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| author | Johannes Ranke <jranke@uni-bremen.de> | 2023-11-16 06:02:05 +0100 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2023-11-16 06:02:05 +0100 |
| commit | 8b7edd4eaf0d196e674a085f744d1a69260a6c91 (patch) | |
| tree | 96d79f504b775d2626ab2a9f700732bd142d66d9 | |
| parent | 6ae6b5230efd2e3d25b68600bd988ded60d3db77 (diff) | |
Update pkgdown docs to bootstrap 5 with search
315 files changed, 20683 insertions, 13204 deletions
diff --git a/_pkgdown.yml b/_pkgdown.yml index f14e6ef3..34220df8 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -5,6 +5,7 @@ development: version_label: default template: + bootstrap: 5 bootswatch: spacelab news: diff --git a/docs/404.html b/docs/404.html index eadf13f5..b85f954e 100644 --- a/docs/404.html +++ b/docs/404.html @@ -4,165 +4,114 @@ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> +<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> <title>Page not found (404) • 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="https://pkgdown.jrwb.de/mkin/bootstrap-toc.css"> -<script src="https://pkgdown.jrwb.de/mkin/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"> +<script src="https://pkgdown.jrwb.de/mkin/deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> +<link 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integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- 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><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" 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and dimethenamid-P</a> - </li> - <li> - <a href="https://pkgdown.jrwb.de/mkin/articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> - </li> - <li> - <a href="https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> - </li> - <li> - <a href="https://pkgdown.jrwb.de/mkin/articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> - </li> - <li> - <a href="https://pkgdown.jrwb.de/mkin/articles/web_only/multistart.html">Short demo of the multistart method</a> - </li> - <li class="divider"> - </li> -<li class="dropdown-header">Performance</li> - <li> - <a href="https://pkgdown.jrwb.de/mkin/articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> - </li> - <li> - <a 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dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="https://pkgdown.jrwb.de/mkin/articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + <a class="dropdown-item" href="https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> + <a class="dropdown-item" href="https://pkgdown.jrwb.de/mkin/articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> + <a class="dropdown-item" href="https://pkgdown.jrwb.de/mkin/articles/web_only/multistart.html">Short demo of the multistart method</a> + <div class="dropdown-divider"></div> + <h6 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-<!--/.navbar --> +</nav><div class="container template-article"> + - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header toc-ignore"> - <h1 data-toc-skip>Example evaluation of FOCUS Example Dataset -D</h1> + +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Example evaluation of FOCUS Example Dataset D</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> <h4 data-toc-skip class="date">Last change 31 January 2019 -(rebuilt 2023-10-30)</h4> +(rebuilt 2023-11-16)</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> - + <div class="d-none name"><code>FOCUS_D.rmd</code></div> </div> @@ -241,9 +200,9 @@ the <code>mkinparplot</code> function.</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: 1.2.6 </span></span> -<span><span class="co">## R version used for fitting: 4.3.1 </span></span> -<span><span class="co">## Date of fit: Mon Oct 30 09:40:58 2023 </span></span> -<span><span class="co">## Date of summary: Mon Oct 30 09:40:58 2023 </span></span> +<span><span class="co">## R version used for fitting: 4.3.2 </span></span> +<span><span class="co">## Date of fit: Thu Nov 16 04:20:11 2023 </span></span> +<span><span class="co">## Date of summary: Thu Nov 16 04:20:11 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> @@ -251,7 +210,7 @@ the <code>mkinparplot</code> function.</p> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 401 model solutions performed in 0.123 s</span></span> +<span><span class="co">## Fitted using 401 model solutions performed in 0.051 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -367,32 +326,27 @@ the <code>mkinparplot</code> function.</p> <span><span class="co">## 100 m1 33.13 31.98162 1.148e+00</span></span> <span><span class="co">## 120 m1 25.15 28.78984 -3.640e+00</span></span> <span><span class="co">## 120 m1 33.31 28.78984 4.520e+00</span></span></code></pre> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - - </div> - + </main><aside 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hierarchical parent degradation kinetics with residue data on mesotrione</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> + <a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> + <a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Performance</h6> + <a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a class="dropdown-item" href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + <a class="dropdown-item" href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + <div class="dropdown-divider"></div> + 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href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> </ul> </div> -<!--/.nav-collapse --> + + </div> -<!--/.container --> -</div> -<!--/.navbar --> +</nav><div class="container template-article"> + - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header toc-ignore"> - <h1 data-toc-skip>Example evaluation of FOCUS Laboratory Data L1 -to L3</h1> + +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Example evaluation of FOCUS Laboratory Data L1 to L3</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> <h4 data-toc-skip class="date">Last change 18 May 2023 -(rebuilt 2023-08-09)</h4> +(rebuilt 2023-11-16)</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> - + <div class="d-none name"><code>FOCUS_L.rmd</code></div> </div> @@ -168,18 +130,18 @@ model fit. This covers the numerical analysis given in the FOCUS 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/r/base/summary.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: 1.2.5 </span></span> -<span><span class="co">## R version used for fitting: 4.3.1 </span></span> -<span><span class="co">## Date of fit: Wed Aug 9 17:55:39 2023 </span></span> -<span><span class="co">## Date of summary: Wed Aug 9 17:55:39 2023 </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: 1.2.6 </span></span> +<span><span class="co">## R version used for fitting: 4.3.2 </span></span> +<span><span class="co">## Date of fit: Thu Nov 16 04:20:13 2023 </span></span> +<span><span class="co">## Date of summary: Thu Nov 16 04:20:13 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> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 133 model solutions performed in 0.031 s</span></span> +<span><span class="co">## Fitted using 133 model solutions performed in 0.011 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -256,7 +218,7 @@ report.</p> <p>A plot of the fit is obtained with the plot function for mkinfit objects.</p> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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">m.L1.SFO</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span>, main <span class="op">=</span> <span class="st">"FOCUS L1 - SFO"</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">m.L1.SFO</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span>, main <span class="op">=</span> <span class="st">"FOCUS L1 - SFO"</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-4-1.png" width="576"></p> <p>The residual plot can be easily obtained by</p> <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> @@ -268,25 +230,25 @@ objects.</p> <pre><code><span><span class="co">## Warning in mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet = TRUE): Optimisation did not converge:</span></span> <span><span class="co">## false convergence (8)</span></span></code></pre> <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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">m.L1.FOMC</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span>, main <span class="op">=</span> <span class="st">"FOCUS L1 - FOMC"</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">m.L1.FOMC</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span>, main <span class="op">=</span> <span class="st">"FOCUS L1 - FOMC"</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-6-1.png" width="576"></p> <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">m.L1.FOMC</span>, data <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> +<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.L1.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">## Warning in sqrt(diag(covar)): NaNs produced</span></span></code></pre> <pre><code><span><span class="co">## Warning in sqrt(1/diag(V)): NaNs produced</span></span></code></pre> <pre><code><span><span class="co">## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result</span></span> <span><span class="co">## is doubtful</span></span></code></pre> -<pre><code><span><span class="co">## mkin version used for fitting: 1.2.5 </span></span> -<span><span class="co">## R version used for fitting: 4.3.1 </span></span> -<span><span class="co">## Date of fit: Wed Aug 9 17:55:39 2023 </span></span> -<span><span class="co">## Date of summary: Wed Aug 9 17:55:39 2023 </span></span> +<pre><code><span><span class="co">## mkin version used for fitting: 1.2.6 </span></span> +<span><span class="co">## R version used for fitting: 4.3.2 </span></span> +<span><span class="co">## Date of fit: Thu Nov 16 04:20:13 2023 </span></span> +<span><span class="co">## Date of summary: Thu Nov 16 04:20:13 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> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 342 model solutions performed in 0.07 s</span></span> +<span><span class="co">## Fitted using 342 model solutions performed in 0.023 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -398,7 +360,7 @@ residual plot can be obtained simply by adding the argument <code>show_residuals</code> to the plot command.</p> <div class="sourceCode" id="cb15"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">m.L2.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_L2_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/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">m.L2.SFO</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<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">m.L2.SFO</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> main <span class="op">=</span> <span class="st">"FOCUS L2 - SFO"</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-8-1.png" width="672"></p> <p>The <span class="math inline">\(\chi^2\)</span> error level of 14% @@ -422,22 +384,22 @@ kinetics.</p> <p>For comparison, the FOMC model is fitted as well, and the <span class="math inline">\(\chi^2\)</span> error level is checked.</p> <div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">m.L2.FOMC</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_L2_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/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">m.L2.FOMC</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<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">m.L2.FOMC</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> main <span class="op">=</span> <span class="st">"FOCUS L2 - FOMC"</span><span class="op">)</span></span></code></pre></div> <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/r/base/summary.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: 1.2.5 </span></span> -<span><span class="co">## R version used for fitting: 4.3.1 </span></span> -<span><span class="co">## Date of fit: Wed Aug 9 17:55:40 2023 </span></span> -<span><span class="co">## Date of summary: Wed Aug 9 17:55:40 2023 </span></span> +<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: 1.2.6 </span></span> +<span><span class="co">## R version used for fitting: 4.3.2 </span></span> +<span><span class="co">## Date of fit: Thu Nov 16 04:20:13 2023 </span></span> +<span><span class="co">## Date of summary: Thu Nov 16 04:20:14 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> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 239 model solutions performed in 0.044 s</span></span> +<span><span class="co">## Fitted using 239 model solutions performed in 0.014 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -506,15 +468,15 @@ the data.</p> <p>Fitting the four parameter DFOP model further reduces the <span class="math inline">\(\chi^2\)</span> error level.</p> <div class="sourceCode" id="cb19"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">m.L2.DFOP</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">FOCUS_2006_L2_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/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">m.L2.DFOP</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span>,</span> +<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">m.L2.DFOP</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> main <span class="op">=</span> <span class="st">"FOCUS L2 - DFOP"</span><span class="op">)</span></span></code></pre></div> <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/r/base/summary.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: 1.2.5 </span></span> -<span><span class="co">## R version used for fitting: 4.3.1 </span></span> -<span><span class="co">## Date of fit: Wed Aug 9 17:55:40 2023 </span></span> -<span><span class="co">## Date of summary: Wed Aug 9 17:55:40 2023 </span></span> +<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: 1.2.6 </span></span> +<span><span class="co">## R version used for fitting: 4.3.2 </span></span> +<span><span class="co">## Date of fit: Thu Nov 16 04:20:14 2023 </span></span> +<span><span class="co">## Date of summary: Thu Nov 16 04:20:14 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> @@ -523,7 +485,7 @@ the data.</p> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 581 model solutions performed in 0.119 s</span></span> +<span><span class="co">## Fitted using 581 model solutions performed in 0.041 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -611,7 +573,7 @@ only the L3 dataset prepared above.</p> <code class="sourceCode R"><span><span class="co"># Only use one core here, not to offend the CRAN checks</span></span> <span><span class="va">mm.L3</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>, cores <span class="op">=</span> <span class="fl">1</span>,</span> <span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS L3"</span> <span class="op">=</span> <span class="va">FOCUS_2006_L3_mkin</span><span class="op">)</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/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">mm.L3</span><span class="op">)</span></span></code></pre></div> +<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">mm.L3</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-12-1.png" width="700"></p> <p>The <span class="math inline">\(\chi^2\)</span> error level of 21% as well as the plot suggest that the SFO model does not fit very well. The @@ -627,11 +589,11 @@ as a row index and datasets as a column index.</p> 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/r/base/summary.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: 1.2.5 </span></span> -<span><span class="co">## R version used for fitting: 4.3.1 </span></span> -<span><span class="co">## Date of fit: Wed Aug 9 17:55:41 2023 </span></span> -<span><span class="co">## Date of summary: Wed Aug 9 17:55:41 2023 </span></span> +<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: 1.2.6 </span></span> +<span><span class="co">## R version used for fitting: 4.3.2 </span></span> +<span><span class="co">## Date of fit: Thu Nov 16 04:20:14 2023 </span></span> +<span><span class="co">## Date of summary: Thu Nov 16 04:20:14 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> @@ -640,7 +602,7 @@ summary and plot functions working on mkinfit objects.</p> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 376 model solutions performed in 0.075 s</span></span> +<span><span class="co">## Fitted using 376 model solutions performed in 0.024 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -715,7 +677,7 @@ summary and plot functions working on mkinfit objects.</p> <span><span class="co">## 91 parent 15.0 15.18 -0.18181</span></span> <span><span class="co">## 120 parent 12.0 10.19 1.81395</span></span></code></pre> <div class="sourceCode" id="cb26"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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">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>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">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>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-13-1.png" width="700"></p> <p>Here, a look to the model plot, the confidence intervals of the parameters and the correlation matrix suggest that the parameter @@ -746,7 +708,7 @@ below:</p> <span><span class="va">mm.L4</span> <span class="op"><-</span> <span class="fu"><a href="../reference/mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span><span class="op">)</span>, cores <span class="op">=</span> <span class="fl">1</span>,</span> <span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="st">"FOCUS L4"</span> <span class="op">=</span> <span class="va">FOCUS_2006_L4_mkin</span><span class="op">)</span>,</span> <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/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">mm.L4</span><span class="op">)</span></span></code></pre></div> +<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">mm.L4</span><span class="op">)</span></span></code></pre></div> <p><img src="FOCUS_L_files/figure-html/unnamed-chunk-15-1.png" width="700"></p> <p>The <span class="math inline">\(\chi^2\)</span> error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error @@ -754,18 +716,18 @@ level at which the <span class="math inline">\(\chi^2\)</span> test passes is slightly lower for the FOMC model. However, the difference appears negligible.</p> <div class="sourceCode" id="cb29"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.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: 1.2.5 </span></span> -<span><span class="co">## R version used for fitting: 4.3.1 </span></span> -<span><span class="co">## Date of fit: Wed Aug 9 17:55:42 2023 </span></span> -<span><span class="co">## Date of summary: Wed Aug 9 17:55:42 2023 </span></span> +<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: 1.2.6 </span></span> +<span><span class="co">## R version used for fitting: 4.3.2 </span></span> +<span><span class="co">## Date of fit: Thu Nov 16 04:20:14 2023 </span></span> +<span><span class="co">## Date of summary: Thu Nov 16 04:20:15 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> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 142 model solutions performed in 0.027 s</span></span> +<span><span class="co">## Fitted using 142 model solutions performed in 0.01 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -819,18 +781,18 @@ appears negligible.</p> <span><span class="co">## DT50 DT90</span></span> <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/r/base/summary.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: 1.2.5 </span></span> -<span><span class="co">## R version used for fitting: 4.3.1 </span></span> -<span><span class="co">## Date of fit: Wed Aug 9 17:55:42 2023 </span></span> -<span><span class="co">## Date of summary: Wed Aug 9 17:55:42 2023 </span></span> +<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: 1.2.6 </span></span> +<span><span class="co">## R version used for fitting: 4.3.2 </span></span> +<span><span class="co">## Date of fit: Thu Nov 16 04:20:15 2023 </span></span> +<span><span class="co">## Date of summary: Thu Nov 16 04:20:15 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> <span><span class="co">## </span></span> <span><span class="co">## Model predictions using solution type analytical </span></span> <span><span class="co">## </span></span> -<span><span class="co">## Fitted using 224 model solutions performed in 0.04 s</span></span> +<span><span class="co">## Fitted using 224 model solutions performed in 0.014 s</span></span> <span><span class="co">## </span></span> <span><span class="co">## Error model: Constant variance </span></span> <span><span class="co">## </span></span> @@ -900,34 +862,27 @@ Validierung von Modellierungssoftware als Alternative zu ModelMaker </div> </div> </div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - - <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2> - </nav> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside> </div> -</div> - - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p> <p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p> <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> + </footer> </div> - </body> diff --git a/docs/articles/index.html b/docs/articles/index.html index f6ad43c2..c6a8604e 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -1,109 +1,74 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta 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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> - + <div class="d-none name"><code>2022_cyan_pathway.rmd</code></div> </div> @@ -2209,9 +2168,9 @@ Hierarchical SFO path 1 fit with constant variance <pre><code> saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.1 -Date of fit: Mon Oct 30 10:03:13 2023 -Date of summary: Mon Oct 30 11:18:26 2023 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:27:41 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - k_cyan * cyan @@ -2224,7 +2183,7 @@ Data: Model predictions using solution type deSolve -Fitted in 1273.632 s +Fitted in 421.347 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -2337,9 +2296,9 @@ Hierarchical SFO path 1 fit with two-component error <pre><code> saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.1 -Date of fit: Mon Oct 30 09:58:51 2023 -Date of summary: Mon Oct 30 11:18:26 2023 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:27:55 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - k_cyan * cyan @@ -2352,7 +2311,7 @@ Data: Model predictions using solution type deSolve -Fitted in 1011.299 s +Fitted in 435.122 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -2467,9 +2426,9 @@ Hierarchical FOMC path 1 fit with constant variance <pre><code> saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.1 -Date of fit: Mon Oct 30 10:04:48 2023 -Date of summary: Mon Oct 30 11:18:26 2023 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:28:33 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -2484,7 +2443,7 @@ Data: Model predictions using solution type deSolve -Fitted in 1368.338 s +Fitted in 473.357 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -2612,9 +2571,9 @@ Hierarchical FOMC path 1 fit with two-component error <pre><code> saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.1 -Date of fit: Mon Oct 30 10:00:40 2023 -Date of summary: Mon Oct 30 11:18:26 2023 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:28:46 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -2629,7 +2588,7 @@ Data: Model predictions using solution type deSolve -Fitted in 1120.168 s +Fitted in 486.031 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -2750,9 +2709,9 @@ Hierarchical DFOP path 1 fit with constant variance <pre><code> saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.1 -Date of fit: Mon Oct 30 10:02:52 2023 -Date of summary: Mon Oct 30 11:18:26 2023 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:29:15 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -2771,7 +2730,7 @@ Data: Model predictions using solution type deSolve -Fitted in 1252.502 s +Fitted in 514.477 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -2896,9 +2855,9 @@ Hierarchical DFOP path 1 fit with two-component error <pre><code> saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.1 -Date of fit: Mon Oct 30 10:12:10 2023 -Date of summary: Mon Oct 30 11:18:26 2023 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:31:58 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -2917,7 +2876,7 @@ Data: Model predictions using solution type deSolve -Fitted in 1809.832 s +Fitted in 677.928 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -3042,9 +3001,9 @@ Hierarchical SFORB path 1 fit with constant variance <pre><code> saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.1 -Date of fit: Mon Oct 30 10:02:30 2023 -Date of summary: Mon Oct 30 11:18:26 2023 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:29:33 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -3062,7 +3021,7 @@ Data: Model predictions using solution type deSolve -Fitted in 1230.946 s +Fitted in 532.937 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -3207,9 +3166,9 @@ Hierarchical SFORB path 1 fit with two-component error <pre><code> saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.1 -Date of fit: Mon Oct 30 10:09:13 2023 -Date of summary: Mon Oct 30 11:18:26 2023 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:31:58 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -3227,7 +3186,7 @@ Data: Model predictions using solution type deSolve -Fitted in 1633.433 s +Fitted in 677.936 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -3372,14 +3331,142 @@ Hierarchical HS path 1 fit with constant variance <pre><code> saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.1 -Date of fit: Mon Oct 30 10:02:52 2023 -Date of summary: Mon Oct 30 11:18:27 2023 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:29:18 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: -d_cyan/dt = - ifelse(time -<p></p></code> -</pre> +d_cyan/dt = - ifelse(time <= tb, k1, k2) * cyan +d_JCZ38/dt = + f_cyan_to_JCZ38 * ifelse(time <= tb, k1, k2) * cyan - + k_JCZ38 * JCZ38 +d_J9Z38/dt = + f_cyan_to_J9Z38 * ifelse(time <= tb, k1, k2) * cyan - + k_J9Z38 * J9Z38 +d_JSE76/dt = + f_JCZ38_to_JSE76 * k_JCZ38 * JCZ38 - k_JSE76 * JSE76 + +Data: +433 observations of 4 variable(s) grouped in 5 datasets + +Model predictions using solution type deSolve + +Fitted in 518.128 s +Using 300, 100 iterations and 10 chains + +Variance model: Constant variance + +Starting values for degradation parameters: + cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 + 102.8845 -3.4495 -4.9355 -5.6040 0.6468 + f_cyan_ilr_2 f_JCZ38_qlogis log_k1 log_k2 log_tb + 1.2396 9.7220 -2.9079 -4.1810 1.7813 + +Fixed degradation parameter values: +None + +Starting values for random effects (square root of initial entries in omega): + cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 +cyan_0 5.406 0.00 0.00 0.000 0.0000 +log_k_JCZ38 0.000 2.33 0.00 0.000 0.0000 +log_k_J9Z38 0.000 0.00 1.59 0.000 0.0000 +log_k_JSE76 0.000 0.00 0.00 1.013 0.0000 +f_cyan_ilr_1 0.000 0.00 0.00 0.000 0.6367 +f_cyan_ilr_2 0.000 0.00 0.00 0.000 0.0000 +f_JCZ38_qlogis 0.000 0.00 0.00 0.000 0.0000 +log_k1 0.000 0.00 0.00 0.000 0.0000 +log_k2 0.000 0.00 0.00 0.000 0.0000 +log_tb 0.000 0.00 0.00 0.000 0.0000 + f_cyan_ilr_2 f_JCZ38_qlogis log_k1 log_k2 log_tb +cyan_0 0.000 0.00 0.0000 0.0000 0.0000 +log_k_JCZ38 0.000 0.00 0.0000 0.0000 0.0000 +log_k_J9Z38 0.000 0.00 0.0000 0.0000 0.0000 +log_k_JSE76 0.000 0.00 0.0000 0.0000 0.0000 +f_cyan_ilr_1 0.000 0.00 0.0000 0.0000 0.0000 +f_cyan_ilr_2 2.038 0.00 0.0000 0.0000 0.0000 +f_JCZ38_qlogis 0.000 10.33 0.0000 0.0000 0.0000 +log_k1 0.000 0.00 0.7006 0.0000 0.0000 +log_k2 0.000 0.00 0.0000 0.8928 0.0000 +log_tb 0.000 0.00 0.0000 0.0000 0.6773 + +Starting values for error model parameters: +a.1 + 1 + +Results: + +Likelihood computed by importance sampling + AIC BIC logLik + 2427 2419 -1194 + +Optimised parameters: + est. lower upper +cyan_0 101.9660 1.005e+02 1.035e+02 +log_k_JCZ38 -3.4698 -4.716e+00 -2.224e+00 +log_k_J9Z38 -5.0947 -5.740e+00 -4.450e+00 +log_k_JSE76 -5.5977 -6.321e+00 -4.875e+00 +f_cyan_ilr_1 0.6595 3.734e-01 9.456e-01 +f_cyan_ilr_2 0.5905 1.664e-01 1.015e+00 +f_JCZ38_qlogis 25.8627 -4.224e+05 4.225e+05 +log_k1 -3.0884 -3.453e+00 -2.723e+00 +log_k2 -4.3877 -4.778e+00 -3.998e+00 +log_tb 2.3057 1.715e+00 2.896e+00 +a.1 3.3228 NA NA +SD.log_k_JCZ38 1.4071 NA NA +SD.log_k_J9Z38 0.5774 NA NA +SD.log_k_JSE76 0.6214 NA NA +SD.f_cyan_ilr_1 0.3058 NA NA +SD.f_cyan_ilr_2 0.3470 NA NA +SD.f_JCZ38_qlogis 0.0644 NA NA +SD.log_k1 0.3994 NA NA +SD.log_k2 0.4373 NA NA +SD.log_tb 0.6419 NA NA + +Correlation is not available + +Random effects: + est. lower upper +SD.log_k_JCZ38 1.4071 NA NA +SD.log_k_J9Z38 0.5774 NA NA +SD.log_k_JSE76 0.6214 NA NA +SD.f_cyan_ilr_1 0.3058 NA NA +SD.f_cyan_ilr_2 0.3470 NA NA +SD.f_JCZ38_qlogis 0.0644 NA NA +SD.log_k1 0.3994 NA NA +SD.log_k2 0.4373 NA NA +SD.log_tb 0.6419 NA NA + +Variance model: + est. lower upper +a.1 3.323 NA NA + +Backtransformed parameters: + est. lower upper +cyan_0 1.020e+02 1.005e+02 1.035e+02 +k_JCZ38 3.112e-02 8.951e-03 1.082e-01 +k_J9Z38 6.129e-03 3.216e-03 1.168e-02 +k_JSE76 3.706e-03 1.798e-03 7.639e-03 +f_cyan_to_JCZ38 5.890e-01 NA NA +f_cyan_to_J9Z38 2.318e-01 NA NA +f_JCZ38_to_JSE76 1.000e+00 0.000e+00 1.000e+00 +k1 4.558e-02 3.164e-02 6.565e-02 +k2 1.243e-02 8.417e-03 1.835e-02 +tb 1.003e+01 5.557e+00 1.811e+01 + +Resulting formation fractions: + ff +cyan_JCZ38 5.890e-01 +cyan_J9Z38 2.318e-01 +cyan_sink 1.793e-01 +JCZ38_JSE76 1.000e+00 +JCZ38_sink 5.861e-12 + +Estimated disappearance times: + DT50 DT90 DT50back DT50_k1 DT50_k2 +cyan 29.02 158.51 47.72 15.21 55.77 +JCZ38 22.27 73.98 NA NA NA +J9Z38 113.09 375.69 NA NA NA +JSE76 187.01 621.23 NA NA NA + +</code></pre> +<p></p> </div> <div class="section level4"> <h4 id="pathway-2">Pathway 2<a class="anchor" aria-label="anchor" href="#pathway-2"></a> @@ -3390,9 +3477,9 @@ Hierarchical FOMC path 2 fit with two-component error <pre><code> saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.1 -Date of fit: Mon Oct 30 10:32:26 2023 -Date of summary: Mon Oct 30 11:18:27 2023 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:40:28 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -3407,7 +3494,7 @@ Data: Model predictions using solution type deSolve -Fitted in 1185.728 s +Fitted in 499.317 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -3556,9 +3643,9 @@ Hierarchical DFOP path 2 fit with constant variance <pre><code> saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.1 -Date of fit: Mon Oct 30 10:34:49 2023 -Date of summary: Mon Oct 30 11:18:27 2023 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:41:25 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -3578,7 +3665,7 @@ Data: Model predictions using solution type deSolve -Fitted in 1329.843 s +Fitted in 555.724 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -3747,9 +3834,9 @@ Hierarchical DFOP path 2 fit with two-component error <pre><code> saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.1 -Date of fit: Mon Oct 30 10:41:05 2023 -Date of summary: Mon Oct 30 11:18:27 2023 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:44:08 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -3769,7 +3856,7 @@ Data: Model predictions using solution type deSolve -Fitted in 1705.043 s +Fitted in 718.988 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -3938,9 +4025,9 @@ Hierarchical SFORB path 2 fit with constant variance <pre><code> saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.1 -Date of fit: Mon Oct 30 10:35:39 2023 -Date of summary: Mon Oct 30 11:18:27 2023 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:41:22 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -3958,7 +4045,7 @@ Data: Model predictions using solution type deSolve -Fitted in 1379.466 s +Fitted in 553.276 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -4134,9 +4221,9 @@ Hierarchical SFORB path 2 fit with two-component error <pre><code> saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.1 -Date of fit: Mon Oct 30 10:41:39 2023 -Date of summary: Mon Oct 30 11:18:27 2023 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:44:02 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -4154,7 +4241,7 @@ Data: Model predictions using solution type deSolve -Fitted in 1739.402 s +Fitted in 713.14 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -4335,9 +4422,9 @@ error <pre><code> saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.1 -Date of fit: Mon Oct 30 11:12:56 2023 -Date of summary: Mon Oct 30 11:18:27 2023 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:57:07 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan @@ -4352,7 +4439,7 @@ Data: Model predictions using solution type deSolve -Fitted in 1872.856 s +Fitted in 776.732 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -4478,9 +4565,9 @@ variance <pre><code> saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.1 -Date of fit: Mon Oct 30 11:17:06 2023 -Date of summary: Mon Oct 30 11:18:27 2023 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:58:51 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -4500,7 +4587,7 @@ Data: Model predictions using solution type deSolve -Fitted in 2122.961 s +Fitted in 880.94 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -4577,12 +4664,12 @@ f_JSE76_qlogis 1.9658 NA NA log_k1 -1.9503 NA NA log_k2 -4.4745 NA NA g_qlogis -0.4967 NA NA -a.1 2.7461 2.59886 2.8932 +a.1 2.7461 2.59274 2.8994 SD.log_k_JCZ38 1.3178 0.47602 2.1596 SD.log_k_J9Z38 0.7022 0.15061 1.2538 -SD.log_k_JSE76 0.6566 0.15614 1.1570 +SD.log_k_JSE76 0.6566 0.15613 1.1570 SD.f_cyan_ilr_1 0.3409 0.11666 0.5652 -SD.f_cyan_ilr_2 0.4385 0.09483 0.7821 +SD.f_cyan_ilr_2 0.4385 0.09482 0.7821 SD.log_k1 0.7381 0.25599 1.2202 SD.log_k2 0.5133 0.18152 0.8450 SD.g_qlogis 0.9866 0.35681 1.6164 @@ -4593,16 +4680,16 @@ Random effects: est. lower upper SD.log_k_JCZ38 1.3178 0.47602 2.1596 SD.log_k_J9Z38 0.7022 0.15061 1.2538 -SD.log_k_JSE76 0.6566 0.15614 1.1570 +SD.log_k_JSE76 0.6566 0.15613 1.1570 SD.f_cyan_ilr_1 0.3409 0.11666 0.5652 -SD.f_cyan_ilr_2 0.4385 0.09483 0.7821 +SD.f_cyan_ilr_2 0.4385 0.09482 0.7821 SD.log_k1 0.7381 0.25599 1.2202 SD.log_k2 0.5133 0.18152 0.8450 SD.g_qlogis 0.9866 0.35681 1.6164 Variance model: est. lower upper -a.1 2.746 2.599 2.893 +a.1 2.746 2.593 2.899 Backtransformed parameters: est. lower upper @@ -4644,9 +4731,9 @@ error <pre><code> saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.1 -Date of fit: Mon Oct 30 11:17:59 2023 -Date of summary: Mon Oct 30 11:18:27 2023 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:58:58 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -4666,7 +4753,7 @@ Data: Model predictions using solution type deSolve -Fitted in 2175.807 s +Fitted in 887.853 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -4810,9 +4897,9 @@ variance <pre><code> saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.1 -Date of fit: Mon Oct 30 11:17:04 2023 -Date of summary: Mon Oct 30 11:18:27 2023 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:58:49 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -4830,7 +4917,7 @@ Data: Model predictions using solution type deSolve -Fitted in 2121.218 s +Fitted in 878.878 s Using 300, 100 iterations and 10 chains Variance model: Constant variance @@ -4981,9 +5068,9 @@ error <pre><code> saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.1 -Date of fit: Mon Oct 30 11:18:24 2023 -Date of summary: Mon Oct 30 11:18:27 2023 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:59:10 2023 +Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * @@ -5001,7 +5088,7 @@ Data: Model predictions using solution type deSolve -Fitted in 2200.603 s +Fitted in 899.539 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function @@ -5150,23 +5237,23 @@ JSE76 25.44 84.51 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 4.3.1 (2023-06-16) +<pre><code>R version 4.3.2 (2023-10-31) Platform: x86_64-pc-linux-gnu (64-bit) -Running under: Ubuntu 22.04.3 LTS +Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default -BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 -LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0 +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=en_US.UTF-8 LC_NUMERIC=C - [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 - [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 - [7] LC_PAPER=en_US.UTF-8 LC_NAME=C + [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=en_US.UTF-8 LC_IDENTIFICATION=C +[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C -time zone: Europe/Zurich +time zone: Europe/Berlin tzcode source: system (glibc) attached base packages: @@ -5174,62 +5261,55 @@ attached base packages: [8] base other attached packages: -[1] saemix_3.2 npde_3.3 knitr_1.44 mkin_1.2.6 +[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.6 loaded via a namespace (and not attached): - [1] sass_0.4.7 utf8_1.2.3 generics_0.1.3 stringi_1.7.12 - [5] lattice_0.21-9 digest_0.6.33 magrittr_2.0.3 evaluate_0.22 - [9] grid_4.3.1 fastmap_1.1.1 cellranger_1.1.0 rprojroot_2.0.3 -[13] jsonlite_1.8.7 processx_3.8.2 pkgbuild_1.4.2 deSolve_1.35 -[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_4.3.1 memoise_2.0.1 dplyr_1.1.2 colorspace_2.1-0 -[37] ggplot2_3.4.2 vctrs_0.6.3 R6_2.5.1 zoo_1.8-12 -[41] lifecycle_1.0.3 stringr_1.5.0 fs_1.6.3 MASS_7.3-60 -[45] ragg_1.2.5 callr_3.7.3 pkgconfig_2.0.3 desc_1.4.2 -[49] pkgdown_2.0.7 bslib_0.5.1 pillar_1.9.0 gtable_0.3.3 -[53] glue_1.6.2 systemfonts_1.0.4 xfun_0.40 tibble_3.2.1 -[57] lmtest_0.9-40 tidyselect_1.2.0 rstudioapi_0.15.0 htmltools_0.5.6.1 -[61] nlme_3.1-163 rmarkdown_2.23 compiler_4.3.1 prettyunits_1.2.0 -[65] readxl_1.4.2 </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_4.3.2 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_4.3.2 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] MASS_7.3-60 ragg_1.2.5 callr_3.7.3 pkgconfig_2.0.3 +[49] desc_1.4.2 pkgdown_2.0.7 bslib_0.4.2 pillar_1.9.0 +[53] gtable_0.3.3 glue_1.6.2 systemfonts_1.0.4 highr_0.10 +[57] xfun_0.39 tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.0 +[61] htmltools_0.5.5 nlme_3.1-163 rmarkdown_2.21 compiler_4.3.2 +[65] prettyunits_1.1.1 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) Xeon(R) Gold 6134 CPU @ 3.20GHz</code></pre> -<pre><code>MemTotal: 247605564 kB</code></pre> +<pre><code>CPU model: AMD Ryzen 9 7950X 16-Core Processor</code></pre> +<pre><code>MemTotal: 64927712 kB</code></pre> </div> </div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - - <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2> - </nav> -</div> - + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside> </div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p> <p>Developed by Johannes Ranke.</p> 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hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="../../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + <a class="dropdown-item" href="../../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> + <a class="dropdown-item" href="../../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> + <a class="dropdown-item" href="../../articles/web_only/multistart.html">Short demo of the multistart method</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Performance</h6> + <a class="dropdown-item" href="../../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a class="dropdown-item" 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navigation" name="search-input" data-search-index="../../search.json" id="search-input" placeholder="Search for" autocomplete="off"> +</form> + + <ul class="navbar-nav"> +<li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> </ul> </div> -<!--/.nav-collapse --> + + </div> -<!--/.container --> -</div> -<!--/.navbar --> +</nav><div class="container template-article"> + + - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header toc-ignore"> - <h1 data-toc-skip>Testing hierarchical parent degradation kinetics -with residue data on dimethenamid and dimethenamid-P</h1> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> <h4 data-toc-skip class="date">Last change on 5 January -2023, last compiled on 30 October 2023</h4> +2023, last compiled on 16 November 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> - + <div class="d-none name"><code>2022_dmta_parent.rmd</code></div> </div> @@ -1290,9 +1249,9 @@ Plot of the final NLHM DFOP fit <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: 1.2.6 -R version used for fitting: 4.3.1 -Date of fit: Mon Oct 30 11:19:13 2023 -Date of summary: Mon Oct 30 11:19:14 2023 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:59:35 2023 +Date of summary: Thu Nov 16 04:59:35 2023 Equations: d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -1304,7 +1263,7 @@ Data: Model predictions using solution type analytical -Fitted in 8.975 s +Fitted in 4.4 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function @@ -1466,9 +1425,9 @@ Hierarchical mkin fit of the SFO model with error model const <pre><code> saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.1 -Date of fit: Mon Oct 30 11:18:56 2023 -Date of summary: Mon Oct 30 11:21:30 2023 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:59:26 2023 +Date of summary: Thu Nov 16 05:00:43 2023 Equations: d_DMTA/dt = - k_DMTA * DMTA @@ -1478,7 +1437,7 @@ Data: Model predictions using solution type analytical -Fitted in 1.899 s +Fitted in 0.788 s Using 300, 100 iterations and 9 chains Variance model: Constant variance @@ -1538,9 +1497,9 @@ Hierarchical mkin fit of the SFO model with error model tc <pre><code> saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.1 -Date of fit: Mon Oct 30 11:19:00 2023 -Date of summary: Mon Oct 30 11:21:30 2023 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:59:28 2023 +Date of summary: Thu Nov 16 05:00:43 2023 Equations: d_DMTA/dt = - k_DMTA * DMTA @@ -1550,7 +1509,7 @@ Data: Model predictions using solution type analytical -Fitted in 5.364 s +Fitted in 2.428 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function @@ -1612,9 +1571,9 @@ Hierarchical mkin fit of the FOMC model with error model const <pre><code> saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.1 -Date of fit: Mon Oct 30 11:18:57 2023 -Date of summary: Mon Oct 30 11:21:30 2023 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:59:27 2023 +Date of summary: Thu Nov 16 05:00:43 2023 Equations: d_DMTA/dt = - (alpha/beta) * 1/((time/beta) + 1) * DMTA @@ -1624,7 +1583,7 @@ Data: Model predictions using solution type analytical -Fitted in 2.944 s +Fitted in 1.28 s Using 300, 100 iterations and 9 chains Variance model: Constant variance @@ -1689,9 +1648,9 @@ Hierarchical mkin fit of the FOMC model with error model tc <pre><code> saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.1 -Date of fit: Mon Oct 30 11:19:01 2023 -Date of summary: Mon Oct 30 11:21:30 2023 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:59:28 2023 +Date of summary: Thu Nov 16 05:00:43 2023 Equations: d_DMTA/dt = - (alpha/beta) * 1/((time/beta) + 1) * DMTA @@ -1701,7 +1660,7 @@ Data: Model predictions using solution type analytical -Fitted in 6.228 s +Fitted in 2.793 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function @@ -1768,9 +1727,9 @@ Hierarchical mkin fit of the DFOP model with error model const <pre><code> saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.1 -Date of fit: Mon Oct 30 11:18:57 2023 -Date of summary: Mon Oct 30 11:21:30 2023 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:59:27 2023 +Date of summary: Thu Nov 16 05:00:43 2023 Equations: d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -1782,7 +1741,7 @@ Data: Model predictions using solution type analytical -Fitted in 3.231 s +Fitted in 1.752 s Using 300, 100 iterations and 9 chains Variance model: Constant variance @@ -1852,9 +1811,9 @@ Hierarchical mkin fit of the DFOP model with error model tc <pre><code> saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.1 -Date of fit: Mon Oct 30 11:19:01 2023 -Date of summary: Mon Oct 30 11:21:30 2023 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:59:29 2023 +Date of summary: Thu Nov 16 05:00:43 2023 Equations: d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -1866,7 +1825,7 @@ Data: Model predictions using solution type analytical -Fitted in 6.71 s +Fitted in 3.186 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function @@ -1938,27 +1897,166 @@ Hierarchical mkin fit of the HS model with error model const <pre><code> saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 -R version used for fitting: 4.3.1 -Date of fit: Mon Oct 30 11:18:59 2023 -Date of summary: Mon Oct 30 11:21:30 2023 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:59:28 2023 +Date of summary: Thu Nov 16 05:00:43 2023 Equations: -d_DMTA/dt = - ifelse(time -<p></p></code> +d_DMTA/dt = - ifelse(time <= tb, k1, k2) * DMTA + +Data: +155 observations of 1 variable(s) grouped in 6 datasets + +Model predictions using solution type analytical + +Fitted in 2.28 s +Using 300, 100 iterations and 9 chains + +Variance model: Constant variance + +Starting values for degradation parameters: + DMTA_0 k1 k2 tb +97.82176 0.06931 0.02997 11.13945 + +Fixed degradation parameter values: +None + +Starting values for random effects (square root of initial entries in omega): + DMTA_0 k1 k2 tb +DMTA_0 97.82 0 0 0 +k1 0.00 1 0 0 +k2 0.00 0 1 0 +tb 0.00 0 0 1 + +Starting values for error model parameters: +a.1 + 1 + +Results: + +Likelihood computed by importance sampling + AIC BIC logLik + 714 712.1 -348 + +Optimised parameters: + est. lower upper +DMTA_0 98.16102 96.47747 99.84456 +k1 0.07876 0.05261 0.10491 +k2 0.02227 0.01706 0.02747 +tb 13.99089 -7.40049 35.38228 +a.1 1.82305 1.60700 2.03910 +SD.DMTA_0 1.88413 0.56204 3.20622 +SD.k1 0.34292 0.10482 0.58102 +SD.k2 0.19851 0.01718 0.37985 +SD.tb 1.68168 0.58064 2.78272 + +Correlation: + DMTA_0 k1 k2 +k1 0.0142 +k2 0.0001 -0.0025 +tb 0.0165 -0.1256 -0.0301 + +Random effects: + est. lower upper +SD.DMTA_0 1.8841 0.56204 3.2062 +SD.k1 0.3429 0.10482 0.5810 +SD.k2 0.1985 0.01718 0.3798 +SD.tb 1.6817 0.58064 2.7827 + +Variance model: + est. lower upper +a.1 1.823 1.607 2.039 + +Estimated disappearance times: + DT50 DT90 DT50back DT50_k1 DT50_k2 +DMTA 8.801 67.91 20.44 8.801 31.13 + +</code></pre> +<p></p> <caption> 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: 1.2.6 -R version used for fitting: 4.3.1 -Date of fit: Mon Oct 30 11:19:02 2023 -Date of summary: Mon Oct 30 11:21:30 2023 +R version used for fitting: 4.3.2 +Date of fit: Thu Nov 16 04:59:29 2023 +Date of summary: Thu Nov 16 05:00:43 2023 Equations: -d_DMTA/dt = - ifelse(time -<p></p></code> -</pre></pre> +d_DMTA/dt = - ifelse(time <= tb, k1, k2) * DMTA + +Data: +155 observations of 1 variable(s) grouped in 6 datasets + +Model predictions using solution type analytical + +Fitted in 3.658 s +Using 300, 100 iterations and 9 chains + +Variance model: Two-component variance function + +Starting values for degradation parameters: + DMTA_0 k1 k2 tb +98.45190 0.07525 0.02576 19.19375 + +Fixed degradation parameter values: +None + +Starting values for random effects (square root of initial entries in omega): + DMTA_0 k1 k2 tb +DMTA_0 98.45 0 0 0 +k1 0.00 1 0 0 +k2 0.00 0 1 0 +tb 0.00 0 0 1 + +Starting values for error model parameters: +a.1 b.1 + 1 1 + +Results: + +Likelihood computed by importance sampling + AIC BIC logLik + 667.1 665 -323.6 + +Optimised parameters: + est. lower upper +DMTA_0 97.76571 95.81350 99.71791 +k1 0.05855 0.03080 0.08630 +k2 0.02337 0.01664 0.03010 +tb 31.09638 29.38289 32.80987 +a.1 1.08835 0.88590 1.29080 +b.1 0.02964 0.02257 0.03671 +SD.DMTA_0 2.04877 0.42607 3.67147 +SD.k1 0.59166 0.25621 0.92711 +SD.k2 0.30698 0.09561 0.51835 +SD.tb 0.01274 -0.10914 0.13462 + +Correlation: + DMTA_0 k1 k2 +k1 0.0160 +k2 -0.0070 -0.0024 +tb -0.0668 -0.0103 -0.2013 + +Random effects: + est. lower upper +SD.DMTA_0 2.04877 0.42607 3.6715 +SD.k1 0.59166 0.25621 0.9271 +SD.k2 0.30698 0.09561 0.5183 +SD.tb 0.01274 -0.10914 0.1346 + +Variance model: + est. lower upper +a.1 1.08835 0.88590 1.29080 +b.1 0.02964 0.02257 0.03671 + +Estimated disappearance times: + DT50 DT90 DT50back DT50_k1 DT50_k2 +DMTA 11.84 51.71 15.57 11.84 29.66 + +</code></pre> +<p></p> </div> <div class="section level3"> <h3 id="hierarchical-model-convergence-plots">Hierarchical model convergence plots<a class="anchor" aria-label="anchor" href="#hierarchical-model-convergence-plots"></a> @@ -2007,23 +2105,23 @@ 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 4.3.1 (2023-06-16) +<pre><code>R version 4.3.2 (2023-10-31) Platform: x86_64-pc-linux-gnu (64-bit) -Running under: Ubuntu 22.04.3 LTS +Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default -BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 -LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0 +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=en_US.UTF-8 LC_NUMERIC=C - [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 - [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 - [7] LC_PAPER=en_US.UTF-8 LC_NAME=C + [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=en_US.UTF-8 LC_IDENTIFICATION=C +[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C -time zone: Europe/Zurich +time zone: Europe/Berlin tzcode source: system (glibc) attached base packages: @@ -2031,59 +2129,52 @@ attached base packages: [8] base other attached packages: -[1] saemix_3.2 npde_3.3 knitr_1.44 mkin_1.2.6 +[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.6 loaded via a namespace (and not attached): - [1] sass_0.4.7 utf8_1.2.3 generics_0.1.3 stringi_1.7.12 - [5] lattice_0.21-9 digest_0.6.33 magrittr_2.0.3 evaluate_0.22 - [9] grid_4.3.1 fastmap_1.1.1 rprojroot_2.0.3 jsonlite_1.8.7 -[13] mclust_6.0.0 gridExtra_2.3 purrr_1.0.1 fansi_1.0.4 -[17] scales_1.2.1 codetools_0.2-19 textshaping_0.3.6 jquerylib_0.1.4 -[21] cli_3.6.1 rlang_1.1.1 munsell_0.5.0 cachem_1.0.8 -[25] yaml_2.3.7 tools_4.3.1 memoise_2.0.1 dplyr_1.1.2 -[29] colorspace_2.1-0 ggplot2_3.4.2 vctrs_0.6.3 R6_2.5.1 -[33] zoo_1.8-12 lifecycle_1.0.3 stringr_1.5.0 fs_1.6.3 -[37] MASS_7.3-60 ragg_1.2.5 pkgconfig_2.0.3 desc_1.4.2 -[41] pkgdown_2.0.7 bslib_0.5.1 pillar_1.9.0 gtable_0.3.3 -[45] glue_1.6.2 systemfonts_1.0.4 xfun_0.40 tibble_3.2.1 -[49] lmtest_0.9-40 tidyselect_1.2.0 rstudioapi_0.15.0 htmltools_0.5.6.1 -[53] nlme_3.1-163 rmarkdown_2.23 compiler_4.3.1 </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_4.3.2 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_4.3.2 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 MASS_7.3-60 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 nlme_3.1-163 rmarkdown_2.21 compiler_4.3.2 </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) Xeon(R) Gold 6134 CPU @ 3.20GHz</code></pre> -<pre><code>MemTotal: 247605564 kB</code></pre> +<pre><code>CPU model: AMD Ryzen 9 7950X 16-Core Processor</code></pre> +<pre><code>MemTotal: 64927712 kB</code></pre> </div> </div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - - <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2> - </nav> -</div> - + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside> </div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p> <p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p> <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> + </footer> </div> - </body> diff --git a/docs/articles/prebuilt/2022_dmta_parent_files/figure-html/convergence-saem-dfop-const-1.png 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hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> <h4 data-toc-skip class="date">Last change on 20 April 2023, -last compiled on 30 October 2023</h4> +last compiled on 16 November 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> - + <div class="d-none name"><code>2022_dmta_pathway.rmd</code></div> </div> @@ -1979,23 +1938,23 @@ 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 4.3.1 (2023-06-16) +<pre><code>R version 4.3.2 (2023-10-31) Platform: x86_64-pc-linux-gnu (64-bit) -Running under: Ubuntu 22.04.3 LTS +Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default -BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 -LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0 +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=en_US.UTF-8 LC_NUMERIC=C - [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 - [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 - [7] LC_PAPER=en_US.UTF-8 LC_NAME=C + [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=en_US.UTF-8 LC_IDENTIFICATION=C +[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C -time zone: Europe/Zurich +time zone: Europe/Berlin tzcode source: system (glibc) attached base packages: @@ -2003,61 +1962,54 @@ attached base packages: [8] base other attached packages: -[1] saemix_3.2 npde_3.3 knitr_1.44 mkin_1.2.6 +[1] saemix_3.2 npde_3.3 knitr_1.42 mkin_1.2.6 loaded via a namespace (and not attached): - [1] sass_0.4.7 utf8_1.2.3 generics_0.1.3 stringi_1.7.12 - [5] lattice_0.21-9 digest_0.6.33 magrittr_2.0.3 evaluate_0.22 - [9] grid_4.3.1 fastmap_1.1.1 rprojroot_2.0.3 jsonlite_1.8.7 -[13] processx_3.8.2 pkgbuild_1.4.2 deSolve_1.35 mclust_6.0.0 -[17] ps_1.7.5 gridExtra_2.3 purrr_1.0.1 fansi_1.0.4 -[21] scales_1.2.1 codetools_0.2-19 textshaping_0.3.6 jquerylib_0.1.4 -[25] cli_3.6.1 crayon_1.5.2 rlang_1.1.1 munsell_0.5.0 -[29] cachem_1.0.8 yaml_2.3.7 inline_0.3.19 tools_4.3.1 -[33] memoise_2.0.1 dplyr_1.1.2 colorspace_2.1-0 ggplot2_3.4.2 -[37] vctrs_0.6.3 R6_2.5.1 zoo_1.8-12 lifecycle_1.0.3 -[41] stringr_1.5.0 fs_1.6.3 MASS_7.3-60 ragg_1.2.5 -[45] callr_3.7.3 pkgconfig_2.0.3 desc_1.4.2 pkgdown_2.0.7 -[49] bslib_0.5.1 pillar_1.9.0 gtable_0.3.3 glue_1.6.2 -[53] systemfonts_1.0.4 xfun_0.40 tibble_3.2.1 lmtest_0.9-40 -[57] tidyselect_1.2.0 rstudioapi_0.15.0 htmltools_0.5.6.1 nlme_3.1-163 -[61] rmarkdown_2.23 compiler_4.3.1 prettyunits_1.2.0</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_4.3.2 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_4.3.2 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 MASS_7.3-60 +[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_3.1-163 rmarkdown_2.21 compiler_4.3.2 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: Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</code></pre> -<pre><code>MemTotal: 247605564 kB</code></pre> +<pre><code>CPU model: AMD Ryzen 9 7950X 16-Core Processor</code></pre> +<pre><code>MemTotal: 64927712 kB</code></pre> </div> </div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - - <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2> - </nav> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside> </div> -</div> - - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p> <p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p> <p>Site built with 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class="fab fa fab fa-github fa-lg"></span> </a> </li> </ul> </div> -<!--/.nav-collapse --> + + </div> -<!--/.container --> -</div> -<!--/.navbar --> +</nav><div class="container template-article"> + - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header toc-ignore"> - <h1 data-toc-skip>Testing covariate modelling in hierarchical -parent degradation kinetics with residue data on mesotrione</h1> + +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>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 13 Oktober 2023</h4> +last compiled on 16 November 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 class="d-none name"><code>2023_mesotrione_parent.rmd</code></div> </div> @@ -2480,7 +2439,7 @@ further refined to make them fully identifiable.</p> <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) +<pre><code>R version 4.3.2 (2023-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 12 (bookworm) @@ -2509,19 +2468,18 @@ other attached packages: 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_0.21-8 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_1.8.4 DBI_1.1.3 mclust_6.0.0 gridExtra_2.3 -[17] purrr_1.0.1 fansi_1.0.4 scales_1.2.1 codetools_0.2-19 -[21] textshaping_0.3.6 jquerylib_0.1.4 cli_3.6.1 rlang_1.1.1 -[25] munsell_0.5.0 cachem_1.0.8 yaml_2.3.7 tools_4.3.1 -[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 MASS_7.3-60 ragg_1.2.5 -[41] pkgconfig_2.0.3 desc_1.4.2 pkgdown_2.0.7 bslib_0.4.2 -[45] pillar_1.9.0 gtable_0.3.3 glue_1.6.2 systemfonts_1.0.4 -[49] highr_0.10 xfun_0.39 tibble_3.2.1 lmtest_0.9-40 -[53] tidyselect_1.2.0 htmltools_0.5.5 nlme_3.1-162 rmarkdown_2.21 -[57] compiler_4.3.1 readxl_1.4.2 </code></pre> + [9] grid_4.3.2 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 textshaping_0.3.6 jquerylib_0.1.4 +[21] cli_3.6.1 rlang_1.1.1 munsell_0.5.0 cachem_1.0.8 +[25] yaml_2.3.7 tools_4.3.2 memoise_2.0.1 dplyr_1.1.2 +[29] colorspace_2.1-0 ggplot2_3.4.2 vctrs_0.6.2 R6_2.5.1 +[33] zoo_1.8-12 lifecycle_1.0.3 stringr_1.5.0 fs_1.6.2 +[37] MASS_7.3-60 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 xfun_0.39 tibble_3.2.1 +[49] lmtest_0.9-40 tidyselect_1.2.0 htmltools_0.5.5 nlme_3.1-163 +[53] rmarkdown_2.21 compiler_4.3.2 </code></pre> </div> <div class="section level3"> <h3 id="hardware-info">Hardware info<a class="anchor" aria-label="anchor" href="#hardware-info"></a> @@ -2530,34 +2488,27 @@ loaded via a namespace (and not attached): <pre><code>MemTotal: 64928100 kB</code></pre> </div> </div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - - <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2> - </nav> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside> </div> -</div> - - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p> <p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> 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class="dropdown-item" href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> + <a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> + <a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <div 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class="page-header"> + <img src="" class="logo" alt=""><h1>Calculation of time weighted average concentrations with mkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> <h4 data-toc-skip class="date">Last change 18 September 2019 -(rebuilt 2023-10-30)</h4> +(rebuilt 2023-11-16)</h4> <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/vignettes/twa.rmd" class="external-link"><code>vignettes/twa.rmd</code></a></small> - <div class="hidden name"><code>twa.rmd</code></div> - + <div class="d-none name"><code>twa.rmd</code></div> </div> @@ -214,32 +173,27 @@ Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration</em>. 1.1 ed. <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>. </div> </div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - - </div> - + 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href="http://esdac.jrc </div> </div> </div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - - <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2> - </nav> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside> </div> -</div> - - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p> <p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p> <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> + </footer> </div> - </body> diff --git a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png b/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png Binary files differindex be652d31..98bc135b 100644 --- a/docs/articles/web_only/FOCUS_Z_files/figure-html/FOCUS_2006_Z_fits_1-1.png +++ 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data-toc-skip>Evaluation of example datasets from Attachment 1 -to the US EPA SOP for the NAFTA guidance</h1> + +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> <h4 data-toc-skip class="date">26 February 2019 (rebuilt -2023-10-30)</h4> +2023-11-16)</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> - + <div class="d-none name"><code>NAFTA_examples.rmd</code></div> </div> @@ -1079,34 +1038,27 @@ Pesticide Degradation.”</span> <a href="https://www.epa.gov/pesticide-science- </div> </div> </div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" 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class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Benchmark timings for mkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> <h4 data-toc-skip class="date">Last change 17 February 2023 -(rebuilt 2023-11-02)</h4> +(rebuilt 2023-11-16)</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> - + <div class="d-none name"><code>benchmarks.rmd</code></div> </div> @@ -465,8 +425,8 @@ models fitted to two datasets, i.e. eight fits for each test.</p> <td align="left">Ryzen 9 7950X</td> <td align="left">4.3.2</td> <td align="left">1.2.6</td> -<td align="right">1.400</td> -<td align="right">2.012</td> +<td align="right">1.408</td> +<td align="right">2.041</td> </tr> </tbody> </table> @@ -736,9 +696,9 @@ for each test.</p> <td align="left">Ryzen 9 7950X</td> <td align="left">4.3.2</td> <td align="left">1.2.6</td> -<td align="right">0.790</td> -<td align="right">2.212</td> -<td align="right">1.173</td> +<td align="right">0.795</td> +<td align="right">2.228</td> +<td align="right">1.178</td> </tr> </tbody> </table> @@ -1092,45 +1052,38 @@ dataset, i.e. one fit for each test.</p> <td align="left">Ryzen 9 7950X</td> <td align="left">4.3.2</td> <td align="left">1.2.6</td> -<td align="right">0.432</td> -<td align="right">0.551</td> -<td align="right">0.580</td> -<td align="right">1.322</td> -<td align="right">0.746</td> -<td align="right">0.996</td> +<td align="right">0.439</td> +<td align="right">0.557</td> +<td align="right">0.585</td> +<td align="right">1.338</td> +<td align="right">0.749</td> +<td align="right">0.999</td> </tr> </tbody> </table> </div> </div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - - <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2> - </nav> -</div> - + 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class="fab fa fab fa-github fa-lg"></span> </a> </li> </ul> </div> -<!--/.nav-collapse --> + + </div> -<!--/.container --> -</div> -<!--/.navbar --> +</nav><div class="container template-article"> + + - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header toc-ignore"> - <h1 data-toc-skip>Performance benefit by using compiled model -definitions in mkin</h1> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Performance benefit by using compiled model definitions in mkin</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> - <h4 data-toc-skip class="date">2023-10-30</h4> + <h4 data-toc-skip class="date">2023-11-16</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> - + <div class="d-none name"><code>compiled_models.rmd</code></div> </div> @@ -216,10 +175,10 @@ 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 0.213</span></span> -<span><span class="co">## 3 deSolve, compiled 1 1.418 0.302</span></span> -<span><span class="co">## 2 Eigenvalue based 1 2.000 0.426</span></span> -<span><span class="co">## 1 deSolve, not compiled 1 23.535 5.013</span></span></code></pre> +<span><span class="co">## 4 analytical 1 1.000 0.109</span></span> +<span><span class="co">## 3 deSolve, compiled 1 1.284 0.140</span></span> +<span><span class="co">## 2 Eigenvalue based 1 1.670 0.182</span></span> +<span><span class="co">## 1 deSolve, not compiled 1 21.927 2.390</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> @@ -250,44 +209,37 @@ 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 0.492</span></span> -<span><span class="co">## 1 deSolve, not compiled 1 20.398 10.036</span></span></code></pre> -<p>Here we get a performance benefit of a factor of 20 using the version +<span><span class="co">## 2 deSolve, compiled 1 1.000 0.181</span></span> +<span><span class="co">## 1 deSolve, not compiled 1 23.646 4.280</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 1.2.6 on</p> -<pre><code><span><span class="co">## R version 4.3.1 (2023-06-16)</span></span> +<pre><code><span><span class="co">## R version 4.3.2 (2023-10-31)</span></span> <span><span class="co">## Platform: x86_64-pc-linux-gnu (64-bit)</span></span> -<span><span class="co">## Running under: Ubuntu 22.04.3 LTS</span></span></code></pre> -<pre><code><span><span class="co">## CPU model: Intel(R) Xeon(R) Gold 6134 CPU @ 3.20GHz</span></span></code></pre> -</div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - - <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2> - </nav> +<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> </div> - + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside> </div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p> <p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p> <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> + </footer> </div> - </body> diff --git a/docs/articles/web_only/dimethenamid_2018.html b/docs/articles/web_only/dimethenamid_2018.html index 1cffd561..4221ba07 100644 --- a/docs/articles/web_only/dimethenamid_2018.html +++ b/docs/articles/web_only/dimethenamid_2018.html @@ -4,145 +4,104 @@ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> 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for" autocomplete="off"> +</form> + + <ul class="navbar-nav"> +<li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> </ul> </div> -<!--/.nav-collapse --> + + </div> -<!--/.container --> -</div> -<!--/.navbar --> +</nav><div class="container template-article"> + - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header toc-ignore"> - <h1 data-toc-skip>Example evaluations of the dimethenamid data -from 2018</h1> + +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Example evaluations of the dimethenamid data from 2018</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> <h4 data-toc-skip class="date">Last change 1 July 2022, -built on 30 Oct 2023</h4> +built on 16 Nov 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> - + <div class="d-none name"><code>dimethenamid_2018.rmd</code></div> </div> @@ -225,12 +184,12 @@ least in some datasets the degradation slows down towards later time points, and that the scatter of the residuals error is smaller for smaller values (panel to the right):</p> <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_sfo_const-1.png" width="700"></p> <p>Using biexponential decline (DFOP) results in a slightly more random scatter of the residuals:</p> <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_dfop_const-1.png" width="700"></p> <p>The population curve (bold line) in the above plot results from taking the mean of the individual transformed parameters, i.e. of log k1 @@ -242,7 +201,7 @@ dominates the average. This is alleviated if only rate constants that pass the t-test for significant difference from zero (on the untransformed scale) are considered in the averaging:</p> <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_dfop_const_test-1.png" width="700"></p> <p>While this is visually much more satisfactory, such an average procedure could introduce a bias, as not all results from the individual @@ -254,7 +213,7 @@ degradation model and the error model (see below).</p> predicted residues is reduced by using the two-component error model:</p> <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="fu"><a href="../../reference/mixed.html">mixed</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span>, test_log_parms <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_mkin_dfop_tc_test-1.png" width="700"></p> <p>However, note that in the case of using this error model, the fits to the Flaach and BBA 2.3 datasets appear to be ill-defined, indicated by @@ -344,7 +303,7 @@ effects does not improve the fits.</p> <p>The selected model (DFOP with two-component error) fitted to the data assuming no correlations between random effects is shown below.</p> <div class="sourceCode" id="cb13"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><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_parent_nlme_dfop_tc</span><span class="op">)</span></span></code></pre></div> +<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_nlme_dfop_tc</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/plot_parent_nlme-1.png" width="700"></p> </div> <div class="section level4"> @@ -361,17 +320,8 @@ implemented in the saemix package, the convergence plots need to be manually checked for every fit. We define control settings that work well for all the parent data fits shown in this vignette.</p> <div class="sourceCode" id="cb14"><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">saemix</span><span class="op">)</span></span></code></pre></div> -<pre><code>Loading required package: npde</code></pre> -<pre><code>Package saemix, version 3.2 - please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr</code></pre> -<pre><code> -Attaching package: 'saemix'</code></pre> -<pre><code>The following objects are masked from 'package:npde': - - kurtosis, skewness</code></pre> -<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r"> -<code class="sourceCode R"><span><span class="va">saemix_control</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/saemixControl.html" class="external-link">saemixControl</a></span><span class="op">(</span>nbiter.saemix <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">800</span>, <span class="fl">300</span><span class="op">)</span>, nb.chains <span class="op">=</span> <span class="fl">15</span>,</span> +<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">saemix</span><span class="op">)</span></span> +<span><span class="va">saemix_control</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/saemixControl.html" class="external-link">saemixControl</a></span><span class="op">(</span>nbiter.saemix <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">800</span>, <span class="fl">300</span><span class="op">)</span>, nb.chains <span class="op">=</span> <span class="fl">15</span>,</span> <span> print <span class="op">=</span> <span class="cn">FALSE</span>, save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span>, displayProgress <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> <span><span class="va">saemix_control_moreiter</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/saemixControl.html" class="external-link">saemixControl</a></span><span class="op">(</span>nbiter.saemix <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1600</span>, <span class="fl">300</span><span class="op">)</span>, nb.chains <span class="op">=</span> <span class="fl">15</span>,</span> <span> print <span class="op">=</span> <span class="cn">FALSE</span>, save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span>, displayProgress <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> @@ -379,7 +329,7 @@ Attaching package: 'saemix'</code></pre> <span> print <span class="op">=</span> <span class="cn">FALSE</span>, save <span class="op">=</span> <span class="cn">FALSE</span>, save.graphs <span class="op">=</span> <span class="cn">FALSE</span>, displayProgress <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> <p>The convergence plot for the SFO model using constant variance is shown below.</p> -<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">f_parent_saemix_sfo_const</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span> <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">f_parent_saemix_sfo_const</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></code></pre></div> @@ -387,19 +337,19 @@ shown below.</p> <p>Obviously the selected number of iterations is sufficient to reach convergence. This can also be said for the SFO fit using the two-component error model.</p> -<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">f_parent_saemix_sfo_tc</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"SFO"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/plot.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">f_parent_saemix_sfo_tc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_saemix_sfo_tc-1.png" width="700"></p> <p>When fitting the DFOP model with constant variance (see below), parameter convergence is not as unambiguous.</p> -<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">f_parent_saemix_dfop_const</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_const</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span> <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">f_parent_saemix_dfop_const</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_saemix_dfop_const-1.png" width="700"></p> -<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_const</span><span class="op">)</span></span></code></pre></div> <pre><code>Kinetic nonlinear mixed-effects model fit by SAEM Structural model: @@ -435,14 +385,14 @@ this model.</p> also observe that the estimated variance of k2 becomes very small, while being ill-defined, as illustrated by the excessive confidence interval of <code>SD.k2</code>.</p> -<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">f_parent_saemix_dfop_tc</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> control <span class="op">=</span> <span class="va">saemix_control</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span> <span><span class="va">f_parent_saemix_dfop_tc_moreiter</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>,</span> <span> control <span class="op">=</span> <span class="va">saemix_control_moreiter</span>, transformations <span class="op">=</span> <span class="st">"saemix"</span><span class="op">)</span></span> <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">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span>, plot.type <span class="op">=</span> <span class="st">"convergence"</span><span class="op">)</span></span></code></pre></div> <p><img src="dimethenamid_2018_files/figure-html/f_parent_saemix_dfop_tc-1.png" width="700"></p> -<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc</span><span class="op">)</span></span></code></pre></div> <pre><code>Kinetic nonlinear mixed-effects model fit by SAEM Structural model: @@ -484,7 +434,7 @@ message.</p> <p>The four combinations (SFO/const, SFO/tc, DFOP/const and DFOP/tc) and the version with increased iterations can be compared using the model comparison function of the saemix package:</p> -<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">AIC_parent_saemix</span> <span class="op"><-</span> <span class="fu">saemix</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/compare.saemix.html" class="external-link">compare.saemix</a></span><span class="op">(</span></span> <span> <span class="va">f_parent_saemix_sfo_const</span><span class="op">$</span><span class="va">so</span>,</span> <span> <span class="va">f_parent_saemix_sfo_tc</span><span class="op">$</span><span class="va">so</span>,</span> @@ -492,7 +442,7 @@ comparison function of the saemix package:</p> <span> <span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span>,</span> <span> <span class="va">f_parent_saemix_dfop_tc_moreiter</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span></code></pre></div> <pre><code>Likelihoods calculated by importance sampling</code></pre> -<div class="sourceCode" id="cb30"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb25"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">AIC_parent_saemix</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span> <span> <span class="st">"SFO const"</span>, <span class="st">"SFO tc"</span>, <span class="st">"DFOP const"</span>, <span class="st">"DFOP tc"</span>, <span class="st">"DFOP tc more iterations"</span><span class="op">)</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">AIC_parent_saemix</span><span class="op">)</span></span></code></pre></div> @@ -506,7 +456,7 @@ DFOP tc more iterations 665.85 663.76</code></pre> algorithms implemented in saemix, the likelihood from Gaussian quadrature is added to the best fit, and the AIC values obtained from the three methods are compared.</p> -<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span> <span class="op"><-</span></span> <span> <span class="fu">saemix</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/llgq.saemix.html" class="external-link">llgq.saemix</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span> <span><span class="va">AIC_parent_saemix_methods</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> @@ -530,7 +480,7 @@ iterations makes a lot of difference. When using the LAPACK version coming with Debian Bullseye, the AIC based on Gaussian quadrature is almost the same as the one obtained with the other methods, also when using defaults for the fit.</p> -<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">f_parent_saemix_dfop_tc_defaults</span> <span class="op"><-</span> <span class="fu">mkin</span><span class="fu">::</span><span class="fu"><a href="../../reference/saem.html">saem</a></span><span class="op">(</span><span class="va">f_parent_mkin_tc</span><span class="op">[</span><span class="st">"DFOP"</span>, <span class="op">]</span><span class="op">)</span></span> <span><span class="va">f_parent_saemix_dfop_tc_defaults</span><span class="op">$</span><span class="va">so</span> <span class="op"><-</span></span> <span> <span class="fu">saemix</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/llgq.saemix.html" class="external-link">llgq.saemix</a></span><span class="op">(</span><span class="va">f_parent_saemix_dfop_tc_defaults</span><span class="op">$</span><span class="va">so</span><span class="op">)</span></span> @@ -550,7 +500,7 @@ using defaults for the fit.</p> <p>The following table gives the AIC values obtained with both backend packages using the same control parameters (800 iterations burn-in, 300 iterations second phase, 15 chains).</p> -<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r"> +<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r"> <code class="sourceCode R"><span><span class="va">AIC_all</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span> <span> check.names <span class="op">=</span> <span class="cn">FALSE</span>,</span> <span> <span class="st">"Degradation model"</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">"SFO"</span>, <span class="st">"DFOP"</span>, <span class="st">"DFOP"</span><span class="op">)</span>,</span> @@ -561,7 +511,7 @@ iterations second phase, 15 chains).</p> <span> saemix_is <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</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_parent_saemix_sfo_const</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_parent_saemix_sfo_tc</span><span class="op">$</span><span class="va">so</span>,</span> <span> <span class="va">f_parent_saemix_dfop_const</span><span class="op">$</span><span class="va">so</span>, <span class="va">f_parent_saemix_dfop_tc</span><span class="op">$</span><span class="va">so</span><span class="op">)</span>, <span class="va">AIC</span>, method <span class="op">=</span> <span class="st">"is"</span><span class="op">)</span></span> <span><span class="op">)</span></span> -<span><span class="fu">kable</span><span class="op">(</span><span class="va">AIC_all</span><span class="op">)</span></span></code></pre></div> +<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">AIC_all</span><span class="op">)</span></span></code></pre></div> <table class="table"> <thead><tr class="header"> <th align="left">Degradation model</th> @@ -624,48 +574,48 @@ satisfactory precision.</p> <div class="section level2"> <h2 id="session-info">Session Info<a class="anchor" aria-label="anchor" href="#session-info"></a> </h2> -<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r"> +<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 4.3.1 (2023-06-16) +<pre><code>R version 4.3.2 (2023-10-31) Platform: x86_64-pc-linux-gnu (64-bit) -Running under: Ubuntu 22.04.3 LTS +Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default -BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 -LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0 +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=en_US.UTF-8 LC_NUMERIC=C - [3] LC_TIME=C LC_COLLATE=en_US.UTF-8 - [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 - [7] LC_PAPER=en_US.UTF-8 LC_NAME=C + [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C + [3] LC_TIME=C 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=en_US.UTF-8 LC_IDENTIFICATION=C +[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C -time zone: Europe/Zurich +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_3.1-163 mkin_1.2.6 knitr_1.44 +[1] saemix_3.2 npde_3.3 nlme_3.1-163 mkin_1.2.6 knitr_1.42 loaded via a namespace (and not attached): - [1] sass_0.4.7 utf8_1.2.3 generics_0.1.3 stringi_1.7.12 - [5] lattice_0.21-9 digest_0.6.33 magrittr_2.0.3 evaluate_0.22 - [9] grid_4.3.1 fastmap_1.1.1 rprojroot_2.0.3 jsonlite_1.8.7 -[13] mclust_6.0.0 gridExtra_2.3 purrr_1.0.1 fansi_1.0.4 -[17] scales_1.2.1 codetools_0.2-19 textshaping_0.3.6 jquerylib_0.1.4 -[21] cli_3.6.1 rlang_1.1.1 munsell_0.5.0 cachem_1.0.8 -[25] yaml_2.3.7 tools_4.3.1 parallel_4.3.1 memoise_2.0.1 -[29] dplyr_1.1.2 colorspace_2.1-0 ggplot2_3.4.2 vctrs_0.6.3 -[33] R6_2.5.1 zoo_1.8-12 lifecycle_1.0.3 stringr_1.5.0 -[37] fs_1.6.3 MASS_7.3-60 ragg_1.2.5 pkgconfig_2.0.3 -[41] desc_1.4.2 pkgdown_2.0.7 bslib_0.5.1 pillar_1.9.0 -[45] gtable_0.3.3 glue_1.6.2 systemfonts_1.0.4 xfun_0.40 -[49] tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.0 rstudioapi_0.15.0 -[53] htmltools_0.5.6.1 rmarkdown_2.23 compiler_4.3.1 </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_4.3.2 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_4.3.2 parallel_4.3.2 +[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 MASS_7.3-60 ragg_1.2.5 +[41] pkgconfig_2.0.3 desc_1.4.2 pkgdown_2.0.7 bslib_0.4.2 +[45] pillar_1.9.0 gtable_0.3.3 glue_1.6.2 systemfonts_1.0.4 +[49] highr_0.10 xfun_0.39 tibble_3.2.1 lmtest_0.9-40 +[53] tidyselect_1.2.0 htmltools_0.5.5 rmarkdown_2.21 compiler_4.3.2 </code></pre> </div> <div class="section level2"> <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a> @@ -690,34 +640,27 @@ November 2017</span>.”</span> <a href="https://open.efsa.europa.eu/study-inven </div> </div> </div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - - <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2> - </nav> -</div> - + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside> </div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p> <p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> 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multistart method</h1> <h4 data-toc-skip class="author">Johannes Ranke</h4> <h4 data-toc-skip class="date">Last change 20 April 2023 -(rebuilt 2023-10-30)</h4> +(rebuilt 2023-11-16)</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> - + <div class="d-none name"><code>multistart.rmd</code></div> </div> @@ -207,32 +167,27 @@ improvement in case of the full model, because it is less well-defined, which impedes convergence. 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definitions in mkin</a> + <a class="dropdown-item" href="../../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + <a class="dropdown-item" href="../../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6> + <a class="dropdown-item" href="../../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a class="dropdown-item" href="../../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </div> </li> -<li> - <a href="../../news/index.html">News</a> +<li class="nav-item"> + <a class="nav-link" href="../../news/index.html">News</a> </li> </ul> -<ul class="nav navbar-nav navbar-right"> -<li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> +<form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" 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2023-11-02)</h4> +(rebuilt 2023-11-16)</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> - + <div class="d-none name"><code>saem_benchmarks.rmd</code></div> </div> @@ -193,7 +153,7 @@ explanation of the following preprocessing.</p> <div class="sourceCode" id="cb4"><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> <span> <span class="va">sfo_const</span>, <span class="va">dfop_const</span>, <span class="va">sforb_const</span>, <span class="va">hs_const</span>,</span> -<span> <span class="va">sfo_tc</span>, <span class="va">dfop_tc</span>, <span class="va">sforb_tc</span>, <span class="va">hs_tc</span><span class="op">)</span> <span class="op">|></span> <span class="fu">kable</span><span class="op">(</span>, digits <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></code></pre></div> +<span> <span class="va">sfo_tc</span>, <span class="va">dfop_tc</span>, <span class="va">sforb_tc</span>, <span class="va">hs_tc</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> @@ -440,10 +400,10 @@ systems. All trademarks belong to their respective owners.</p> <td align="left">Linux</td> <td align="left">1.2.6</td> <td align="left">3.2</td> -<td align="right">1.126</td> -<td align="right">1.971</td> -<td align="right">2.359</td> -<td align="right">2.424</td> +<td align="right">1.135</td> +<td align="right">2.025</td> +<td align="right">2.406</td> +<td align="right">2.478</td> </tr> </tbody> </table> @@ -555,10 +515,10 @@ systems. All trademarks belong to their respective owners.</p> <td align="left">Linux</td> <td align="left">1.2.6</td> <td align="left">3.2</td> -<td align="right">2.116</td> -<td align="right">3.246</td> -<td align="right">3.602</td> -<td align="right">3.036</td> +<td align="right">2.161</td> +<td align="right">3.325</td> +<td align="right">3.669</td> +<td align="right">3.153</td> </tr> </tbody> </table> @@ -654,8 +614,8 @@ systems. All trademarks belong to their respective owners.</p> <td align="left">Linux</td> <td align="left">1.2.6</td> <td align="left">3.2</td> -<td align="right">11.712</td> -<td align="right">290.532</td> +<td align="right">12.007</td> +<td align="right">286.757</td> </tr> </tbody> </table> @@ -741,40 +701,33 @@ systems. All trademarks belong to their respective owners.</p> <td align="left">Linux</td> <td align="left">1.2.6</td> <td align="left">3.2</td> -<td align="right">479.161</td> +<td align="right">480.577</td> </tr> </tbody> </table> </div> </div> - </div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - - <nav id="toc" data-toggle="toc"><h2 data-toc-skip>Contents</h2> - </nav> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside> </div> -</div> - - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p> <p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p> <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> + </footer> </div> - </body> diff --git a/docs/authors.html b/docs/authors.html index 2e97a0dc..088db2aa 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -1,112 +1,78 @@ <!DOCTYPE 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class="dropdown-item" href="articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </div> +</li> +<li class="nav-item"> + <a class="nav-link" href="news/index.html">News</a> </li> - </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - + </ul></div> - </header><div class="row"> - <div class="contents col-md-9"> - <div class="section level2 authors-section"> - <div class="page-header"> - <h1>Authors</h1> - </div> + + </div> +</nav><div class="container template-citation-authors"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Authors and Citation</h1> + </div> + <div class="section level2 citation"> + <h2>Authors</h2> <ul class="list-unstyled"><li> <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright holder. <a href="https://orcid.org/0000-0003-4371-6538" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> @@ -125,45 +91,39 @@ <br><small>copyright for some of the contributions of JR 2012-2014</small></p> </li> </ul></div> - <div class="section level2 citation-section"> - <div> - <h1 id="citation">Citation</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/DESCRIPTION" class="external-link"><code>DESCRIPTION</code></a></small> - </div> - </div> + <div class="section level2 citation"> + <h2 id="citation">Citation</h2> + <p><small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/DESCRIPTION" class="external-link"><code>DESCRIPTION</code></a></small></p> - <p>Ranke J (2023). + <p>Ranke J (2023). <em>mkin: Kinetic Evaluation of Chemical Degradation Data</em>. R package version 1.2.6, <a href="https://pkgdown.jrwb.de/mkin/">https://pkgdown.jrwb.de/mkin/</a>. </p> - <pre>@Manual{, + <pre>@Manual{, title = {mkin: Kinetic Evaluation of Chemical Degradation Data}, author = {Johannes Ranke}, year = {2023}, note = {R package version 1.2.6}, url = {https://pkgdown.jrwb.de/mkin/}, }</pre> - - </div> - -</div> - + </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js b/docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js new file mode 100644 index 00000000..1d138863 --- /dev/null +++ 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g?g(Object.assign({},e.rects,{placement:e.placement})):g,O="number"==typeof C?{mainAxis:C,altAxis:C}:Object.assign({mainAxis:0,altAxis:0},C),x=e.modifiersData.offset?e.modifiersData.offset[e.placement]:null,k={x:0,y:0};if(A){if(o){var L,D="y"===y?gt:bt,S="y"===y?mt:_t,I="y"===y?"height":"width",N=A[y],P=N+m[D],j=N-m[S],M=f?-T[I]/2:0,H=b===wt?E[I]:T[I],$=b===wt?-T[I]:-E[I],W=e.elements.arrow,B=f&&W?Jt(W):{width:0,height:0},F=e.modifiersData["arrow#persistent"]?e.modifiersData["arrow#persistent"].padding:{top:0,right:0,bottom:0,left:0},z=F[D],q=F[S],R=ae(0,E[I],B[I]),V=v?E[I]/2-M-R-z-O.mainAxis:H-R-z-O.mainAxis,K=v?-E[I]/2+M+R+q+O.mainAxis:$+R+q+O.mainAxis,Q=e.elements.arrow&&oe(e.elements.arrow),X=Q?"y"===y?Q.clientTop||0:Q.clientLeft||0:0,Y=null!=(L=null==x?void 0:x[y])?L:0,U=N+K-Y,G=ae(f?Qt(P,N+V-Y-X):P,N,f?Kt(j,U):j);A[y]=G,k[y]=G-N}if(a){var J,Z="x"===y?gt:bt,tt="x"===y?mt:_t,et=A[w],it="y"===w?"height":"width",nt=et+m[Z],st=et-m[tt],ot=-1!==[gt,bt].indexOf(_),rt=null!=(J=null==x?void 0:x[w])?J:0,at=ot?nt:et-E[it]-T[it]-rt+O.altAxis,lt=ot?et+E[it]+T[it]-rt-O.altAxis:st,ct=f&&ot?function(t,e,i){var n=ae(t,e,i);return n>i?i:n}(at,et,lt):ae(f?at:nt,et,f?lt:st);A[w]=ct,k[w]=ct-et}e.modifiersData[n]=k}},requiresIfExists:["offset"]};function $e(t,e,i){void 0===i&&(i=!1);var n,s,o=zt(e),r=zt(e)&&function(t){var e=t.getBoundingClientRect(),i=Xt(e.width)/t.offsetWidth||1,n=Xt(e.height)/t.offsetHeight||1;return 1!==i||1!==n}(e),a=ie(e),l=Gt(t,r,i),c={scrollLeft:0,scrollTop:0},h={x:0,y:0};return(o||!o&&!i)&&(("body"!==Wt(e)||Ee(a))&&(c=(n=e)!==Bt(n)&&zt(n)?{scrollLeft:(s=n).scrollLeft,scrollTop:s.scrollTop}:we(n)),zt(e)?((h=Gt(e,!0)).x+=e.clientLeft,h.y+=e.clientTop):a&&(h.x=Ae(a))),{x:l.left+c.scrollLeft-h.x,y:l.top+c.scrollTop-h.y,width:l.width,height:l.height}}function We(t){var e=new Map,i=new Set,n=[];function s(t){i.add(t.name),[].concat(t.requires||[],t.requiresIfExists||[]).forEach((function(t){if(!i.has(t)){var n=e.get(t);n&&s(n)}})),n.push(t)}return t.forEach((function(t){e.set(t.name,t)})),t.forEach((function(t){i.has(t.name)||s(t)})),n}var Be={placement:"bottom",modifiers:[],strategy:"absolute"};function Fe(){for(var t=arguments.length,e=new Array(t),i=0;i<t;i++)e[i]=arguments[i];return!e.some((function(t){return!(t&&"function"==typeof t.getBoundingClientRect)}))}function ze(t){void 0===t&&(t={});var e=t,i=e.defaultModifiers,n=void 0===i?[]:i,s=e.defaultOptions,o=void 0===s?Be:s;return function(t,e,i){void 0===i&&(i=o);var s,r,a={placement:"bottom",orderedModifiers:[],options:Object.assign({},Be,o),modifiersData:{},elements:{reference:t,popper:e},attributes:{},styles:{}},l=[],c=!1,h={state:a,setOptions:function(i){var s="function"==typeof i?i(a.options):i;d(),a.options=Object.assign({},o,a.options,s),a.scrollParents={reference:Ft(t)?Ce(t):t.contextElement?Ce(t.contextElement):[],popper:Ce(e)};var r,c,u=function(t){var e=We(t);return $t.reduce((function(t,i){return t.concat(e.filter((function(t){return t.phase===i})))}),[])}((r=[].concat(n,a.options.modifiers),c=r.reduce((function(t,e){var i=t[e.name];return t[e.name]=i?Object.assign({},i,e,{options:Object.assign({},i.options,e.options),data:Object.assign({},i.data,e.data)}):e,t}),{}),Object.keys(c).map((function(t){return c[t]}))));return a.orderedModifiers=u.filter((function(t){return t.enabled})),a.orderedModifiers.forEach((function(t){var e=t.name,i=t.options,n=void 0===i?{}:i,s=t.effect;if("function"==typeof s){var o=s({state:a,name:e,instance:h,options:n});l.push(o||function(){})}})),h.update()},forceUpdate:function(){if(!c){var t=a.elements,e=t.reference,i=t.popper;if(Fe(e,i)){a.rects={reference:$e(e,oe(i),"fixed"===a.options.strategy),popper:Jt(i)},a.reset=!1,a.placement=a.options.placement,a.orderedModifiers.forEach((function(t){return a.modifiersData[t.name]=Object.assign({},t.data)}));for(var n=0;n<a.orderedModifiers.length;n++)if(!0!==a.reset){var s=a.orderedModifiers[n],o=s.fn,r=s.options,l=void 0===r?{}:r,d=s.name;"function"==typeof o&&(a=o({state:a,options:l,name:d,instance:h})||a)}else a.reset=!1,n=-1}}},update:(s=function(){return new Promise((function(t){h.forceUpdate(),t(a)}))},function(){return r||(r=new Promise((function(t){Promise.resolve().then((function(){r=void 0,t(s())}))}))),r}),destroy:function(){d(),c=!0}};if(!Fe(t,e))return h;function d(){l.forEach((function(t){return t()})),l=[]}return h.setOptions(i).then((function(t){!c&&i.onFirstUpdate&&i.onFirstUpdate(t)})),h}}var qe=ze(),Re=ze({defaultModifiers:[me,Me,pe,Rt]}),Ve=ze({defaultModifiers:[me,Me,pe,Rt,je,Se,He,he,Pe]});const Ke=Object.freeze(Object.defineProperty({__proto__:null,popperGenerator:ze,detectOverflow:Le,createPopperBase:qe,createPopper:Ve,createPopperLite:Re,top:gt,bottom:mt,right:_t,left:bt,auto:vt,basePlacements:yt,start:wt,end:At,clippingParents:Et,viewport:Tt,popper:Ct,reference:Ot,variationPlacements:xt,placements:kt,beforeRead:Lt,read:Dt,afterRead:St,beforeMain:It,main:Nt,afterMain:Pt,beforeWrite:jt,write:Mt,afterWrite:Ht,modifierPhases:$t,applyStyles:Rt,arrow:he,computeStyles:pe,eventListeners:me,flip:Se,hide:Pe,offset:je,popperOffsets:Me,preventOverflow:He},Symbol.toStringTag,{value:"Module"})),Qe="dropdown",Xe="ArrowUp",Ye="ArrowDown",Ue="click.bs.dropdown.data-api",Ge="keydown.bs.dropdown.data-api",Je="show",Ze='[data-bs-toggle="dropdown"]:not(.disabled):not(:disabled)',ti=`${Ze}.show`,ei=".dropdown-menu",ii=p()?"top-end":"top-start",ni=p()?"top-start":"top-end",si=p()?"bottom-end":"bottom-start",oi=p()?"bottom-start":"bottom-end",ri=p()?"left-start":"right-start",ai=p()?"right-start":"left-start",li={autoClose:!0,boundary:"clippingParents",display:"dynamic",offset:[0,2],popperConfig:null,reference:"toggle"},ci={autoClose:"(boolean|string)",boundary:"(string|element)",display:"string",offset:"(array|string|function)",popperConfig:"(null|object|function)",reference:"(string|element|object)"};class hi extends z{constructor(t,e){super(t,e),this._popper=null,this._parent=this._element.parentNode,this._menu=Q.next(this._element,ei)[0]||Q.prev(this._element,ei)[0]||Q.findOne(ei,this._parent),this._inNavbar=this._detectNavbar()}static get Default(){return li}static get DefaultType(){return ci}static get NAME(){return Qe}toggle(){return this._isShown()?this.hide():this.show()}show(){if(l(this._element)||this._isShown())return;const t={relatedTarget:this._element};if(!P.trigger(this._element,"show.bs.dropdown",t).defaultPrevented){if(this._createPopper(),"ontouchstart"in document.documentElement&&!this._parent.closest(".navbar-nav"))for(const t of[].concat(...document.body.children))P.on(t,"mouseover",h);this._element.focus(),this._element.setAttribute("aria-expanded",!0),this._menu.classList.add(Je),this._element.classList.add(Je),P.trigger(this._element,"shown.bs.dropdown",t)}}hide(){if(l(this._element)||!this._isShown())return;const t={relatedTarget:this._element};this._completeHide(t)}dispose(){this._popper&&this._popper.destroy(),super.dispose()}update(){this._inNavbar=this._detectNavbar(),this._popper&&this._popper.update()}_completeHide(t){if(!P.trigger(this._element,"hide.bs.dropdown",t).defaultPrevented){if("ontouchstart"in document.documentElement)for(const t of[].concat(...document.body.children))P.off(t,"mouseover",h);this._popper&&this._popper.destroy(),this._menu.classList.remove(Je),this._element.classList.remove(Je),this._element.setAttribute("aria-expanded","false"),B.removeDataAttribute(this._menu,"popper"),P.trigger(this._element,"hidden.bs.dropdown",t)}}_getConfig(t){if("object"==typeof(t=super._getConfig(t)).reference&&!o(t.reference)&&"function"!=typeof t.reference.getBoundingClientRect)throw new TypeError(`${Qe.toUpperCase()}: Option "reference" provided type "object" without a required "getBoundingClientRect" method.`);return t}_createPopper(){if(void 0===Ke)throw new TypeError("Bootstrap's dropdowns require Popper (https://popper.js.org)");let t=this._element;"parent"===this._config.reference?t=this._parent:o(this._config.reference)?t=r(this._config.reference):"object"==typeof this._config.reference&&(t=this._config.reference);const e=this._getPopperConfig();this._popper=Ve(t,this._menu,e)}_isShown(){return this._menu.classList.contains(Je)}_getPlacement(){const t=this._parent;if(t.classList.contains("dropend"))return ri;if(t.classList.contains("dropstart"))return ai;if(t.classList.contains("dropup-center"))return"top";if(t.classList.contains("dropdown-center"))return"bottom";const e="end"===getComputedStyle(this._menu).getPropertyValue("--bs-position").trim();return t.classList.contains("dropup")?e?ni:ii:e?oi:si}_detectNavbar(){return null!==this._element.closest(".navbar")}_getOffset(){const{offset:t}=this._config;return"string"==typeof t?t.split(",").map((t=>Number.parseInt(t,10))):"function"==typeof t?e=>t(e,this._element):t}_getPopperConfig(){const t={placement:this._getPlacement(),modifiers:[{name:"preventOverflow",options:{boundary:this._config.boundary}},{name:"offset",options:{offset:this._getOffset()}}]};return(this._inNavbar||"static"===this._config.display)&&(B.setDataAttribute(this._menu,"popper","static"),t.modifiers=[{name:"applyStyles",enabled:!1}]),{...t,..."function"==typeof this._config.popperConfig?this._config.popperConfig(t):this._config.popperConfig}}_selectMenuItem({key:t,target:e}){const i=Q.find(".dropdown-menu .dropdown-item:not(.disabled):not(:disabled)",this._menu).filter((t=>a(t)));i.length&&b(i,e,t===Ye,!i.includes(e)).focus()}static jQueryInterface(t){return this.each((function(){const e=hi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}static clearMenus(t){if(2===t.button||"keyup"===t.type&&"Tab"!==t.key)return;const e=Q.find(ti);for(const i of e){const e=hi.getInstance(i);if(!e||!1===e._config.autoClose)continue;const n=t.composedPath(),s=n.includes(e._menu);if(n.includes(e._element)||"inside"===e._config.autoClose&&!s||"outside"===e._config.autoClose&&s)continue;if(e._menu.contains(t.target)&&("keyup"===t.type&&"Tab"===t.key||/input|select|option|textarea|form/i.test(t.target.tagName)))continue;const o={relatedTarget:e._element};"click"===t.type&&(o.clickEvent=t),e._completeHide(o)}}static dataApiKeydownHandler(t){const e=/input|textarea/i.test(t.target.tagName),i="Escape"===t.key,n=[Xe,Ye].includes(t.key);if(!n&&!i)return;if(e&&!i)return;t.preventDefault();const s=this.matches(Ze)?this:Q.prev(this,Ze)[0]||Q.next(this,Ze)[0]||Q.findOne(Ze,t.delegateTarget.parentNode),o=hi.getOrCreateInstance(s);if(n)return t.stopPropagation(),o.show(),void o._selectMenuItem(t);o._isShown()&&(t.stopPropagation(),o.hide(),s.focus())}}P.on(document,Ge,Ze,hi.dataApiKeydownHandler),P.on(document,Ge,ei,hi.dataApiKeydownHandler),P.on(document,Ue,hi.clearMenus),P.on(document,"keyup.bs.dropdown.data-api",hi.clearMenus),P.on(document,Ue,Ze,(function(t){t.preventDefault(),hi.getOrCreateInstance(this).toggle()})),g(hi);const di=".fixed-top, .fixed-bottom, .is-fixed, .sticky-top",ui=".sticky-top",fi="padding-right",pi="margin-right";class gi{constructor(){this._element=document.body}getWidth(){const t=document.documentElement.clientWidth;return Math.abs(window.innerWidth-t)}hide(){const t=this.getWidth();this._disableOverFlow(),this._setElementAttributes(this._element,fi,(e=>e+t)),this._setElementAttributes(di,fi,(e=>e+t)),this._setElementAttributes(ui,pi,(e=>e-t))}reset(){this._resetElementAttributes(this._element,"overflow"),this._resetElementAttributes(this._element,fi),this._resetElementAttributes(di,fi),this._resetElementAttributes(ui,pi)}isOverflowing(){return this.getWidth()>0}_disableOverFlow(){this._saveInitialAttribute(this._element,"overflow"),this._element.style.overflow="hidden"}_setElementAttributes(t,e,i){const n=this.getWidth();this._applyManipulationCallback(t,(t=>{if(t!==this._element&&window.innerWidth>t.clientWidth+n)return;this._saveInitialAttribute(t,e);const s=window.getComputedStyle(t).getPropertyValue(e);t.style.setProperty(e,`${i(Number.parseFloat(s))}px`)}))}_saveInitialAttribute(t,e){const i=t.style.getPropertyValue(e);i&&B.setDataAttribute(t,e,i)}_resetElementAttributes(t,e){this._applyManipulationCallback(t,(t=>{const i=B.getDataAttribute(t,e);null!==i?(B.removeDataAttribute(t,e),t.style.setProperty(e,i)):t.style.removeProperty(e)}))}_applyManipulationCallback(t,e){if(o(t))e(t);else for(const i of Q.find(t,this._element))e(i)}}const mi="show",_i="mousedown.bs.backdrop",bi={className:"modal-backdrop",clickCallback:null,isAnimated:!1,isVisible:!0,rootElement:"body"},vi={className:"string",clickCallback:"(function|null)",isAnimated:"boolean",isVisible:"boolean",rootElement:"(element|string)"};class yi extends F{constructor(t){super(),this._config=this._getConfig(t),this._isAppended=!1,this._element=null}static get Default(){return bi}static get DefaultType(){return vi}static get NAME(){return"backdrop"}show(t){if(!this._config.isVisible)return void m(t);this._append();const e=this._getElement();this._config.isAnimated&&d(e),e.classList.add(mi),this._emulateAnimation((()=>{m(t)}))}hide(t){this._config.isVisible?(this._getElement().classList.remove(mi),this._emulateAnimation((()=>{this.dispose(),m(t)}))):m(t)}dispose(){this._isAppended&&(P.off(this._element,_i),this._element.remove(),this._isAppended=!1)}_getElement(){if(!this._element){const t=document.createElement("div");t.className=this._config.className,this._config.isAnimated&&t.classList.add("fade"),this._element=t}return this._element}_configAfterMerge(t){return t.rootElement=r(t.rootElement),t}_append(){if(this._isAppended)return;const t=this._getElement();this._config.rootElement.append(t),P.on(t,_i,(()=>{m(this._config.clickCallback)})),this._isAppended=!0}_emulateAnimation(t){_(t,this._getElement(),this._config.isAnimated)}}const wi=".bs.focustrap",Ai="backward",Ei={autofocus:!0,trapElement:null},Ti={autofocus:"boolean",trapElement:"element"};class Ci extends F{constructor(t){super(),this._config=this._getConfig(t),this._isActive=!1,this._lastTabNavDirection=null}static get Default(){return Ei}static get DefaultType(){return Ti}static get NAME(){return"focustrap"}activate(){this._isActive||(this._config.autofocus&&this._config.trapElement.focus(),P.off(document,wi),P.on(document,"focusin.bs.focustrap",(t=>this._handleFocusin(t))),P.on(document,"keydown.tab.bs.focustrap",(t=>this._handleKeydown(t))),this._isActive=!0)}deactivate(){this._isActive&&(this._isActive=!1,P.off(document,wi))}_handleFocusin(t){const{trapElement:e}=this._config;if(t.target===document||t.target===e||e.contains(t.target))return;const i=Q.focusableChildren(e);0===i.length?e.focus():this._lastTabNavDirection===Ai?i[i.length-1].focus():i[0].focus()}_handleKeydown(t){"Tab"===t.key&&(this._lastTabNavDirection=t.shiftKey?Ai:"forward")}}const Oi="hidden.bs.modal",xi="show.bs.modal",ki="modal-open",Li="show",Di="modal-static",Si={backdrop:!0,focus:!0,keyboard:!0},Ii={backdrop:"(boolean|string)",focus:"boolean",keyboard:"boolean"};class Ni extends z{constructor(t,e){super(t,e),this._dialog=Q.findOne(".modal-dialog",this._element),this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._isShown=!1,this._isTransitioning=!1,this._scrollBar=new gi,this._addEventListeners()}static get Default(){return Si}static get DefaultType(){return Ii}static get NAME(){return"modal"}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||this._isTransitioning||P.trigger(this._element,xi,{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._isTransitioning=!0,this._scrollBar.hide(),document.body.classList.add(ki),this._adjustDialog(),this._backdrop.show((()=>this._showElement(t))))}hide(){this._isShown&&!this._isTransitioning&&(P.trigger(this._element,"hide.bs.modal").defaultPrevented||(this._isShown=!1,this._isTransitioning=!0,this._focustrap.deactivate(),this._element.classList.remove(Li),this._queueCallback((()=>this._hideModal()),this._element,this._isAnimated())))}dispose(){for(const t of[window,this._dialog])P.off(t,".bs.modal");this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}handleUpdate(){this._adjustDialog()}_initializeBackDrop(){return new yi({isVisible:Boolean(this._config.backdrop),isAnimated:this._isAnimated()})}_initializeFocusTrap(){return new Ci({trapElement:this._element})}_showElement(t){document.body.contains(this._element)||document.body.append(this._element),this._element.style.display="block",this._element.removeAttribute("aria-hidden"),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.scrollTop=0;const e=Q.findOne(".modal-body",this._dialog);e&&(e.scrollTop=0),d(this._element),this._element.classList.add(Li),this._queueCallback((()=>{this._config.focus&&this._focustrap.activate(),this._isTransitioning=!1,P.trigger(this._element,"shown.bs.modal",{relatedTarget:t})}),this._dialog,this._isAnimated())}_addEventListeners(){P.on(this._element,"keydown.dismiss.bs.modal",(t=>{if("Escape"===t.key)return this._config.keyboard?(t.preventDefault(),void this.hide()):void this._triggerBackdropTransition()})),P.on(window,"resize.bs.modal",(()=>{this._isShown&&!this._isTransitioning&&this._adjustDialog()})),P.on(this._element,"mousedown.dismiss.bs.modal",(t=>{P.one(this._element,"click.dismiss.bs.modal",(e=>{this._element===t.target&&this._element===e.target&&("static"!==this._config.backdrop?this._config.backdrop&&this.hide():this._triggerBackdropTransition())}))}))}_hideModal(){this._element.style.display="none",this._element.setAttribute("aria-hidden",!0),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._isTransitioning=!1,this._backdrop.hide((()=>{document.body.classList.remove(ki),this._resetAdjustments(),this._scrollBar.reset(),P.trigger(this._element,Oi)}))}_isAnimated(){return this._element.classList.contains("fade")}_triggerBackdropTransition(){if(P.trigger(this._element,"hidePrevented.bs.modal").defaultPrevented)return;const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._element.style.overflowY;"hidden"===e||this._element.classList.contains(Di)||(t||(this._element.style.overflowY="hidden"),this._element.classList.add(Di),this._queueCallback((()=>{this._element.classList.remove(Di),this._queueCallback((()=>{this._element.style.overflowY=e}),this._dialog)}),this._dialog),this._element.focus())}_adjustDialog(){const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._scrollBar.getWidth(),i=e>0;if(i&&!t){const t=p()?"paddingLeft":"paddingRight";this._element.style[t]=`${e}px`}if(!i&&t){const t=p()?"paddingRight":"paddingLeft";this._element.style[t]=`${e}px`}}_resetAdjustments(){this._element.style.paddingLeft="",this._element.style.paddingRight=""}static jQueryInterface(t,e){return this.each((function(){const i=Ni.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===i[t])throw new TypeError(`No method named "${t}"`);i[t](e)}}))}}P.on(document,"click.bs.modal.data-api",'[data-bs-toggle="modal"]',(function(t){const e=n(this);["A","AREA"].includes(this.tagName)&&t.preventDefault(),P.one(e,xi,(t=>{t.defaultPrevented||P.one(e,Oi,(()=>{a(this)&&this.focus()}))}));const i=Q.findOne(".modal.show");i&&Ni.getInstance(i).hide(),Ni.getOrCreateInstance(e).toggle(this)})),q(Ni),g(Ni);const Pi="show",ji="showing",Mi="hiding",Hi=".offcanvas.show",$i="hidePrevented.bs.offcanvas",Wi="hidden.bs.offcanvas",Bi={backdrop:!0,keyboard:!0,scroll:!1},Fi={backdrop:"(boolean|string)",keyboard:"boolean",scroll:"boolean"};class zi extends z{constructor(t,e){super(t,e),this._isShown=!1,this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._addEventListeners()}static get Default(){return Bi}static get DefaultType(){return Fi}static get NAME(){return"offcanvas"}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||P.trigger(this._element,"show.bs.offcanvas",{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._backdrop.show(),this._config.scroll||(new gi).hide(),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.classList.add(ji),this._queueCallback((()=>{this._config.scroll&&!this._config.backdrop||this._focustrap.activate(),this._element.classList.add(Pi),this._element.classList.remove(ji),P.trigger(this._element,"shown.bs.offcanvas",{relatedTarget:t})}),this._element,!0))}hide(){this._isShown&&(P.trigger(this._element,"hide.bs.offcanvas").defaultPrevented||(this._focustrap.deactivate(),this._element.blur(),this._isShown=!1,this._element.classList.add(Mi),this._backdrop.hide(),this._queueCallback((()=>{this._element.classList.remove(Pi,Mi),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._config.scroll||(new gi).reset(),P.trigger(this._element,Wi)}),this._element,!0)))}dispose(){this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}_initializeBackDrop(){const t=Boolean(this._config.backdrop);return new yi({className:"offcanvas-backdrop",isVisible:t,isAnimated:!0,rootElement:this._element.parentNode,clickCallback:t?()=>{"static"!==this._config.backdrop?this.hide():P.trigger(this._element,$i)}:null})}_initializeFocusTrap(){return new Ci({trapElement:this._element})}_addEventListeners(){P.on(this._element,"keydown.dismiss.bs.offcanvas",(t=>{"Escape"===t.key&&(this._config.keyboard?this.hide():P.trigger(this._element,$i))}))}static jQueryInterface(t){return this.each((function(){const e=zi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t]||t.startsWith("_")||"constructor"===t)throw new TypeError(`No method named "${t}"`);e[t](this)}}))}}P.on(document,"click.bs.offcanvas.data-api",'[data-bs-toggle="offcanvas"]',(function(t){const e=n(this);if(["A","AREA"].includes(this.tagName)&&t.preventDefault(),l(this))return;P.one(e,Wi,(()=>{a(this)&&this.focus()}));const i=Q.findOne(Hi);i&&i!==e&&zi.getInstance(i).hide(),zi.getOrCreateInstance(e).toggle(this)})),P.on(window,"load.bs.offcanvas.data-api",(()=>{for(const t of Q.find(Hi))zi.getOrCreateInstance(t).show()})),P.on(window,"resize.bs.offcanvas",(()=>{for(const t of Q.find("[aria-modal][class*=show][class*=offcanvas-]"))"fixed"!==getComputedStyle(t).position&&zi.getOrCreateInstance(t).hide()})),q(zi),g(zi);const qi=new Set(["background","cite","href","itemtype","longdesc","poster","src","xlink:href"]),Ri=/^(?:(?:https?|mailto|ftp|tel|file|sms):|[^#&/:?]*(?:[#/?]|$))/i,Vi=/^data:(?:image\/(?:bmp|gif|jpeg|jpg|png|tiff|webp)|video\/(?:mpeg|mp4|ogg|webm)|audio\/(?:mp3|oga|ogg|opus));base64,[\d+/a-z]+=*$/i,Ki=(t,e)=>{const i=t.nodeName.toLowerCase();return e.includes(i)?!qi.has(i)||Boolean(Ri.test(t.nodeValue)||Vi.test(t.nodeValue)):e.filter((t=>t instanceof RegExp)).some((t=>t.test(i)))},Qi={"*":["class","dir","id","lang","role",/^aria-[\w-]*$/i],a:["target","href","title","rel"],area:[],b:[],br:[],col:[],code:[],div:[],em:[],hr:[],h1:[],h2:[],h3:[],h4:[],h5:[],h6:[],i:[],img:["src","srcset","alt","title","width","height"],li:[],ol:[],p:[],pre:[],s:[],small:[],span:[],sub:[],sup:[],strong:[],u:[],ul:[]},Xi={allowList:Qi,content:{},extraClass:"",html:!1,sanitize:!0,sanitizeFn:null,template:"<div></div>"},Yi={allowList:"object",content:"object",extraClass:"(string|function)",html:"boolean",sanitize:"boolean",sanitizeFn:"(null|function)",template:"string"},Ui={entry:"(string|element|function|null)",selector:"(string|element)"};class Gi extends F{constructor(t){super(),this._config=this._getConfig(t)}static get Default(){return Xi}static get DefaultType(){return Yi}static get NAME(){return"TemplateFactory"}getContent(){return Object.values(this._config.content).map((t=>this._resolvePossibleFunction(t))).filter(Boolean)}hasContent(){return this.getContent().length>0}changeContent(t){return this._checkContent(t),this._config.content={...this._config.content,...t},this}toHtml(){const t=document.createElement("div");t.innerHTML=this._maybeSanitize(this._config.template);for(const[e,i]of Object.entries(this._config.content))this._setContent(t,i,e);const e=t.children[0],i=this._resolvePossibleFunction(this._config.extraClass);return i&&e.classList.add(...i.split(" ")),e}_typeCheckConfig(t){super._typeCheckConfig(t),this._checkContent(t.content)}_checkContent(t){for(const[e,i]of Object.entries(t))super._typeCheckConfig({selector:e,entry:i},Ui)}_setContent(t,e,i){const n=Q.findOne(i,t);n&&((e=this._resolvePossibleFunction(e))?o(e)?this._putElementInTemplate(r(e),n):this._config.html?n.innerHTML=this._maybeSanitize(e):n.textContent=e:n.remove())}_maybeSanitize(t){return this._config.sanitize?function(t,e,i){if(!t.length)return t;if(i&&"function"==typeof i)return i(t);const n=(new window.DOMParser).parseFromString(t,"text/html"),s=[].concat(...n.body.querySelectorAll("*"));for(const t of s){const i=t.nodeName.toLowerCase();if(!Object.keys(e).includes(i)){t.remove();continue}const n=[].concat(...t.attributes),s=[].concat(e["*"]||[],e[i]||[]);for(const e of n)Ki(e,s)||t.removeAttribute(e.nodeName)}return n.body.innerHTML}(t,this._config.allowList,this._config.sanitizeFn):t}_resolvePossibleFunction(t){return"function"==typeof t?t(this):t}_putElementInTemplate(t,e){if(this._config.html)return e.innerHTML="",void e.append(t);e.textContent=t.textContent}}const Ji=new Set(["sanitize","allowList","sanitizeFn"]),Zi="fade",tn="show",en=".modal",nn="hide.bs.modal",sn="hover",on="focus",rn={AUTO:"auto",TOP:"top",RIGHT:p()?"left":"right",BOTTOM:"bottom",LEFT:p()?"right":"left"},an={allowList:Qi,animation:!0,boundary:"clippingParents",container:!1,customClass:"",delay:0,fallbackPlacements:["top","right","bottom","left"],html:!1,offset:[0,0],placement:"top",popperConfig:null,sanitize:!0,sanitizeFn:null,selector:!1,template:'<div class="tooltip" role="tooltip"><div class="tooltip-arrow"></div><div class="tooltip-inner"></div></div>',title:"",trigger:"hover focus"},ln={allowList:"object",animation:"boolean",boundary:"(string|element)",container:"(string|element|boolean)",customClass:"(string|function)",delay:"(number|object)",fallbackPlacements:"array",html:"boolean",offset:"(array|string|function)",placement:"(string|function)",popperConfig:"(null|object|function)",sanitize:"boolean",sanitizeFn:"(null|function)",selector:"(string|boolean)",template:"string",title:"(string|element|function)",trigger:"string"};class cn extends z{constructor(t,e){if(void 0===Ke)throw new TypeError("Bootstrap's tooltips require Popper (https://popper.js.org)");super(t,e),this._isEnabled=!0,this._timeout=0,this._isHovered=null,this._activeTrigger={},this._popper=null,this._templateFactory=null,this._newContent=null,this.tip=null,this._setListeners(),this._config.selector||this._fixTitle()}static get Default(){return an}static get DefaultType(){return ln}static get NAME(){return"tooltip"}enable(){this._isEnabled=!0}disable(){this._isEnabled=!1}toggleEnabled(){this._isEnabled=!this._isEnabled}toggle(){this._isEnabled&&(this._activeTrigger.click=!this._activeTrigger.click,this._isShown()?this._leave():this._enter())}dispose(){clearTimeout(this._timeout),P.off(this._element.closest(en),nn,this._hideModalHandler),this.tip&&this.tip.remove(),this._element.getAttribute("data-bs-original-title")&&this._element.setAttribute("title",this._element.getAttribute("data-bs-original-title")),this._disposePopper(),super.dispose()}show(){if("none"===this._element.style.display)throw new Error("Please use show on visible elements");if(!this._isWithContent()||!this._isEnabled)return;const t=P.trigger(this._element,this.constructor.eventName("show")),e=(c(this._element)||this._element.ownerDocument.documentElement).contains(this._element);if(t.defaultPrevented||!e)return;this.tip&&(this.tip.remove(),this.tip=null);const i=this._getTipElement();this._element.setAttribute("aria-describedby",i.getAttribute("id"));const{container:n}=this._config;if(this._element.ownerDocument.documentElement.contains(this.tip)||(n.append(i),P.trigger(this._element,this.constructor.eventName("inserted"))),this._popper?this._popper.update():this._popper=this._createPopper(i),i.classList.add(tn),"ontouchstart"in document.documentElement)for(const t of[].concat(...document.body.children))P.on(t,"mouseover",h);this._queueCallback((()=>{P.trigger(this._element,this.constructor.eventName("shown")),!1===this._isHovered&&this._leave(),this._isHovered=!1}),this.tip,this._isAnimated())}hide(){if(!this._isShown())return;if(P.trigger(this._element,this.constructor.eventName("hide")).defaultPrevented)return;const t=this._getTipElement();if(t.classList.remove(tn),"ontouchstart"in document.documentElement)for(const t of[].concat(...document.body.children))P.off(t,"mouseover",h);this._activeTrigger.click=!1,this._activeTrigger.focus=!1,this._activeTrigger.hover=!1,this._isHovered=null,this._queueCallback((()=>{this._isWithActiveTrigger()||(this._isHovered||t.remove(),this._element.removeAttribute("aria-describedby"),P.trigger(this._element,this.constructor.eventName("hidden")),this._disposePopper())}),this.tip,this._isAnimated())}update(){this._popper&&this._popper.update()}_isWithContent(){return Boolean(this._getTitle())}_getTipElement(){return this.tip||(this.tip=this._createTipElement(this._newContent||this._getContentForTemplate())),this.tip}_createTipElement(t){const e=this._getTemplateFactory(t).toHtml();if(!e)return null;e.classList.remove(Zi,tn),e.classList.add(`bs-${this.constructor.NAME}-auto`);const i=(t=>{do{t+=Math.floor(1e6*Math.random())}while(document.getElementById(t));return t})(this.constructor.NAME).toString();return e.setAttribute("id",i),this._isAnimated()&&e.classList.add(Zi),e}setContent(t){this._newContent=t,this._isShown()&&(this._disposePopper(),this.show())}_getTemplateFactory(t){return this._templateFactory?this._templateFactory.changeContent(t):this._templateFactory=new Gi({...this._config,content:t,extraClass:this._resolvePossibleFunction(this._config.customClass)}),this._templateFactory}_getContentForTemplate(){return{".tooltip-inner":this._getTitle()}}_getTitle(){return this._resolvePossibleFunction(this._config.title)||this._element.getAttribute("data-bs-original-title")}_initializeOnDelegatedTarget(t){return this.constructor.getOrCreateInstance(t.delegateTarget,this._getDelegateConfig())}_isAnimated(){return this._config.animation||this.tip&&this.tip.classList.contains(Zi)}_isShown(){return this.tip&&this.tip.classList.contains(tn)}_createPopper(t){const e="function"==typeof this._config.placement?this._config.placement.call(this,t,this._element):this._config.placement,i=rn[e.toUpperCase()];return Ve(this._element,t,this._getPopperConfig(i))}_getOffset(){const{offset:t}=this._config;return"string"==typeof t?t.split(",").map((t=>Number.parseInt(t,10))):"function"==typeof t?e=>t(e,this._element):t}_resolvePossibleFunction(t){return"function"==typeof t?t.call(this._element):t}_getPopperConfig(t){const e={placement:t,modifiers:[{name:"flip",options:{fallbackPlacements:this._config.fallbackPlacements}},{name:"offset",options:{offset:this._getOffset()}},{name:"preventOverflow",options:{boundary:this._config.boundary}},{name:"arrow",options:{element:`.${this.constructor.NAME}-arrow`}},{name:"preSetPlacement",enabled:!0,phase:"beforeMain",fn:t=>{this._getTipElement().setAttribute("data-popper-placement",t.state.placement)}}]};return{...e,..."function"==typeof this._config.popperConfig?this._config.popperConfig(e):this._config.popperConfig}}_setListeners(){const t=this._config.trigger.split(" ");for(const e of t)if("click"===e)P.on(this._element,this.constructor.eventName("click"),this._config.selector,(t=>{this._initializeOnDelegatedTarget(t).toggle()}));else if("manual"!==e){const t=e===sn?this.constructor.eventName("mouseenter"):this.constructor.eventName("focusin"),i=e===sn?this.constructor.eventName("mouseleave"):this.constructor.eventName("focusout");P.on(this._element,t,this._config.selector,(t=>{const e=this._initializeOnDelegatedTarget(t);e._activeTrigger["focusin"===t.type?on:sn]=!0,e._enter()})),P.on(this._element,i,this._config.selector,(t=>{const e=this._initializeOnDelegatedTarget(t);e._activeTrigger["focusout"===t.type?on:sn]=e._element.contains(t.relatedTarget),e._leave()}))}this._hideModalHandler=()=>{this._element&&this.hide()},P.on(this._element.closest(en),nn,this._hideModalHandler)}_fixTitle(){const t=this._element.getAttribute("title");t&&(this._element.getAttribute("aria-label")||this._element.textContent.trim()||this._element.setAttribute("aria-label",t),this._element.setAttribute("data-bs-original-title",t),this._element.removeAttribute("title"))}_enter(){this._isShown()||this._isHovered?this._isHovered=!0:(this._isHovered=!0,this._setTimeout((()=>{this._isHovered&&this.show()}),this._config.delay.show))}_leave(){this._isWithActiveTrigger()||(this._isHovered=!1,this._setTimeout((()=>{this._isHovered||this.hide()}),this._config.delay.hide))}_setTimeout(t,e){clearTimeout(this._timeout),this._timeout=setTimeout(t,e)}_isWithActiveTrigger(){return Object.values(this._activeTrigger).includes(!0)}_getConfig(t){const e=B.getDataAttributes(this._element);for(const t of Object.keys(e))Ji.has(t)&&delete e[t];return t={...e,..."object"==typeof t&&t?t:{}},t=this._mergeConfigObj(t),t=this._configAfterMerge(t),this._typeCheckConfig(t),t}_configAfterMerge(t){return t.container=!1===t.container?document.body:r(t.container),"number"==typeof t.delay&&(t.delay={show:t.delay,hide:t.delay}),"number"==typeof t.title&&(t.title=t.title.toString()),"number"==typeof t.content&&(t.content=t.content.toString()),t}_getDelegateConfig(){const t={};for(const e in this._config)this.constructor.Default[e]!==this._config[e]&&(t[e]=this._config[e]);return t.selector=!1,t.trigger="manual",t}_disposePopper(){this._popper&&(this._popper.destroy(),this._popper=null)}static jQueryInterface(t){return this.each((function(){const e=cn.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}}g(cn);const hn={...cn.Default,content:"",offset:[0,8],placement:"right",template:'<div class="popover" role="tooltip"><div class="popover-arrow"></div><h3 class="popover-header"></h3><div class="popover-body"></div></div>',trigger:"click"},dn={...cn.DefaultType,content:"(null|string|element|function)"};class un extends cn{static get Default(){return hn}static get DefaultType(){return dn}static get NAME(){return"popover"}_isWithContent(){return this._getTitle()||this._getContent()}_getContentForTemplate(){return{".popover-header":this._getTitle(),".popover-body":this._getContent()}}_getContent(){return this._resolvePossibleFunction(this._config.content)}static jQueryInterface(t){return this.each((function(){const e=un.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}}g(un);const fn="click.bs.scrollspy",pn="active",gn="[href]",mn={offset:null,rootMargin:"0px 0px -25%",smoothScroll:!1,target:null,threshold:[.1,.5,1]},_n={offset:"(number|null)",rootMargin:"string",smoothScroll:"boolean",target:"element",threshold:"array"};class bn extends z{constructor(t,e){super(t,e),this._targetLinks=new Map,this._observableSections=new Map,this._rootElement="visible"===getComputedStyle(this._element).overflowY?null:this._element,this._activeTarget=null,this._observer=null,this._previousScrollData={visibleEntryTop:0,parentScrollTop:0},this.refresh()}static get Default(){return mn}static get DefaultType(){return _n}static get NAME(){return"scrollspy"}refresh(){this._initializeTargetsAndObservables(),this._maybeEnableSmoothScroll(),this._observer?this._observer.disconnect():this._observer=this._getNewObserver();for(const t of this._observableSections.values())this._observer.observe(t)}dispose(){this._observer.disconnect(),super.dispose()}_configAfterMerge(t){return t.target=r(t.target)||document.body,t.rootMargin=t.offset?`${t.offset}px 0px -30%`:t.rootMargin,"string"==typeof t.threshold&&(t.threshold=t.threshold.split(",").map((t=>Number.parseFloat(t)))),t}_maybeEnableSmoothScroll(){this._config.smoothScroll&&(P.off(this._config.target,fn),P.on(this._config.target,fn,gn,(t=>{const e=this._observableSections.get(t.target.hash);if(e){t.preventDefault();const i=this._rootElement||window,n=e.offsetTop-this._element.offsetTop;if(i.scrollTo)return void i.scrollTo({top:n,behavior:"smooth"});i.scrollTop=n}})))}_getNewObserver(){const t={root:this._rootElement,threshold:this._config.threshold,rootMargin:this._config.rootMargin};return new IntersectionObserver((t=>this._observerCallback(t)),t)}_observerCallback(t){const e=t=>this._targetLinks.get(`#${t.target.id}`),i=t=>{this._previousScrollData.visibleEntryTop=t.target.offsetTop,this._process(e(t))},n=(this._rootElement||document.documentElement).scrollTop,s=n>=this._previousScrollData.parentScrollTop;this._previousScrollData.parentScrollTop=n;for(const o of t){if(!o.isIntersecting){this._activeTarget=null,this._clearActiveClass(e(o));continue}const t=o.target.offsetTop>=this._previousScrollData.visibleEntryTop;if(s&&t){if(i(o),!n)return}else s||t||i(o)}}_initializeTargetsAndObservables(){this._targetLinks=new Map,this._observableSections=new Map;const t=Q.find(gn,this._config.target);for(const e of t){if(!e.hash||l(e))continue;const t=Q.findOne(e.hash,this._element);a(t)&&(this._targetLinks.set(e.hash,e),this._observableSections.set(e.hash,t))}}_process(t){this._activeTarget!==t&&(this._clearActiveClass(this._config.target),this._activeTarget=t,t.classList.add(pn),this._activateParents(t),P.trigger(this._element,"activate.bs.scrollspy",{relatedTarget:t}))}_activateParents(t){if(t.classList.contains("dropdown-item"))Q.findOne(".dropdown-toggle",t.closest(".dropdown")).classList.add(pn);else for(const e of Q.parents(t,".nav, .list-group"))for(const t of Q.prev(e,".nav-link, .nav-item > .nav-link, .list-group-item"))t.classList.add(pn)}_clearActiveClass(t){t.classList.remove(pn);const e=Q.find("[href].active",t);for(const t of e)t.classList.remove(pn)}static jQueryInterface(t){return this.each((function(){const e=bn.getOrCreateInstance(this,t);if("string"==typeof t){if(void 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* --------------------------------------------------------------------------\n * Bootstrap (v5.2.2): util/index.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nconst MAX_UID = 1_000_000\nconst MILLISECONDS_MULTIPLIER = 1000\nconst TRANSITION_END = 'transitionend'\n\n// Shout-out Angus Croll (https://goo.gl/pxwQGp)\nconst toType = object => {\n if (object === null || object === undefined) {\n return `${object}`\n }\n\n return Object.prototype.toString.call(object).match(/\\s([a-z]+)/i)[1].toLowerCase()\n}\n\n/**\n * Public Util API\n */\n\nconst getUID = prefix => {\n do {\n prefix += Math.floor(Math.random() * MAX_UID)\n } while (document.getElementById(prefix))\n\n return prefix\n}\n\nconst getSelector = element => {\n let selector = element.getAttribute('data-bs-target')\n\n if (!selector || selector === '#') {\n let hrefAttribute = element.getAttribute('href')\n\n // The only valid content that could double as a selector are IDs or classes,\n // so everything starting with `#` or `.`. If a \"real\" URL is used as the selector,\n // `document.querySelector` will rightfully complain it is invalid.\n // See https://github.com/twbs/bootstrap/issues/32273\n if (!hrefAttribute || (!hrefAttribute.includes('#') && !hrefAttribute.startsWith('.'))) {\n return null\n }\n\n // Just in case some CMS puts out a full URL with the anchor appended\n if (hrefAttribute.includes('#') && !hrefAttribute.startsWith('#')) {\n hrefAttribute = `#${hrefAttribute.split('#')[1]}`\n }\n\n selector = hrefAttribute && hrefAttribute !== '#' ? hrefAttribute.trim() : null\n }\n\n return selector\n}\n\nconst getSelectorFromElement = element => {\n const selector = getSelector(element)\n\n if (selector) {\n return document.querySelector(selector) ? selector : null\n }\n\n return null\n}\n\nconst getElementFromSelector = element => {\n const selector = getSelector(element)\n\n return selector ? document.querySelector(selector) : null\n}\n\nconst getTransitionDurationFromElement = element => {\n if (!element) {\n return 0\n }\n\n // Get transition-duration of the element\n let { transitionDuration, transitionDelay } = window.getComputedStyle(element)\n\n const floatTransitionDuration = Number.parseFloat(transitionDuration)\n const floatTransitionDelay = Number.parseFloat(transitionDelay)\n\n // Return 0 if element or transition duration is not found\n if (!floatTransitionDuration && !floatTransitionDelay) {\n return 0\n }\n\n // If multiple durations are defined, take the first\n transitionDuration = transitionDuration.split(',')[0]\n transitionDelay = transitionDelay.split(',')[0]\n\n return (Number.parseFloat(transitionDuration) + Number.parseFloat(transitionDelay)) * MILLISECONDS_MULTIPLIER\n}\n\nconst triggerTransitionEnd = element => {\n element.dispatchEvent(new Event(TRANSITION_END))\n}\n\nconst isElement = object => {\n if (!object || typeof object !== 'object') {\n return false\n }\n\n if (typeof object.jquery !== 'undefined') {\n object = object[0]\n }\n\n return typeof object.nodeType !== 'undefined'\n}\n\nconst getElement = object => {\n // it's a jQuery object or a node element\n if (isElement(object)) {\n return object.jquery ? object[0] : object\n }\n\n if (typeof object === 'string' && object.length > 0) {\n return document.querySelector(object)\n }\n\n return null\n}\n\nconst isVisible = element => {\n if (!isElement(element) || element.getClientRects().length === 0) {\n return false\n }\n\n const elementIsVisible = getComputedStyle(element).getPropertyValue('visibility') === 'visible'\n // Handle `details` element as its content may falsie appear visible when it is closed\n const closedDetails = element.closest('details:not([open])')\n\n if (!closedDetails) {\n return elementIsVisible\n }\n\n if (closedDetails !== element) {\n const summary = element.closest('summary')\n if (summary && summary.parentNode !== closedDetails) {\n return false\n }\n\n if (summary === null) {\n return false\n }\n }\n\n return elementIsVisible\n}\n\nconst isDisabled = element => {\n if (!element || element.nodeType !== Node.ELEMENT_NODE) {\n return true\n }\n\n if (element.classList.contains('disabled')) {\n return true\n }\n\n if (typeof element.disabled !== 'undefined') {\n return element.disabled\n }\n\n return element.hasAttribute('disabled') && element.getAttribute('disabled') !== 'false'\n}\n\nconst findShadowRoot = element => {\n if (!document.documentElement.attachShadow) {\n return null\n }\n\n // Can find the shadow root otherwise it'll return the document\n if (typeof element.getRootNode === 'function') {\n const root = element.getRootNode()\n return root instanceof ShadowRoot ? root : null\n }\n\n if (element instanceof ShadowRoot) {\n return element\n }\n\n // when we don't find a shadow root\n if (!element.parentNode) {\n return null\n }\n\n return findShadowRoot(element.parentNode)\n}\n\nconst noop = () => {}\n\n/**\n * Trick to restart an element's animation\n *\n * @param {HTMLElement} element\n * @return void\n *\n * @see https://www.charistheo.io/blog/2021/02/restart-a-css-animation-with-javascript/#restarting-a-css-animation\n */\nconst reflow = element => {\n element.offsetHeight // eslint-disable-line no-unused-expressions\n}\n\nconst getjQuery = () => {\n if (window.jQuery && !document.body.hasAttribute('data-bs-no-jquery')) {\n return window.jQuery\n }\n\n return null\n}\n\nconst DOMContentLoadedCallbacks = []\n\nconst onDOMContentLoaded = callback => {\n if (document.readyState === 'loading') {\n // add listener on the first call when the document is in loading state\n if (!DOMContentLoadedCallbacks.length) {\n document.addEventListener('DOMContentLoaded', () => {\n for (const callback of DOMContentLoadedCallbacks) {\n callback()\n }\n })\n }\n\n DOMContentLoadedCallbacks.push(callback)\n } else {\n callback()\n }\n}\n\nconst isRTL = () => document.documentElement.dir === 'rtl'\n\nconst defineJQueryPlugin = plugin => {\n onDOMContentLoaded(() => {\n const $ = getjQuery()\n /* istanbul ignore if */\n if ($) {\n const name = plugin.NAME\n const JQUERY_NO_CONFLICT = $.fn[name]\n $.fn[name] = plugin.jQueryInterface\n $.fn[name].Constructor = plugin\n $.fn[name].noConflict = () => {\n $.fn[name] = JQUERY_NO_CONFLICT\n return plugin.jQueryInterface\n }\n }\n })\n}\n\nconst execute = callback => {\n if (typeof callback === 'function') {\n callback()\n }\n}\n\nconst executeAfterTransition = (callback, transitionElement, waitForTransition = true) => {\n if (!waitForTransition) {\n execute(callback)\n return\n }\n\n const durationPadding = 5\n const emulatedDuration = getTransitionDurationFromElement(transitionElement) + durationPadding\n\n let called = false\n\n const handler = ({ target }) => {\n if (target !== transitionElement) {\n return\n }\n\n called = true\n transitionElement.removeEventListener(TRANSITION_END, handler)\n execute(callback)\n }\n\n transitionElement.addEventListener(TRANSITION_END, handler)\n setTimeout(() => {\n if (!called) {\n triggerTransitionEnd(transitionElement)\n }\n }, emulatedDuration)\n}\n\n/**\n * Return the previous/next element of a list.\n *\n * @param {array} list The list of elements\n * @param activeElement The active element\n * @param shouldGetNext Choose to get next or previous element\n * @param isCycleAllowed\n * @return {Element|elem} The proper element\n */\nconst getNextActiveElement = (list, activeElement, shouldGetNext, isCycleAllowed) => {\n const listLength = list.length\n let index = list.indexOf(activeElement)\n\n // if the element does not exist in the list return an element\n // depending on the direction and if cycle is allowed\n if (index === -1) {\n return !shouldGetNext && isCycleAllowed ? list[listLength - 1] : list[0]\n }\n\n index += shouldGetNext ? 1 : -1\n\n if (isCycleAllowed) {\n index = (index + listLength) % listLength\n }\n\n return list[Math.max(0, Math.min(index, listLength - 1))]\n}\n\nexport {\n defineJQueryPlugin,\n execute,\n executeAfterTransition,\n findShadowRoot,\n getElement,\n getElementFromSelector,\n getjQuery,\n getNextActiveElement,\n getSelectorFromElement,\n getTransitionDurationFromElement,\n getUID,\n isDisabled,\n isElement,\n isRTL,\n isVisible,\n noop,\n onDOMContentLoaded,\n reflow,\n triggerTransitionEnd,\n toType\n}\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap (v5.2.2): dom/event-handler.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport { getjQuery } from '../util/index'\n\n/**\n * Constants\n */\n\nconst namespaceRegex = /[^.]*(?=\\..*)\\.|.*/\nconst stripNameRegex = /\\..*/\nconst stripUidRegex = /::\\d+$/\nconst eventRegistry = {} // Events storage\nlet uidEvent = 1\nconst customEvents = {\n mouseenter: 'mouseover',\n mouseleave: 'mouseout'\n}\n\nconst nativeEvents = new Set([\n 'click',\n 'dblclick',\n 'mouseup',\n 'mousedown',\n 'contextmenu',\n 'mousewheel',\n 'DOMMouseScroll',\n 'mouseover',\n 'mouseout',\n 'mousemove',\n 'selectstart',\n 'selectend',\n 'keydown',\n 'keypress',\n 'keyup',\n 'orientationchange',\n 'touchstart',\n 'touchmove',\n 'touchend',\n 'touchcancel',\n 'pointerdown',\n 'pointermove',\n 'pointerup',\n 'pointerleave',\n 'pointercancel',\n 'gesturestart',\n 'gesturechange',\n 'gestureend',\n 'focus',\n 'blur',\n 'change',\n 'reset',\n 'select',\n 'submit',\n 'focusin',\n 'focusout',\n 'load',\n 'unload',\n 'beforeunload',\n 'resize',\n 'move',\n 'DOMContentLoaded',\n 'readystatechange',\n 'error',\n 'abort',\n 'scroll'\n])\n\n/**\n * Private methods\n */\n\nfunction makeEventUid(element, uid) {\n return (uid && `${uid}::${uidEvent++}`) || element.uidEvent || uidEvent++\n}\n\nfunction getElementEvents(element) {\n const uid = makeEventUid(element)\n\n element.uidEvent = uid\n eventRegistry[uid] = eventRegistry[uid] || {}\n\n return eventRegistry[uid]\n}\n\nfunction bootstrapHandler(element, fn) {\n return function handler(event) {\n hydrateObj(event, { delegateTarget: element })\n\n if (handler.oneOff) {\n EventHandler.off(element, event.type, fn)\n }\n\n return fn.apply(element, [event])\n }\n}\n\nfunction bootstrapDelegationHandler(element, selector, fn) {\n return function handler(event) {\n const domElements = element.querySelectorAll(selector)\n\n for (let { target } = event; target && target !== this; target = target.parentNode) {\n for (const domElement of domElements) {\n if (domElement !== target) {\n continue\n }\n\n hydrateObj(event, { delegateTarget: target })\n\n if (handler.oneOff) {\n EventHandler.off(element, event.type, selector, fn)\n }\n\n return fn.apply(target, [event])\n }\n }\n }\n}\n\nfunction findHandler(events, callable, delegationSelector = null) {\n return Object.values(events)\n .find(event => event.callable === callable && event.delegationSelector === delegationSelector)\n}\n\nfunction normalizeParameters(originalTypeEvent, handler, delegationFunction) {\n const isDelegated = typeof handler === 'string'\n // todo: tooltip passes `false` instead of selector, so we need to check\n const callable = isDelegated ? delegationFunction : (handler || delegationFunction)\n let typeEvent = getTypeEvent(originalTypeEvent)\n\n if (!nativeEvents.has(typeEvent)) {\n typeEvent = originalTypeEvent\n }\n\n return [isDelegated, callable, typeEvent]\n}\n\nfunction addHandler(element, originalTypeEvent, handler, delegationFunction, oneOff) {\n if (typeof originalTypeEvent !== 'string' || !element) {\n return\n }\n\n let [isDelegated, callable, typeEvent] = normalizeParameters(originalTypeEvent, handler, delegationFunction)\n\n // in case of mouseenter or mouseleave wrap the handler within a function that checks for its DOM position\n // this prevents the handler from being dispatched the same way as mouseover or mouseout does\n if (originalTypeEvent in customEvents) {\n const wrapFunction = fn => {\n return function (event) {\n if (!event.relatedTarget || (event.relatedTarget !== event.delegateTarget && !event.delegateTarget.contains(event.relatedTarget))) {\n return fn.call(this, event)\n }\n }\n }\n\n callable = wrapFunction(callable)\n }\n\n const events = getElementEvents(element)\n const handlers = events[typeEvent] || (events[typeEvent] = {})\n const previousFunction = findHandler(handlers, callable, isDelegated ? handler : null)\n\n if (previousFunction) {\n previousFunction.oneOff = previousFunction.oneOff && oneOff\n\n return\n }\n\n const uid = makeEventUid(callable, originalTypeEvent.replace(namespaceRegex, ''))\n const fn = isDelegated ?\n bootstrapDelegationHandler(element, handler, callable) :\n bootstrapHandler(element, callable)\n\n fn.delegationSelector = isDelegated ? handler : null\n fn.callable = callable\n fn.oneOff = oneOff\n fn.uidEvent = uid\n handlers[uid] = fn\n\n element.addEventListener(typeEvent, fn, isDelegated)\n}\n\nfunction removeHandler(element, events, typeEvent, handler, delegationSelector) {\n const fn = findHandler(events[typeEvent], handler, delegationSelector)\n\n if (!fn) {\n return\n }\n\n element.removeEventListener(typeEvent, fn, Boolean(delegationSelector))\n delete events[typeEvent][fn.uidEvent]\n}\n\nfunction removeNamespacedHandlers(element, events, typeEvent, namespace) {\n const storeElementEvent = events[typeEvent] || {}\n\n for (const handlerKey of Object.keys(storeElementEvent)) {\n if (handlerKey.includes(namespace)) {\n const event = storeElementEvent[handlerKey]\n removeHandler(element, events, typeEvent, event.callable, event.delegationSelector)\n }\n }\n}\n\nfunction getTypeEvent(event) {\n // allow to get the native events from namespaced events ('click.bs.button' --> 'click')\n event = event.replace(stripNameRegex, '')\n return customEvents[event] || event\n}\n\nconst EventHandler = {\n on(element, event, handler, delegationFunction) {\n addHandler(element, event, handler, delegationFunction, false)\n },\n\n one(element, event, handler, delegationFunction) {\n addHandler(element, event, handler, delegationFunction, true)\n },\n\n off(element, originalTypeEvent, handler, delegationFunction) {\n if (typeof originalTypeEvent !== 'string' || !element) {\n return\n }\n\n const [isDelegated, callable, typeEvent] = normalizeParameters(originalTypeEvent, handler, delegationFunction)\n const inNamespace = typeEvent !== originalTypeEvent\n const events = getElementEvents(element)\n const storeElementEvent = events[typeEvent] || {}\n const isNamespace = originalTypeEvent.startsWith('.')\n\n if (typeof callable !== 'undefined') {\n // Simplest case: handler is passed, remove that listener ONLY.\n if (!Object.keys(storeElementEvent).length) {\n return\n }\n\n removeHandler(element, events, typeEvent, callable, isDelegated ? handler : null)\n return\n }\n\n if (isNamespace) {\n for (const elementEvent of Object.keys(events)) {\n removeNamespacedHandlers(element, events, elementEvent, originalTypeEvent.slice(1))\n }\n }\n\n for (const keyHandlers of Object.keys(storeElementEvent)) {\n const handlerKey = keyHandlers.replace(stripUidRegex, '')\n\n if (!inNamespace || originalTypeEvent.includes(handlerKey)) {\n const event = storeElementEvent[keyHandlers]\n removeHandler(element, events, typeEvent, event.callable, event.delegationSelector)\n }\n }\n },\n\n trigger(element, event, args) {\n if (typeof event !== 'string' || !element) {\n return null\n }\n\n const $ = getjQuery()\n const typeEvent = getTypeEvent(event)\n const inNamespace = event !== typeEvent\n\n let jQueryEvent = null\n let bubbles = true\n let nativeDispatch = true\n let defaultPrevented = false\n\n if (inNamespace && $) {\n jQueryEvent = $.Event(event, args)\n\n $(element).trigger(jQueryEvent)\n bubbles = !jQueryEvent.isPropagationStopped()\n nativeDispatch = !jQueryEvent.isImmediatePropagationStopped()\n defaultPrevented = jQueryEvent.isDefaultPrevented()\n }\n\n let evt = new Event(event, { bubbles, cancelable: true })\n evt = hydrateObj(evt, args)\n\n if (defaultPrevented) {\n evt.preventDefault()\n }\n\n if (nativeDispatch) {\n element.dispatchEvent(evt)\n }\n\n if (evt.defaultPrevented && jQueryEvent) {\n jQueryEvent.preventDefault()\n }\n\n return evt\n }\n}\n\nfunction hydrateObj(obj, meta) {\n for (const [key, value] of Object.entries(meta || {})) {\n try {\n obj[key] = value\n } catch {\n Object.defineProperty(obj, key, {\n configurable: true,\n get() {\n return value\n }\n })\n }\n }\n\n return obj\n}\n\nexport default EventHandler\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap (v5.2.2): dom/data.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\n/**\n * Constants\n */\n\nconst elementMap = new Map()\n\nexport default {\n set(element, key, instance) {\n if (!elementMap.has(element)) {\n elementMap.set(element, new Map())\n }\n\n const instanceMap = elementMap.get(element)\n\n // make it clear we only want one instance per element\n // can be removed later when multiple key/instances are fine to be used\n if (!instanceMap.has(key) && instanceMap.size !== 0) {\n // eslint-disable-next-line no-console\n console.error(`Bootstrap doesn't allow more than one instance per element. Bound instance: ${Array.from(instanceMap.keys())[0]}.`)\n return\n }\n\n instanceMap.set(key, instance)\n },\n\n get(element, key) {\n if (elementMap.has(element)) {\n return elementMap.get(element).get(key) || null\n }\n\n return null\n },\n\n remove(element, key) {\n if (!elementMap.has(element)) {\n return\n }\n\n const instanceMap = elementMap.get(element)\n\n instanceMap.delete(key)\n\n // free up element references if there are no instances left for an element\n if (instanceMap.size === 0) {\n elementMap.delete(element)\n }\n }\n}\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap (v5.2.2): dom/manipulator.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nfunction normalizeData(value) {\n if (value === 'true') {\n return true\n }\n\n if (value === 'false') {\n return false\n }\n\n if (value === Number(value).toString()) {\n return Number(value)\n }\n\n if (value === '' || value === 'null') {\n return null\n }\n\n if (typeof value !== 'string') {\n return value\n }\n\n try {\n return JSON.parse(decodeURIComponent(value))\n } catch {\n return value\n }\n}\n\nfunction normalizeDataKey(key) {\n return key.replace(/[A-Z]/g, chr => `-${chr.toLowerCase()}`)\n}\n\nconst Manipulator = {\n setDataAttribute(element, key, value) {\n element.setAttribute(`data-bs-${normalizeDataKey(key)}`, value)\n },\n\n removeDataAttribute(element, key) {\n element.removeAttribute(`data-bs-${normalizeDataKey(key)}`)\n },\n\n getDataAttributes(element) {\n if (!element) {\n return {}\n }\n\n const attributes = {}\n const bsKeys = Object.keys(element.dataset).filter(key => key.startsWith('bs') && !key.startsWith('bsConfig'))\n\n for (const key of bsKeys) {\n let pureKey = key.replace(/^bs/, '')\n pureKey = pureKey.charAt(0).toLowerCase() + pureKey.slice(1, pureKey.length)\n attributes[pureKey] = normalizeData(element.dataset[key])\n }\n\n return attributes\n },\n\n getDataAttribute(element, key) {\n return normalizeData(element.getAttribute(`data-bs-${normalizeDataKey(key)}`))\n }\n}\n\nexport default Manipulator\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap (v5.2.2): util/config.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport { isElement, toType } from './index'\nimport Manipulator from '../dom/manipulator'\n\n/**\n * Class definition\n */\n\nclass Config {\n // Getters\n static get Default() {\n return {}\n }\n\n static get DefaultType() {\n return {}\n }\n\n static get NAME() {\n throw new Error('You have to implement the static method \"NAME\", for each component!')\n }\n\n _getConfig(config) {\n config = this._mergeConfigObj(config)\n config = this._configAfterMerge(config)\n this._typeCheckConfig(config)\n return config\n }\n\n _configAfterMerge(config) {\n return config\n }\n\n _mergeConfigObj(config, element) {\n const jsonConfig = isElement(element) ? Manipulator.getDataAttribute(element, 'config') : {} // try to parse\n\n return {\n ...this.constructor.Default,\n ...(typeof jsonConfig === 'object' ? jsonConfig : {}),\n ...(isElement(element) ? Manipulator.getDataAttributes(element) : {}),\n ...(typeof config === 'object' ? config : {})\n }\n }\n\n _typeCheckConfig(config, configTypes = this.constructor.DefaultType) {\n for (const property of Object.keys(configTypes)) {\n const expectedTypes = configTypes[property]\n const value = config[property]\n const valueType = isElement(value) ? 'element' : toType(value)\n\n if (!new RegExp(expectedTypes).test(valueType)) {\n throw new TypeError(\n `${this.constructor.NAME.toUpperCase()}: Option \"${property}\" provided type \"${valueType}\" but expected type \"${expectedTypes}\".`\n )\n }\n }\n }\n}\n\nexport default Config\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap (v5.2.2): base-component.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport Data from './dom/data'\nimport { executeAfterTransition, getElement } from './util/index'\nimport EventHandler from './dom/event-handler'\nimport Config from './util/config'\n\n/**\n * Constants\n */\n\nconst VERSION = '5.2.2'\n\n/**\n * Class definition\n */\n\nclass BaseComponent extends Config {\n constructor(element, config) {\n super()\n\n element = getElement(element)\n if (!element) {\n return\n }\n\n this._element = element\n this._config = this._getConfig(config)\n\n Data.set(this._element, this.constructor.DATA_KEY, this)\n }\n\n // Public\n dispose() {\n Data.remove(this._element, this.constructor.DATA_KEY)\n EventHandler.off(this._element, this.constructor.EVENT_KEY)\n\n for (const propertyName of Object.getOwnPropertyNames(this)) {\n this[propertyName] = null\n }\n }\n\n _queueCallback(callback, element, isAnimated = true) {\n executeAfterTransition(callback, element, isAnimated)\n }\n\n _getConfig(config) {\n config = this._mergeConfigObj(config, this._element)\n config = this._configAfterMerge(config)\n this._typeCheckConfig(config)\n return config\n }\n\n // Static\n static getInstance(element) {\n return Data.get(getElement(element), this.DATA_KEY)\n }\n\n static getOrCreateInstance(element, config = {}) {\n return this.getInstance(element) || new this(element, typeof config === 'object' ? config : null)\n }\n\n static get VERSION() {\n return VERSION\n }\n\n static get DATA_KEY() {\n return `bs.${this.NAME}`\n }\n\n static get EVENT_KEY() {\n return `.${this.DATA_KEY}`\n }\n\n static eventName(name) {\n return `${name}${this.EVENT_KEY}`\n }\n}\n\nexport default BaseComponent\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap (v5.2.2): util/component-functions.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport EventHandler from '../dom/event-handler'\nimport { getElementFromSelector, isDisabled } from './index'\n\nconst enableDismissTrigger = (component, method = 'hide') => {\n const clickEvent = `click.dismiss${component.EVENT_KEY}`\n const name = component.NAME\n\n EventHandler.on(document, clickEvent, `[data-bs-dismiss=\"${name}\"]`, function (event) {\n if (['A', 'AREA'].includes(this.tagName)) {\n event.preventDefault()\n }\n\n if (isDisabled(this)) {\n return\n }\n\n const target = getElementFromSelector(this) || this.closest(`.${name}`)\n const instance = component.getOrCreateInstance(target)\n\n // Method argument is left, for Alert and only, as it doesn't implement the 'hide' method\n instance[method]()\n })\n}\n\nexport {\n enableDismissTrigger\n}\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap (v5.2.2): alert.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport { defineJQueryPlugin } from './util/index'\nimport EventHandler from './dom/event-handler'\nimport BaseComponent from './base-component'\nimport { enableDismissTrigger } from './util/component-functions'\n\n/**\n * Constants\n */\n\nconst NAME = 'alert'\nconst DATA_KEY = 'bs.alert'\nconst EVENT_KEY = `.${DATA_KEY}`\n\nconst EVENT_CLOSE = `close${EVENT_KEY}`\nconst EVENT_CLOSED = `closed${EVENT_KEY}`\nconst CLASS_NAME_FADE = 'fade'\nconst CLASS_NAME_SHOW = 'show'\n\n/**\n * Class definition\n */\n\nclass Alert extends BaseComponent {\n // Getters\n static get NAME() {\n return NAME\n }\n\n // Public\n close() {\n const closeEvent = EventHandler.trigger(this._element, EVENT_CLOSE)\n\n if (closeEvent.defaultPrevented) {\n return\n }\n\n this._element.classList.remove(CLASS_NAME_SHOW)\n\n const isAnimated = this._element.classList.contains(CLASS_NAME_FADE)\n this._queueCallback(() => this._destroyElement(), this._element, isAnimated)\n }\n\n // Private\n _destroyElement() {\n this._element.remove()\n EventHandler.trigger(this._element, EVENT_CLOSED)\n this.dispose()\n }\n\n // Static\n static jQueryInterface(config) {\n return this.each(function () {\n const data = Alert.getOrCreateInstance(this)\n\n if (typeof config !== 'string') {\n return\n }\n\n if (data[config] === undefined || config.startsWith('_') || config === 'constructor') {\n throw new TypeError(`No method named \"${config}\"`)\n }\n\n data[config](this)\n })\n }\n}\n\n/**\n * Data API implementation\n */\n\nenableDismissTrigger(Alert, 'close')\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Alert)\n\nexport default Alert\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap (v5.2.2): button.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport { defineJQueryPlugin } from './util/index'\nimport EventHandler from './dom/event-handler'\nimport BaseComponent from './base-component'\n\n/**\n * Constants\n */\n\nconst NAME = 'button'\nconst DATA_KEY = 'bs.button'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst DATA_API_KEY = '.data-api'\n\nconst CLASS_NAME_ACTIVE = 'active'\nconst SELECTOR_DATA_TOGGLE = '[data-bs-toggle=\"button\"]'\nconst EVENT_CLICK_DATA_API = `click${EVENT_KEY}${DATA_API_KEY}`\n\n/**\n * Class definition\n */\n\nclass Button extends BaseComponent {\n // Getters\n static get NAME() {\n return NAME\n }\n\n // Public\n toggle() {\n // Toggle class and sync the `aria-pressed` attribute with the return value of the `.toggle()` method\n this._element.setAttribute('aria-pressed', this._element.classList.toggle(CLASS_NAME_ACTIVE))\n }\n\n // Static\n static jQueryInterface(config) {\n return this.each(function () {\n const data = Button.getOrCreateInstance(this)\n\n if (config === 'toggle') {\n data[config]()\n }\n })\n }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(document, EVENT_CLICK_DATA_API, SELECTOR_DATA_TOGGLE, event => {\n event.preventDefault()\n\n const button = event.target.closest(SELECTOR_DATA_TOGGLE)\n const data = Button.getOrCreateInstance(button)\n\n data.toggle()\n})\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Button)\n\nexport default Button\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap (v5.2.2): dom/selector-engine.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport { isDisabled, isVisible } from '../util/index'\n\n/**\n * Constants\n */\n\nconst SelectorEngine = {\n find(selector, element = document.documentElement) {\n return [].concat(...Element.prototype.querySelectorAll.call(element, selector))\n },\n\n findOne(selector, element = document.documentElement) {\n return Element.prototype.querySelector.call(element, selector)\n },\n\n children(element, selector) {\n return [].concat(...element.children).filter(child => child.matches(selector))\n },\n\n parents(element, selector) {\n const parents = []\n let ancestor = element.parentNode.closest(selector)\n\n while (ancestor) {\n parents.push(ancestor)\n ancestor = ancestor.parentNode.closest(selector)\n }\n\n return parents\n },\n\n prev(element, selector) {\n let previous = element.previousElementSibling\n\n while (previous) {\n if (previous.matches(selector)) {\n return [previous]\n }\n\n previous = previous.previousElementSibling\n }\n\n return []\n },\n // TODO: this is now unused; remove later along with prev()\n next(element, selector) {\n let next = element.nextElementSibling\n\n while (next) {\n if (next.matches(selector)) {\n return [next]\n }\n\n next = next.nextElementSibling\n }\n\n return []\n },\n\n focusableChildren(element) {\n const focusables = [\n 'a',\n 'button',\n 'input',\n 'textarea',\n 'select',\n 'details',\n '[tabindex]',\n '[contenteditable=\"true\"]'\n ].map(selector => `${selector}:not([tabindex^=\"-\"])`).join(',')\n\n return this.find(focusables, element).filter(el => !isDisabled(el) && isVisible(el))\n }\n}\n\nexport default SelectorEngine\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap (v5.2.2): util/swipe.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport Config from './config'\nimport EventHandler from '../dom/event-handler'\nimport { execute } from './index'\n\n/**\n * Constants\n */\n\nconst NAME = 'swipe'\nconst EVENT_KEY = '.bs.swipe'\nconst EVENT_TOUCHSTART = `touchstart${EVENT_KEY}`\nconst EVENT_TOUCHMOVE = `touchmove${EVENT_KEY}`\nconst EVENT_TOUCHEND = `touchend${EVENT_KEY}`\nconst EVENT_POINTERDOWN = `pointerdown${EVENT_KEY}`\nconst EVENT_POINTERUP = `pointerup${EVENT_KEY}`\nconst POINTER_TYPE_TOUCH = 'touch'\nconst POINTER_TYPE_PEN = 'pen'\nconst CLASS_NAME_POINTER_EVENT = 'pointer-event'\nconst SWIPE_THRESHOLD = 40\n\nconst Default = {\n endCallback: null,\n leftCallback: null,\n rightCallback: null\n}\n\nconst DefaultType = {\n endCallback: '(function|null)',\n leftCallback: '(function|null)',\n rightCallback: '(function|null)'\n}\n\n/**\n * Class definition\n */\n\nclass Swipe extends Config {\n constructor(element, config) {\n super()\n this._element = element\n\n if (!element || !Swipe.isSupported()) {\n return\n }\n\n this._config = this._getConfig(config)\n this._deltaX = 0\n this._supportPointerEvents = Boolean(window.PointerEvent)\n this._initEvents()\n }\n\n // Getters\n static get Default() {\n return Default\n }\n\n static get DefaultType() {\n return DefaultType\n }\n\n static get NAME() {\n return NAME\n }\n\n // Public\n dispose() {\n EventHandler.off(this._element, EVENT_KEY)\n }\n\n // Private\n _start(event) {\n if (!this._supportPointerEvents) {\n this._deltaX = event.touches[0].clientX\n\n return\n }\n\n if (this._eventIsPointerPenTouch(event)) {\n this._deltaX = event.clientX\n }\n }\n\n _end(event) {\n if (this._eventIsPointerPenTouch(event)) {\n this._deltaX = event.clientX - this._deltaX\n }\n\n this._handleSwipe()\n execute(this._config.endCallback)\n }\n\n _move(event) {\n this._deltaX = event.touches && event.touches.length > 1 ?\n 0 :\n event.touches[0].clientX - this._deltaX\n }\n\n _handleSwipe() {\n const absDeltaX = Math.abs(this._deltaX)\n\n if (absDeltaX <= SWIPE_THRESHOLD) {\n return\n }\n\n const direction = absDeltaX / this._deltaX\n\n this._deltaX = 0\n\n if (!direction) {\n return\n }\n\n execute(direction > 0 ? this._config.rightCallback : this._config.leftCallback)\n }\n\n _initEvents() {\n if (this._supportPointerEvents) {\n EventHandler.on(this._element, EVENT_POINTERDOWN, event => this._start(event))\n EventHandler.on(this._element, EVENT_POINTERUP, event => this._end(event))\n\n this._element.classList.add(CLASS_NAME_POINTER_EVENT)\n } else {\n EventHandler.on(this._element, EVENT_TOUCHSTART, event => this._start(event))\n EventHandler.on(this._element, EVENT_TOUCHMOVE, event => this._move(event))\n EventHandler.on(this._element, EVENT_TOUCHEND, event => this._end(event))\n }\n }\n\n _eventIsPointerPenTouch(event) {\n return this._supportPointerEvents && (event.pointerType === POINTER_TYPE_PEN || event.pointerType === POINTER_TYPE_TOUCH)\n }\n\n // Static\n static isSupported() {\n return 'ontouchstart' in document.documentElement || navigator.maxTouchPoints > 0\n }\n}\n\nexport default Swipe\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap (v5.2.2): carousel.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport {\n defineJQueryPlugin,\n getElementFromSelector,\n getNextActiveElement,\n isRTL,\n isVisible,\n reflow,\n triggerTransitionEnd\n} from './util/index'\nimport EventHandler from './dom/event-handler'\nimport Manipulator from './dom/manipulator'\nimport SelectorEngine from './dom/selector-engine'\nimport Swipe from './util/swipe'\nimport BaseComponent from './base-component'\n\n/**\n * Constants\n */\n\nconst NAME = 'carousel'\nconst DATA_KEY = 'bs.carousel'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst DATA_API_KEY = '.data-api'\n\nconst ARROW_LEFT_KEY = 'ArrowLeft'\nconst ARROW_RIGHT_KEY = 'ArrowRight'\nconst TOUCHEVENT_COMPAT_WAIT = 500 // Time for mouse compat events to fire after touch\n\nconst ORDER_NEXT = 'next'\nconst ORDER_PREV = 'prev'\nconst DIRECTION_LEFT = 'left'\nconst DIRECTION_RIGHT = 'right'\n\nconst EVENT_SLIDE = `slide${EVENT_KEY}`\nconst EVENT_SLID = `slid${EVENT_KEY}`\nconst EVENT_KEYDOWN = `keydown${EVENT_KEY}`\nconst EVENT_MOUSEENTER = `mouseenter${EVENT_KEY}`\nconst EVENT_MOUSELEAVE = `mouseleave${EVENT_KEY}`\nconst EVENT_DRAG_START = `dragstart${EVENT_KEY}`\nconst EVENT_LOAD_DATA_API = `load${EVENT_KEY}${DATA_API_KEY}`\nconst EVENT_CLICK_DATA_API = `click${EVENT_KEY}${DATA_API_KEY}`\n\nconst CLASS_NAME_CAROUSEL = 'carousel'\nconst CLASS_NAME_ACTIVE = 'active'\nconst CLASS_NAME_SLIDE = 'slide'\nconst CLASS_NAME_END = 'carousel-item-end'\nconst CLASS_NAME_START = 'carousel-item-start'\nconst CLASS_NAME_NEXT = 'carousel-item-next'\nconst CLASS_NAME_PREV = 'carousel-item-prev'\n\nconst SELECTOR_ACTIVE = '.active'\nconst SELECTOR_ITEM = '.carousel-item'\nconst SELECTOR_ACTIVE_ITEM = SELECTOR_ACTIVE + SELECTOR_ITEM\nconst SELECTOR_ITEM_IMG = '.carousel-item img'\nconst SELECTOR_INDICATORS = '.carousel-indicators'\nconst SELECTOR_DATA_SLIDE = '[data-bs-slide], [data-bs-slide-to]'\nconst SELECTOR_DATA_RIDE = '[data-bs-ride=\"carousel\"]'\n\nconst KEY_TO_DIRECTION = {\n [ARROW_LEFT_KEY]: DIRECTION_RIGHT,\n [ARROW_RIGHT_KEY]: DIRECTION_LEFT\n}\n\nconst Default = {\n interval: 5000,\n keyboard: true,\n pause: 'hover',\n ride: false,\n touch: true,\n wrap: true\n}\n\nconst DefaultType = {\n interval: '(number|boolean)', // TODO:v6 remove boolean support\n keyboard: 'boolean',\n pause: '(string|boolean)',\n ride: '(boolean|string)',\n touch: 'boolean',\n wrap: 'boolean'\n}\n\n/**\n * Class definition\n */\n\nclass Carousel extends BaseComponent {\n constructor(element, config) {\n super(element, config)\n\n this._interval = null\n this._activeElement = null\n this._isSliding = false\n this.touchTimeout = null\n this._swipeHelper = null\n\n this._indicatorsElement = SelectorEngine.findOne(SELECTOR_INDICATORS, this._element)\n this._addEventListeners()\n\n if (this._config.ride === CLASS_NAME_CAROUSEL) {\n this.cycle()\n }\n }\n\n // Getters\n static get Default() {\n return Default\n }\n\n static get DefaultType() {\n return DefaultType\n }\n\n static get NAME() {\n return NAME\n }\n\n // Public\n next() {\n this._slide(ORDER_NEXT)\n }\n\n nextWhenVisible() {\n // FIXME TODO use `document.visibilityState`\n // Don't call next when the page isn't visible\n // or the carousel or its parent isn't visible\n if (!document.hidden && isVisible(this._element)) {\n this.next()\n }\n }\n\n prev() {\n this._slide(ORDER_PREV)\n }\n\n pause() {\n if (this._isSliding) {\n triggerTransitionEnd(this._element)\n }\n\n this._clearInterval()\n }\n\n cycle() {\n this._clearInterval()\n this._updateInterval()\n\n this._interval = setInterval(() => this.nextWhenVisible(), this._config.interval)\n }\n\n _maybeEnableCycle() {\n if (!this._config.ride) {\n return\n }\n\n if (this._isSliding) {\n EventHandler.one(this._element, EVENT_SLID, () => this.cycle())\n return\n }\n\n this.cycle()\n }\n\n to(index) {\n const items = this._getItems()\n if (index > items.length - 1 || index < 0) {\n return\n }\n\n if (this._isSliding) {\n EventHandler.one(this._element, EVENT_SLID, () => this.to(index))\n return\n }\n\n const activeIndex = this._getItemIndex(this._getActive())\n if (activeIndex === index) {\n return\n }\n\n const order = index > activeIndex ? ORDER_NEXT : ORDER_PREV\n\n this._slide(order, items[index])\n }\n\n dispose() {\n if (this._swipeHelper) {\n this._swipeHelper.dispose()\n }\n\n super.dispose()\n }\n\n // Private\n _configAfterMerge(config) {\n config.defaultInterval = config.interval\n return config\n }\n\n _addEventListeners() {\n if (this._config.keyboard) {\n EventHandler.on(this._element, EVENT_KEYDOWN, event => this._keydown(event))\n }\n\n if (this._config.pause === 'hover') {\n EventHandler.on(this._element, EVENT_MOUSEENTER, () => this.pause())\n EventHandler.on(this._element, EVENT_MOUSELEAVE, () => this._maybeEnableCycle())\n }\n\n if (this._config.touch && Swipe.isSupported()) {\n this._addTouchEventListeners()\n }\n }\n\n _addTouchEventListeners() {\n for (const img of SelectorEngine.find(SELECTOR_ITEM_IMG, this._element)) {\n EventHandler.on(img, EVENT_DRAG_START, event => event.preventDefault())\n }\n\n const endCallBack = () => {\n if (this._config.pause !== 'hover') {\n return\n }\n\n // If it's a touch-enabled device, mouseenter/leave are fired as\n // part of the mouse compatibility events on first tap - the carousel\n // would stop cycling until user tapped out of it;\n // here, we listen for touchend, explicitly pause the carousel\n // (as if it's the second time we tap on it, mouseenter compat event\n // is NOT fired) and after a timeout (to allow for mouse compatibility\n // events to fire) we explicitly restart cycling\n\n this.pause()\n if (this.touchTimeout) {\n clearTimeout(this.touchTimeout)\n }\n\n this.touchTimeout = setTimeout(() => this._maybeEnableCycle(), TOUCHEVENT_COMPAT_WAIT + this._config.interval)\n }\n\n const swipeConfig = {\n leftCallback: () => this._slide(this._directionToOrder(DIRECTION_LEFT)),\n rightCallback: () => this._slide(this._directionToOrder(DIRECTION_RIGHT)),\n endCallback: endCallBack\n }\n\n this._swipeHelper = new Swipe(this._element, swipeConfig)\n }\n\n _keydown(event) {\n if (/input|textarea/i.test(event.target.tagName)) {\n return\n }\n\n const direction = KEY_TO_DIRECTION[event.key]\n if (direction) {\n event.preventDefault()\n this._slide(this._directionToOrder(direction))\n }\n }\n\n _getItemIndex(element) {\n return this._getItems().indexOf(element)\n }\n\n _setActiveIndicatorElement(index) {\n if (!this._indicatorsElement) {\n return\n }\n\n const activeIndicator = SelectorEngine.findOne(SELECTOR_ACTIVE, this._indicatorsElement)\n\n activeIndicator.classList.remove(CLASS_NAME_ACTIVE)\n activeIndicator.removeAttribute('aria-current')\n\n const newActiveIndicator = SelectorEngine.findOne(`[data-bs-slide-to=\"${index}\"]`, this._indicatorsElement)\n\n if (newActiveIndicator) {\n newActiveIndicator.classList.add(CLASS_NAME_ACTIVE)\n newActiveIndicator.setAttribute('aria-current', 'true')\n }\n }\n\n _updateInterval() {\n const element = this._activeElement || this._getActive()\n\n if (!element) {\n return\n }\n\n const elementInterval = Number.parseInt(element.getAttribute('data-bs-interval'), 10)\n\n this._config.interval = elementInterval || this._config.defaultInterval\n }\n\n _slide(order, element = null) {\n if (this._isSliding) {\n return\n }\n\n const activeElement = this._getActive()\n const isNext = order === ORDER_NEXT\n const nextElement = element || getNextActiveElement(this._getItems(), activeElement, isNext, this._config.wrap)\n\n if (nextElement === activeElement) {\n return\n }\n\n const nextElementIndex = this._getItemIndex(nextElement)\n\n const triggerEvent = eventName => {\n return EventHandler.trigger(this._element, eventName, {\n relatedTarget: nextElement,\n direction: this._orderToDirection(order),\n from: this._getItemIndex(activeElement),\n to: nextElementIndex\n })\n }\n\n const slideEvent = triggerEvent(EVENT_SLIDE)\n\n if (slideEvent.defaultPrevented) {\n return\n }\n\n if (!activeElement || !nextElement) {\n // Some weirdness is happening, so we bail\n // todo: change tests that use empty divs to avoid this check\n return\n }\n\n const isCycling = Boolean(this._interval)\n this.pause()\n\n this._isSliding = true\n\n this._setActiveIndicatorElement(nextElementIndex)\n this._activeElement = nextElement\n\n const directionalClassName = isNext ? CLASS_NAME_START : CLASS_NAME_END\n const orderClassName = isNext ? CLASS_NAME_NEXT : CLASS_NAME_PREV\n\n nextElement.classList.add(orderClassName)\n\n reflow(nextElement)\n\n activeElement.classList.add(directionalClassName)\n nextElement.classList.add(directionalClassName)\n\n const completeCallBack = () => {\n nextElement.classList.remove(directionalClassName, orderClassName)\n nextElement.classList.add(CLASS_NAME_ACTIVE)\n\n activeElement.classList.remove(CLASS_NAME_ACTIVE, orderClassName, directionalClassName)\n\n this._isSliding = false\n\n triggerEvent(EVENT_SLID)\n }\n\n this._queueCallback(completeCallBack, activeElement, this._isAnimated())\n\n if (isCycling) {\n this.cycle()\n }\n }\n\n _isAnimated() {\n return this._element.classList.contains(CLASS_NAME_SLIDE)\n }\n\n _getActive() {\n return SelectorEngine.findOne(SELECTOR_ACTIVE_ITEM, this._element)\n }\n\n _getItems() {\n return SelectorEngine.find(SELECTOR_ITEM, this._element)\n }\n\n _clearInterval() {\n if (this._interval) {\n clearInterval(this._interval)\n this._interval = null\n }\n }\n\n _directionToOrder(direction) {\n if (isRTL()) {\n return direction === DIRECTION_LEFT ? ORDER_PREV : ORDER_NEXT\n }\n\n return direction === DIRECTION_LEFT ? ORDER_NEXT : ORDER_PREV\n }\n\n _orderToDirection(order) {\n if (isRTL()) {\n return order === ORDER_PREV ? DIRECTION_LEFT : DIRECTION_RIGHT\n }\n\n return order === ORDER_PREV ? DIRECTION_RIGHT : DIRECTION_LEFT\n }\n\n // Static\n static jQueryInterface(config) {\n return this.each(function () {\n const data = Carousel.getOrCreateInstance(this, config)\n\n if (typeof config === 'number') {\n data.to(config)\n return\n }\n\n if (typeof config === 'string') {\n if (data[config] === undefined || config.startsWith('_') || config === 'constructor') {\n throw new TypeError(`No method named \"${config}\"`)\n }\n\n data[config]()\n }\n })\n }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(document, EVENT_CLICK_DATA_API, SELECTOR_DATA_SLIDE, function (event) {\n const target = getElementFromSelector(this)\n\n if (!target || !target.classList.contains(CLASS_NAME_CAROUSEL)) {\n return\n }\n\n event.preventDefault()\n\n const carousel = Carousel.getOrCreateInstance(target)\n const slideIndex = this.getAttribute('data-bs-slide-to')\n\n if (slideIndex) {\n carousel.to(slideIndex)\n carousel._maybeEnableCycle()\n return\n }\n\n if (Manipulator.getDataAttribute(this, 'slide') === 'next') {\n carousel.next()\n carousel._maybeEnableCycle()\n return\n }\n\n carousel.prev()\n carousel._maybeEnableCycle()\n})\n\nEventHandler.on(window, EVENT_LOAD_DATA_API, () => {\n const carousels = SelectorEngine.find(SELECTOR_DATA_RIDE)\n\n for (const carousel of carousels) {\n Carousel.getOrCreateInstance(carousel)\n }\n})\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Carousel)\n\nexport default Carousel\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap (v5.2.2): collapse.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport {\n defineJQueryPlugin,\n getElement,\n getElementFromSelector,\n getSelectorFromElement,\n reflow\n} from './util/index'\nimport EventHandler from './dom/event-handler'\nimport SelectorEngine from './dom/selector-engine'\nimport BaseComponent from './base-component'\n\n/**\n * Constants\n */\n\nconst NAME = 'collapse'\nconst DATA_KEY = 'bs.collapse'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst DATA_API_KEY = '.data-api'\n\nconst EVENT_SHOW = `show${EVENT_KEY}`\nconst EVENT_SHOWN = `shown${EVENT_KEY}`\nconst EVENT_HIDE = `hide${EVENT_KEY}`\nconst EVENT_HIDDEN = `hidden${EVENT_KEY}`\nconst EVENT_CLICK_DATA_API = `click${EVENT_KEY}${DATA_API_KEY}`\n\nconst CLASS_NAME_SHOW = 'show'\nconst CLASS_NAME_COLLAPSE = 'collapse'\nconst CLASS_NAME_COLLAPSING = 'collapsing'\nconst CLASS_NAME_COLLAPSED = 'collapsed'\nconst CLASS_NAME_DEEPER_CHILDREN = `:scope .${CLASS_NAME_COLLAPSE} .${CLASS_NAME_COLLAPSE}`\nconst CLASS_NAME_HORIZONTAL = 'collapse-horizontal'\n\nconst WIDTH = 'width'\nconst HEIGHT = 'height'\n\nconst SELECTOR_ACTIVES = '.collapse.show, .collapse.collapsing'\nconst SELECTOR_DATA_TOGGLE = '[data-bs-toggle=\"collapse\"]'\n\nconst Default = {\n parent: null,\n toggle: true\n}\n\nconst DefaultType = {\n parent: '(null|element)',\n toggle: 'boolean'\n}\n\n/**\n * Class definition\n */\n\nclass Collapse extends BaseComponent {\n constructor(element, config) {\n super(element, config)\n\n this._isTransitioning = false\n this._triggerArray = []\n\n const toggleList = SelectorEngine.find(SELECTOR_DATA_TOGGLE)\n\n for (const elem of toggleList) {\n const selector = getSelectorFromElement(elem)\n const filterElement = SelectorEngine.find(selector)\n .filter(foundElement => foundElement === this._element)\n\n if (selector !== null && filterElement.length) {\n this._triggerArray.push(elem)\n }\n }\n\n this._initializeChildren()\n\n if (!this._config.parent) {\n this._addAriaAndCollapsedClass(this._triggerArray, this._isShown())\n }\n\n if (this._config.toggle) {\n this.toggle()\n }\n }\n\n // Getters\n static get Default() {\n return Default\n }\n\n static get DefaultType() {\n return DefaultType\n }\n\n static get NAME() {\n return NAME\n }\n\n // Public\n toggle() {\n if (this._isShown()) {\n this.hide()\n } else {\n this.show()\n }\n }\n\n show() {\n if (this._isTransitioning || this._isShown()) {\n return\n }\n\n let activeChildren = []\n\n // find active children\n if (this._config.parent) {\n activeChildren = this._getFirstLevelChildren(SELECTOR_ACTIVES)\n .filter(element => element !== this._element)\n .map(element => Collapse.getOrCreateInstance(element, { toggle: false }))\n }\n\n if (activeChildren.length && activeChildren[0]._isTransitioning) {\n return\n }\n\n const startEvent = EventHandler.trigger(this._element, EVENT_SHOW)\n if (startEvent.defaultPrevented) {\n return\n }\n\n for (const activeInstance of activeChildren) {\n activeInstance.hide()\n }\n\n const dimension = this._getDimension()\n\n this._element.classList.remove(CLASS_NAME_COLLAPSE)\n this._element.classList.add(CLASS_NAME_COLLAPSING)\n\n this._element.style[dimension] = 0\n\n this._addAriaAndCollapsedClass(this._triggerArray, true)\n this._isTransitioning = true\n\n const complete = () => {\n this._isTransitioning = false\n\n this._element.classList.remove(CLASS_NAME_COLLAPSING)\n this._element.classList.add(CLASS_NAME_COLLAPSE, CLASS_NAME_SHOW)\n\n this._element.style[dimension] = ''\n\n EventHandler.trigger(this._element, EVENT_SHOWN)\n }\n\n const capitalizedDimension = dimension[0].toUpperCase() + dimension.slice(1)\n const scrollSize = `scroll${capitalizedDimension}`\n\n this._queueCallback(complete, this._element, true)\n this._element.style[dimension] = `${this._element[scrollSize]}px`\n }\n\n hide() {\n if (this._isTransitioning || !this._isShown()) {\n return\n }\n\n const startEvent = EventHandler.trigger(this._element, EVENT_HIDE)\n if (startEvent.defaultPrevented) {\n return\n }\n\n const dimension = this._getDimension()\n\n this._element.style[dimension] = `${this._element.getBoundingClientRect()[dimension]}px`\n\n reflow(this._element)\n\n this._element.classList.add(CLASS_NAME_COLLAPSING)\n this._element.classList.remove(CLASS_NAME_COLLAPSE, CLASS_NAME_SHOW)\n\n for (const trigger of this._triggerArray) {\n const element = getElementFromSelector(trigger)\n\n if (element && !this._isShown(element)) {\n this._addAriaAndCollapsedClass([trigger], false)\n }\n }\n\n this._isTransitioning = true\n\n const complete = () => {\n this._isTransitioning = false\n this._element.classList.remove(CLASS_NAME_COLLAPSING)\n this._element.classList.add(CLASS_NAME_COLLAPSE)\n EventHandler.trigger(this._element, EVENT_HIDDEN)\n }\n\n this._element.style[dimension] = ''\n\n this._queueCallback(complete, this._element, true)\n }\n\n _isShown(element = this._element) {\n return element.classList.contains(CLASS_NAME_SHOW)\n }\n\n // Private\n _configAfterMerge(config) {\n config.toggle = Boolean(config.toggle) // Coerce string values\n config.parent = getElement(config.parent)\n return config\n }\n\n _getDimension() {\n return this._element.classList.contains(CLASS_NAME_HORIZONTAL) ? WIDTH : HEIGHT\n }\n\n _initializeChildren() {\n if (!this._config.parent) {\n return\n }\n\n const children = this._getFirstLevelChildren(SELECTOR_DATA_TOGGLE)\n\n for (const element of children) {\n const selected = getElementFromSelector(element)\n\n if (selected) {\n this._addAriaAndCollapsedClass([element], this._isShown(selected))\n }\n }\n }\n\n _getFirstLevelChildren(selector) {\n const children = SelectorEngine.find(CLASS_NAME_DEEPER_CHILDREN, this._config.parent)\n // remove children if greater depth\n return SelectorEngine.find(selector, this._config.parent).filter(element => !children.includes(element))\n }\n\n _addAriaAndCollapsedClass(triggerArray, isOpen) {\n if (!triggerArray.length) {\n return\n }\n\n for (const element of triggerArray) {\n element.classList.toggle(CLASS_NAME_COLLAPSED, !isOpen)\n element.setAttribute('aria-expanded', isOpen)\n }\n }\n\n // Static\n static jQueryInterface(config) {\n const _config = {}\n if (typeof config === 'string' && /show|hide/.test(config)) {\n _config.toggle = false\n }\n\n return this.each(function () {\n const data = Collapse.getOrCreateInstance(this, _config)\n\n if (typeof config === 'string') {\n if (typeof data[config] === 'undefined') {\n throw new TypeError(`No method named \"${config}\"`)\n }\n\n data[config]()\n }\n })\n }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(document, EVENT_CLICK_DATA_API, SELECTOR_DATA_TOGGLE, function (event) {\n // preventDefault only for <a> elements (which change the URL) not inside the collapsible element\n if (event.target.tagName === 'A' || (event.delegateTarget && event.delegateTarget.tagName === 'A')) {\n event.preventDefault()\n }\n\n const selector = getSelectorFromElement(this)\n const selectorElements = SelectorEngine.find(selector)\n\n for (const element of selectorElements) {\n Collapse.getOrCreateInstance(element, { toggle: false }).toggle()\n }\n})\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Collapse)\n\nexport default Collapse\n","export var top = 'top';\nexport var bottom = 'bottom';\nexport var right = 'right';\nexport var left = 'left';\nexport var auto = 'auto';\nexport var basePlacements = [top, bottom, right, left];\nexport var start = 'start';\nexport var end = 'end';\nexport var clippingParents = 'clippingParents';\nexport var viewport = 'viewport';\nexport var popper = 'popper';\nexport var reference = 'reference';\nexport var variationPlacements = /*#__PURE__*/basePlacements.reduce(function (acc, placement) {\n return acc.concat([placement + \"-\" + start, placement + \"-\" + end]);\n}, []);\nexport var placements = /*#__PURE__*/[].concat(basePlacements, [auto]).reduce(function (acc, placement) {\n return acc.concat([placement, placement + \"-\" + start, placement + \"-\" + end]);\n}, []); // modifiers that need to read the DOM\n\nexport var beforeRead = 'beforeRead';\nexport var read = 'read';\nexport var afterRead = 'afterRead'; // pure-logic modifiers\n\nexport var beforeMain = 'beforeMain';\nexport var main = 'main';\nexport var afterMain = 'afterMain'; // modifier with the purpose to write to the DOM (or write into a framework state)\n\nexport var beforeWrite = 'beforeWrite';\nexport var write = 'write';\nexport var afterWrite = 'afterWrite';\nexport var modifierPhases = [beforeRead, read, afterRead, beforeMain, main, afterMain, beforeWrite, write, afterWrite];","export default function getNodeName(element) {\n return element ? (element.nodeName || '').toLowerCase() : null;\n}","export default function getWindow(node) {\n if (node == null) {\n return window;\n }\n\n if (node.toString() !== '[object Window]') {\n var ownerDocument = node.ownerDocument;\n return ownerDocument ? ownerDocument.defaultView || window : window;\n }\n\n return node;\n}","import getWindow from \"./getWindow.js\";\n\nfunction isElement(node) {\n var OwnElement = getWindow(node).Element;\n return node instanceof OwnElement || node instanceof Element;\n}\n\nfunction isHTMLElement(node) {\n var OwnElement = getWindow(node).HTMLElement;\n return node instanceof OwnElement || node instanceof HTMLElement;\n}\n\nfunction isShadowRoot(node) {\n // IE 11 has no ShadowRoot\n if (typeof ShadowRoot === 'undefined') {\n return false;\n }\n\n var OwnElement = getWindow(node).ShadowRoot;\n return node instanceof OwnElement || node instanceof ShadowRoot;\n}\n\nexport { isElement, isHTMLElement, isShadowRoot };","import getNodeName from \"../dom-utils/getNodeName.js\";\nimport { isHTMLElement } from \"../dom-utils/instanceOf.js\"; // This modifier takes the styles prepared by the `computeStyles` modifier\n// and applies them to the HTMLElements such as popper and arrow\n\nfunction applyStyles(_ref) {\n var state = _ref.state;\n Object.keys(state.elements).forEach(function (name) {\n var style = state.styles[name] || {};\n var attributes = state.attributes[name] || {};\n var element = state.elements[name]; // arrow is optional + virtual elements\n\n if (!isHTMLElement(element) || !getNodeName(element)) {\n return;\n } // Flow doesn't support to extend this property, but it's the most\n // effective way to apply styles to an HTMLElement\n // $FlowFixMe[cannot-write]\n\n\n Object.assign(element.style, style);\n Object.keys(attributes).forEach(function (name) {\n var value = attributes[name];\n\n if (value === false) {\n element.removeAttribute(name);\n } else {\n element.setAttribute(name, value === true ? '' : value);\n }\n });\n });\n}\n\nfunction effect(_ref2) {\n var state = _ref2.state;\n var initialStyles = {\n popper: {\n position: state.options.strategy,\n left: '0',\n top: '0',\n margin: '0'\n },\n arrow: {\n position: 'absolute'\n },\n reference: {}\n };\n Object.assign(state.elements.popper.style, initialStyles.popper);\n state.styles = initialStyles;\n\n if (state.elements.arrow) {\n Object.assign(state.elements.arrow.style, initialStyles.arrow);\n }\n\n return function () {\n Object.keys(state.elements).forEach(function (name) {\n var element = state.elements[name];\n var attributes = state.attributes[name] || {};\n var styleProperties = Object.keys(state.styles.hasOwnProperty(name) ? state.styles[name] : initialStyles[name]); // Set all values to an empty string to unset them\n\n var style = styleProperties.reduce(function (style, property) {\n style[property] = '';\n return style;\n }, {}); // arrow is optional + virtual elements\n\n if (!isHTMLElement(element) || !getNodeName(element)) {\n return;\n }\n\n Object.assign(element.style, style);\n Object.keys(attributes).forEach(function (attribute) {\n element.removeAttribute(attribute);\n });\n });\n };\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n name: 'applyStyles',\n enabled: true,\n phase: 'write',\n fn: applyStyles,\n effect: effect,\n requires: ['computeStyles']\n};","import { auto } from \"../enums.js\";\nexport default function getBasePlacement(placement) {\n return placement.split('-')[0];\n}","export var max = Math.max;\nexport var min = Math.min;\nexport var round = Math.round;","export default function getUAString() {\n var uaData = navigator.userAgentData;\n\n if (uaData != null && uaData.brands) {\n return uaData.brands.map(function (item) {\n return item.brand + \"/\" + item.version;\n }).join(' ');\n }\n\n return navigator.userAgent;\n}","import getUAString from \"../utils/userAgent.js\";\nexport default function isLayoutViewport() {\n return !/^((?!chrome|android).)*safari/i.test(getUAString());\n}","import { isElement, isHTMLElement } from \"./instanceOf.js\";\nimport { round } from \"../utils/math.js\";\nimport getWindow from \"./getWindow.js\";\nimport isLayoutViewport from \"./isLayoutViewport.js\";\nexport default function getBoundingClientRect(element, includeScale, isFixedStrategy) {\n if (includeScale === void 0) {\n includeScale = false;\n }\n\n if (isFixedStrategy === void 0) {\n isFixedStrategy = false;\n }\n\n var clientRect = element.getBoundingClientRect();\n var scaleX = 1;\n var scaleY = 1;\n\n if (includeScale && isHTMLElement(element)) {\n scaleX = element.offsetWidth > 0 ? round(clientRect.width) / element.offsetWidth || 1 : 1;\n scaleY = element.offsetHeight > 0 ? round(clientRect.height) / element.offsetHeight || 1 : 1;\n }\n\n var _ref = isElement(element) ? getWindow(element) : window,\n visualViewport = _ref.visualViewport;\n\n var addVisualOffsets = !isLayoutViewport() && isFixedStrategy;\n var x = (clientRect.left + (addVisualOffsets && visualViewport ? visualViewport.offsetLeft : 0)) / scaleX;\n var y = (clientRect.top + (addVisualOffsets && visualViewport ? visualViewport.offsetTop : 0)) / scaleY;\n var width = clientRect.width / scaleX;\n var height = clientRect.height / scaleY;\n return {\n width: width,\n height: height,\n top: y,\n right: x + width,\n bottom: y + height,\n left: x,\n x: x,\n y: y\n };\n}","import getBoundingClientRect from \"./getBoundingClientRect.js\"; // Returns the layout rect of an element relative to its offsetParent. Layout\n// means it doesn't take into account transforms.\n\nexport default function getLayoutRect(element) {\n var clientRect = getBoundingClientRect(element); // Use the clientRect sizes if it's not been transformed.\n // Fixes https://github.com/popperjs/popper-core/issues/1223\n\n var width = element.offsetWidth;\n var height = element.offsetHeight;\n\n if (Math.abs(clientRect.width - width) <= 1) {\n width = clientRect.width;\n }\n\n if (Math.abs(clientRect.height - height) <= 1) {\n height = clientRect.height;\n }\n\n return {\n x: element.offsetLeft,\n y: element.offsetTop,\n width: width,\n height: height\n };\n}","import { isShadowRoot } from \"./instanceOf.js\";\nexport default function contains(parent, child) {\n var rootNode = child.getRootNode && child.getRootNode(); // First, attempt with faster native method\n\n if (parent.contains(child)) {\n return true;\n } // then fallback to custom implementation with Shadow DOM support\n else if (rootNode && isShadowRoot(rootNode)) {\n var next = child;\n\n do {\n if (next && parent.isSameNode(next)) {\n return true;\n } // $FlowFixMe[prop-missing]: need a better way to handle this...\n\n\n next = next.parentNode || next.host;\n } while (next);\n } // Give up, the result is false\n\n\n return false;\n}","import getWindow from \"./getWindow.js\";\nexport default function getComputedStyle(element) {\n return getWindow(element).getComputedStyle(element);\n}","import getNodeName from \"./getNodeName.js\";\nexport default function isTableElement(element) {\n return ['table', 'td', 'th'].indexOf(getNodeName(element)) >= 0;\n}","import { isElement } from \"./instanceOf.js\";\nexport default function getDocumentElement(element) {\n // $FlowFixMe[incompatible-return]: assume body is always available\n return ((isElement(element) ? element.ownerDocument : // $FlowFixMe[prop-missing]\n element.document) || window.document).documentElement;\n}","import getNodeName from \"./getNodeName.js\";\nimport getDocumentElement from \"./getDocumentElement.js\";\nimport { isShadowRoot } from \"./instanceOf.js\";\nexport default function getParentNode(element) {\n if (getNodeName(element) === 'html') {\n return element;\n }\n\n return (// this is a quicker (but less type safe) way to save quite some bytes from the bundle\n // $FlowFixMe[incompatible-return]\n // $FlowFixMe[prop-missing]\n element.assignedSlot || // step into the shadow DOM of the parent of a slotted node\n element.parentNode || ( // DOM Element detected\n isShadowRoot(element) ? element.host : null) || // ShadowRoot detected\n // $FlowFixMe[incompatible-call]: HTMLElement is a Node\n getDocumentElement(element) // fallback\n\n );\n}","import getWindow from \"./getWindow.js\";\nimport getNodeName from \"./getNodeName.js\";\nimport getComputedStyle from \"./getComputedStyle.js\";\nimport { isHTMLElement, isShadowRoot } from \"./instanceOf.js\";\nimport isTableElement from \"./isTableElement.js\";\nimport getParentNode from \"./getParentNode.js\";\nimport getUAString from \"../utils/userAgent.js\";\n\nfunction getTrueOffsetParent(element) {\n if (!isHTMLElement(element) || // https://github.com/popperjs/popper-core/issues/837\n getComputedStyle(element).position === 'fixed') {\n return null;\n }\n\n return element.offsetParent;\n} // `.offsetParent` reports `null` for fixed elements, while absolute elements\n// return the containing block\n\n\nfunction getContainingBlock(element) {\n var isFirefox = /firefox/i.test(getUAString());\n var isIE = /Trident/i.test(getUAString());\n\n if (isIE && isHTMLElement(element)) {\n // In IE 9, 10 and 11 fixed elements containing block is always established by the viewport\n var elementCss = getComputedStyle(element);\n\n if (elementCss.position === 'fixed') {\n return null;\n }\n }\n\n var currentNode = getParentNode(element);\n\n if (isShadowRoot(currentNode)) {\n currentNode = currentNode.host;\n }\n\n while (isHTMLElement(currentNode) && ['html', 'body'].indexOf(getNodeName(currentNode)) < 0) {\n var css = getComputedStyle(currentNode); // This is non-exhaustive but covers the most common CSS properties that\n // create a containing block.\n // https://developer.mozilla.org/en-US/docs/Web/CSS/Containing_block#identifying_the_containing_block\n\n if (css.transform !== 'none' || css.perspective !== 'none' || css.contain === 'paint' || ['transform', 'perspective'].indexOf(css.willChange) !== -1 || isFirefox && css.willChange === 'filter' || isFirefox && css.filter && css.filter !== 'none') {\n return currentNode;\n } else {\n currentNode = currentNode.parentNode;\n }\n }\n\n return null;\n} // Gets the closest ancestor positioned element. Handles some edge cases,\n// such as table ancestors and cross browser bugs.\n\n\nexport default function getOffsetParent(element) {\n var window = getWindow(element);\n var offsetParent = getTrueOffsetParent(element);\n\n while (offsetParent && isTableElement(offsetParent) && getComputedStyle(offsetParent).position === 'static') {\n offsetParent = getTrueOffsetParent(offsetParent);\n }\n\n if (offsetParent && (getNodeName(offsetParent) === 'html' || getNodeName(offsetParent) === 'body' && getComputedStyle(offsetParent).position === 'static')) {\n return window;\n }\n\n return offsetParent || getContainingBlock(element) || window;\n}","export default function getMainAxisFromPlacement(placement) {\n return ['top', 'bottom'].indexOf(placement) >= 0 ? 'x' : 'y';\n}","import { max as mathMax, min as mathMin } from \"./math.js\";\nexport function within(min, value, max) {\n return mathMax(min, mathMin(value, max));\n}\nexport function withinMaxClamp(min, value, max) {\n var v = within(min, value, max);\n return v > max ? max : v;\n}","import getFreshSideObject from \"./getFreshSideObject.js\";\nexport default function mergePaddingObject(paddingObject) {\n return Object.assign({}, getFreshSideObject(), paddingObject);\n}","export default function getFreshSideObject() {\n return {\n top: 0,\n right: 0,\n bottom: 0,\n left: 0\n };\n}","export default function expandToHashMap(value, keys) {\n return keys.reduce(function (hashMap, key) {\n hashMap[key] = value;\n return hashMap;\n }, {});\n}","import getBasePlacement from \"../utils/getBasePlacement.js\";\nimport getLayoutRect from \"../dom-utils/getLayoutRect.js\";\nimport contains from \"../dom-utils/contains.js\";\nimport getOffsetParent from \"../dom-utils/getOffsetParent.js\";\nimport getMainAxisFromPlacement from \"../utils/getMainAxisFromPlacement.js\";\nimport { within } from \"../utils/within.js\";\nimport mergePaddingObject from \"../utils/mergePaddingObject.js\";\nimport expandToHashMap from \"../utils/expandToHashMap.js\";\nimport { left, right, basePlacements, top, bottom } from \"../enums.js\";\nimport { isHTMLElement } from \"../dom-utils/instanceOf.js\"; // eslint-disable-next-line import/no-unused-modules\n\nvar toPaddingObject = function toPaddingObject(padding, state) {\n padding = typeof padding === 'function' ? padding(Object.assign({}, state.rects, {\n placement: state.placement\n })) : padding;\n return mergePaddingObject(typeof padding !== 'number' ? padding : expandToHashMap(padding, basePlacements));\n};\n\nfunction arrow(_ref) {\n var _state$modifiersData$;\n\n var state = _ref.state,\n name = _ref.name,\n options = _ref.options;\n var arrowElement = state.elements.arrow;\n var popperOffsets = state.modifiersData.popperOffsets;\n var basePlacement = getBasePlacement(state.placement);\n var axis = getMainAxisFromPlacement(basePlacement);\n var isVertical = [left, right].indexOf(basePlacement) >= 0;\n var len = isVertical ? 'height' : 'width';\n\n if (!arrowElement || !popperOffsets) {\n return;\n }\n\n var paddingObject = toPaddingObject(options.padding, state);\n var arrowRect = getLayoutRect(arrowElement);\n var minProp = axis === 'y' ? top : left;\n var maxProp = axis === 'y' ? bottom : right;\n var endDiff = state.rects.reference[len] + state.rects.reference[axis] - popperOffsets[axis] - state.rects.popper[len];\n var startDiff = popperOffsets[axis] - state.rects.reference[axis];\n var arrowOffsetParent = getOffsetParent(arrowElement);\n var clientSize = arrowOffsetParent ? axis === 'y' ? arrowOffsetParent.clientHeight || 0 : arrowOffsetParent.clientWidth || 0 : 0;\n var centerToReference = endDiff / 2 - startDiff / 2; // Make sure the arrow doesn't overflow the popper if the center point is\n // outside of the popper bounds\n\n var min = paddingObject[minProp];\n var max = clientSize - arrowRect[len] - paddingObject[maxProp];\n var center = clientSize / 2 - arrowRect[len] / 2 + centerToReference;\n var offset = within(min, center, max); // Prevents breaking syntax highlighting...\n\n var axisProp = axis;\n state.modifiersData[name] = (_state$modifiersData$ = {}, _state$modifiersData$[axisProp] = offset, _state$modifiersData$.centerOffset = offset - center, _state$modifiersData$);\n}\n\nfunction effect(_ref2) {\n var state = _ref2.state,\n options = _ref2.options;\n var _options$element = options.element,\n arrowElement = _options$element === void 0 ? '[data-popper-arrow]' : _options$element;\n\n if (arrowElement == null) {\n return;\n } // CSS selector\n\n\n if (typeof arrowElement === 'string') {\n arrowElement = state.elements.popper.querySelector(arrowElement);\n\n if (!arrowElement) {\n return;\n }\n }\n\n if (process.env.NODE_ENV !== \"production\") {\n if (!isHTMLElement(arrowElement)) {\n console.error(['Popper: \"arrow\" element must be an HTMLElement (not an SVGElement).', 'To use an SVG arrow, wrap it in an HTMLElement that will be used as', 'the arrow.'].join(' '));\n }\n }\n\n if (!contains(state.elements.popper, arrowElement)) {\n if (process.env.NODE_ENV !== \"production\") {\n console.error(['Popper: \"arrow\" modifier\\'s `element` must be a child of the popper', 'element.'].join(' '));\n }\n\n return;\n }\n\n state.elements.arrow = arrowElement;\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n name: 'arrow',\n enabled: true,\n phase: 'main',\n fn: arrow,\n effect: effect,\n requires: ['popperOffsets'],\n requiresIfExists: ['preventOverflow']\n};","export default function getVariation(placement) {\n return placement.split('-')[1];\n}","import { top, left, right, bottom, end } from \"../enums.js\";\nimport getOffsetParent from \"../dom-utils/getOffsetParent.js\";\nimport getWindow from \"../dom-utils/getWindow.js\";\nimport getDocumentElement from \"../dom-utils/getDocumentElement.js\";\nimport getComputedStyle from \"../dom-utils/getComputedStyle.js\";\nimport getBasePlacement from \"../utils/getBasePlacement.js\";\nimport getVariation from \"../utils/getVariation.js\";\nimport { round } from \"../utils/math.js\"; // eslint-disable-next-line import/no-unused-modules\n\nvar unsetSides = {\n top: 'auto',\n right: 'auto',\n bottom: 'auto',\n left: 'auto'\n}; // Round the offsets to the nearest suitable subpixel based on the DPR.\n// Zooming can change the DPR, but it seems to report a value that will\n// cleanly divide the values into the appropriate subpixels.\n\nfunction roundOffsetsByDPR(_ref) {\n var x = _ref.x,\n y = _ref.y;\n var win = window;\n var dpr = win.devicePixelRatio || 1;\n return {\n x: round(x * dpr) / dpr || 0,\n y: round(y * dpr) / dpr || 0\n };\n}\n\nexport function mapToStyles(_ref2) {\n var _Object$assign2;\n\n var popper = _ref2.popper,\n popperRect = _ref2.popperRect,\n placement = _ref2.placement,\n variation = _ref2.variation,\n offsets = _ref2.offsets,\n position = _ref2.position,\n gpuAcceleration = _ref2.gpuAcceleration,\n adaptive = _ref2.adaptive,\n roundOffsets = _ref2.roundOffsets,\n isFixed = _ref2.isFixed;\n var _offsets$x = offsets.x,\n x = _offsets$x === void 0 ? 0 : _offsets$x,\n _offsets$y = offsets.y,\n y = _offsets$y === void 0 ? 0 : _offsets$y;\n\n var _ref3 = typeof roundOffsets === 'function' ? roundOffsets({\n x: x,\n y: y\n }) : {\n x: x,\n y: y\n };\n\n x = _ref3.x;\n y = _ref3.y;\n var hasX = offsets.hasOwnProperty('x');\n var hasY = offsets.hasOwnProperty('y');\n var sideX = left;\n var sideY = top;\n var win = window;\n\n if (adaptive) {\n var offsetParent = getOffsetParent(popper);\n var heightProp = 'clientHeight';\n var widthProp = 'clientWidth';\n\n if (offsetParent === getWindow(popper)) {\n offsetParent = getDocumentElement(popper);\n\n if (getComputedStyle(offsetParent).position !== 'static' && position === 'absolute') {\n heightProp = 'scrollHeight';\n widthProp = 'scrollWidth';\n }\n } // $FlowFixMe[incompatible-cast]: force type refinement, we compare offsetParent with window above, but Flow doesn't detect it\n\n\n offsetParent = offsetParent;\n\n if (placement === top || (placement === left || placement === right) && variation === end) {\n sideY = bottom;\n var offsetY = isFixed && offsetParent === win && win.visualViewport ? win.visualViewport.height : // $FlowFixMe[prop-missing]\n offsetParent[heightProp];\n y -= offsetY - popperRect.height;\n y *= gpuAcceleration ? 1 : -1;\n }\n\n if (placement === left || (placement === top || placement === bottom) && variation === end) {\n sideX = right;\n var offsetX = isFixed && offsetParent === win && win.visualViewport ? win.visualViewport.width : // $FlowFixMe[prop-missing]\n offsetParent[widthProp];\n x -= offsetX - popperRect.width;\n x *= gpuAcceleration ? 1 : -1;\n }\n }\n\n var commonStyles = Object.assign({\n position: position\n }, adaptive && unsetSides);\n\n var _ref4 = roundOffsets === true ? roundOffsetsByDPR({\n x: x,\n y: y\n }) : {\n x: x,\n y: y\n };\n\n x = _ref4.x;\n y = _ref4.y;\n\n if (gpuAcceleration) {\n var _Object$assign;\n\n return Object.assign({}, commonStyles, (_Object$assign = {}, _Object$assign[sideY] = hasY ? '0' : '', _Object$assign[sideX] = hasX ? '0' : '', _Object$assign.transform = (win.devicePixelRatio || 1) <= 1 ? \"translate(\" + x + \"px, \" + y + \"px)\" : \"translate3d(\" + x + \"px, \" + y + \"px, 0)\", _Object$assign));\n }\n\n return Object.assign({}, commonStyles, (_Object$assign2 = {}, _Object$assign2[sideY] = hasY ? y + \"px\" : '', _Object$assign2[sideX] = hasX ? x + \"px\" : '', _Object$assign2.transform = '', _Object$assign2));\n}\n\nfunction computeStyles(_ref5) {\n var state = _ref5.state,\n options = _ref5.options;\n var _options$gpuAccelerat = options.gpuAcceleration,\n gpuAcceleration = _options$gpuAccelerat === void 0 ? true : _options$gpuAccelerat,\n _options$adaptive = options.adaptive,\n adaptive = _options$adaptive === void 0 ? true : _options$adaptive,\n _options$roundOffsets = options.roundOffsets,\n roundOffsets = _options$roundOffsets === void 0 ? true : _options$roundOffsets;\n\n if (process.env.NODE_ENV !== \"production\") {\n var transitionProperty = getComputedStyle(state.elements.popper).transitionProperty || '';\n\n if (adaptive && ['transform', 'top', 'right', 'bottom', 'left'].some(function (property) {\n return transitionProperty.indexOf(property) >= 0;\n })) {\n console.warn(['Popper: Detected CSS transitions on at least one of the following', 'CSS properties: \"transform\", \"top\", \"right\", \"bottom\", \"left\".', '\\n\\n', 'Disable the \"computeStyles\" modifier\\'s `adaptive` option to allow', 'for smooth transitions, or remove these properties from the CSS', 'transition declaration on the popper element if only transitioning', 'opacity or background-color for example.', '\\n\\n', 'We recommend using the popper element as a wrapper around an inner', 'element that can have any CSS property transitioned for animations.'].join(' '));\n }\n }\n\n var commonStyles = {\n placement: getBasePlacement(state.placement),\n variation: getVariation(state.placement),\n popper: state.elements.popper,\n popperRect: state.rects.popper,\n gpuAcceleration: gpuAcceleration,\n isFixed: state.options.strategy === 'fixed'\n };\n\n if (state.modifiersData.popperOffsets != null) {\n state.styles.popper = Object.assign({}, state.styles.popper, mapToStyles(Object.assign({}, commonStyles, {\n offsets: state.modifiersData.popperOffsets,\n position: state.options.strategy,\n adaptive: adaptive,\n roundOffsets: roundOffsets\n })));\n }\n\n if (state.modifiersData.arrow != null) {\n state.styles.arrow = Object.assign({}, state.styles.arrow, mapToStyles(Object.assign({}, commonStyles, {\n offsets: state.modifiersData.arrow,\n position: 'absolute',\n adaptive: false,\n roundOffsets: roundOffsets\n })));\n }\n\n state.attributes.popper = Object.assign({}, state.attributes.popper, {\n 'data-popper-placement': state.placement\n });\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n name: 'computeStyles',\n enabled: true,\n phase: 'beforeWrite',\n fn: computeStyles,\n data: {}\n};","import getWindow from \"../dom-utils/getWindow.js\"; // eslint-disable-next-line import/no-unused-modules\n\nvar passive = {\n passive: true\n};\n\nfunction effect(_ref) {\n var state = _ref.state,\n instance = _ref.instance,\n options = _ref.options;\n var _options$scroll = options.scroll,\n scroll = _options$scroll === void 0 ? true : _options$scroll,\n _options$resize = options.resize,\n resize = _options$resize === void 0 ? true : _options$resize;\n var window = getWindow(state.elements.popper);\n var scrollParents = [].concat(state.scrollParents.reference, state.scrollParents.popper);\n\n if (scroll) {\n scrollParents.forEach(function (scrollParent) {\n scrollParent.addEventListener('scroll', instance.update, passive);\n });\n }\n\n if (resize) {\n window.addEventListener('resize', instance.update, passive);\n }\n\n return function () {\n if (scroll) {\n scrollParents.forEach(function (scrollParent) {\n scrollParent.removeEventListener('scroll', instance.update, passive);\n });\n }\n\n if (resize) {\n window.removeEventListener('resize', instance.update, passive);\n }\n };\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n name: 'eventListeners',\n enabled: true,\n phase: 'write',\n fn: function fn() {},\n effect: effect,\n data: {}\n};","var hash = {\n left: 'right',\n right: 'left',\n bottom: 'top',\n top: 'bottom'\n};\nexport default function getOppositePlacement(placement) {\n return placement.replace(/left|right|bottom|top/g, function (matched) {\n return hash[matched];\n });\n}","var hash = {\n start: 'end',\n end: 'start'\n};\nexport default function getOppositeVariationPlacement(placement) {\n return placement.replace(/start|end/g, function (matched) {\n return hash[matched];\n });\n}","import getWindow from \"./getWindow.js\";\nexport default function getWindowScroll(node) {\n var win = getWindow(node);\n var scrollLeft = win.pageXOffset;\n var scrollTop = win.pageYOffset;\n return {\n scrollLeft: scrollLeft,\n scrollTop: scrollTop\n };\n}","import getBoundingClientRect from \"./getBoundingClientRect.js\";\nimport getDocumentElement from \"./getDocumentElement.js\";\nimport getWindowScroll from \"./getWindowScroll.js\";\nexport default function getWindowScrollBarX(element) {\n // If <html> has a CSS width greater than the viewport, then this will be\n // incorrect for RTL.\n // Popper 1 is broken in this case and never had a bug report so let's assume\n // it's not an issue. I don't think anyone ever specifies width on <html>\n // anyway.\n // Browsers where the left scrollbar doesn't cause an issue report `0` for\n // this (e.g. Edge 2019, IE11, Safari)\n return getBoundingClientRect(getDocumentElement(element)).left + getWindowScroll(element).scrollLeft;\n}","import getComputedStyle from \"./getComputedStyle.js\";\nexport default function isScrollParent(element) {\n // Firefox wants us to check `-x` and `-y` variations as well\n var _getComputedStyle = getComputedStyle(element),\n overflow = _getComputedStyle.overflow,\n overflowX = _getComputedStyle.overflowX,\n overflowY = _getComputedStyle.overflowY;\n\n return /auto|scroll|overlay|hidden/.test(overflow + overflowY + overflowX);\n}","import getParentNode from \"./getParentNode.js\";\nimport isScrollParent from \"./isScrollParent.js\";\nimport getNodeName from \"./getNodeName.js\";\nimport { isHTMLElement } from \"./instanceOf.js\";\nexport default function getScrollParent(node) {\n if (['html', 'body', '#document'].indexOf(getNodeName(node)) >= 0) {\n // $FlowFixMe[incompatible-return]: assume body is always available\n return node.ownerDocument.body;\n }\n\n if (isHTMLElement(node) && isScrollParent(node)) {\n return node;\n }\n\n return getScrollParent(getParentNode(node));\n}","import getScrollParent from \"./getScrollParent.js\";\nimport getParentNode from \"./getParentNode.js\";\nimport getWindow from \"./getWindow.js\";\nimport isScrollParent from \"./isScrollParent.js\";\n/*\ngiven a DOM element, return the list of all scroll parents, up the list of ancesors\nuntil we get to the top window object. This list is what we attach scroll listeners\nto, because if any of these parent elements scroll, we'll need to re-calculate the\nreference element's position.\n*/\n\nexport default function listScrollParents(element, list) {\n var _element$ownerDocumen;\n\n if (list === void 0) {\n list = [];\n }\n\n var scrollParent = getScrollParent(element);\n var isBody = scrollParent === ((_element$ownerDocumen = element.ownerDocument) == null ? void 0 : _element$ownerDocumen.body);\n var win = getWindow(scrollParent);\n var target = isBody ? [win].concat(win.visualViewport || [], isScrollParent(scrollParent) ? scrollParent : []) : scrollParent;\n var updatedList = list.concat(target);\n return isBody ? updatedList : // $FlowFixMe[incompatible-call]: isBody tells us target will be an HTMLElement here\n updatedList.concat(listScrollParents(getParentNode(target)));\n}","export default function rectToClientRect(rect) {\n return Object.assign({}, rect, {\n left: rect.x,\n top: rect.y,\n right: rect.x + rect.width,\n bottom: rect.y + rect.height\n });\n}","import { viewport } from \"../enums.js\";\nimport getViewportRect from \"./getViewportRect.js\";\nimport getDocumentRect from \"./getDocumentRect.js\";\nimport listScrollParents from \"./listScrollParents.js\";\nimport getOffsetParent from \"./getOffsetParent.js\";\nimport getDocumentElement from \"./getDocumentElement.js\";\nimport getComputedStyle from \"./getComputedStyle.js\";\nimport { isElement, isHTMLElement } from \"./instanceOf.js\";\nimport getBoundingClientRect from \"./getBoundingClientRect.js\";\nimport getParentNode from \"./getParentNode.js\";\nimport contains from \"./contains.js\";\nimport getNodeName from \"./getNodeName.js\";\nimport rectToClientRect from \"../utils/rectToClientRect.js\";\nimport { max, min } from \"../utils/math.js\";\n\nfunction getInnerBoundingClientRect(element, strategy) {\n var rect = getBoundingClientRect(element, false, strategy === 'fixed');\n rect.top = rect.top + element.clientTop;\n rect.left = rect.left + element.clientLeft;\n rect.bottom = rect.top + element.clientHeight;\n rect.right = rect.left + element.clientWidth;\n rect.width = element.clientWidth;\n rect.height = element.clientHeight;\n rect.x = rect.left;\n rect.y = rect.top;\n return rect;\n}\n\nfunction getClientRectFromMixedType(element, clippingParent, strategy) {\n return clippingParent === viewport ? rectToClientRect(getViewportRect(element, strategy)) : isElement(clippingParent) ? getInnerBoundingClientRect(clippingParent, strategy) : rectToClientRect(getDocumentRect(getDocumentElement(element)));\n} // A \"clipping parent\" is an overflowable container with the characteristic of\n// clipping (or hiding) overflowing elements with a position different from\n// `initial`\n\n\nfunction getClippingParents(element) {\n var clippingParents = listScrollParents(getParentNode(element));\n var canEscapeClipping = ['absolute', 'fixed'].indexOf(getComputedStyle(element).position) >= 0;\n var clipperElement = canEscapeClipping && isHTMLElement(element) ? getOffsetParent(element) : element;\n\n if (!isElement(clipperElement)) {\n return [];\n } // $FlowFixMe[incompatible-return]: https://github.com/facebook/flow/issues/1414\n\n\n return clippingParents.filter(function (clippingParent) {\n return isElement(clippingParent) && contains(clippingParent, clipperElement) && getNodeName(clippingParent) !== 'body';\n });\n} // Gets the maximum area that the element is visible in due to any number of\n// clipping parents\n\n\nexport default function getClippingRect(element, boundary, rootBoundary, strategy) {\n var mainClippingParents = boundary === 'clippingParents' ? getClippingParents(element) : [].concat(boundary);\n var clippingParents = [].concat(mainClippingParents, [rootBoundary]);\n var firstClippingParent = clippingParents[0];\n var clippingRect = clippingParents.reduce(function (accRect, clippingParent) {\n var rect = getClientRectFromMixedType(element, clippingParent, strategy);\n accRect.top = max(rect.top, accRect.top);\n accRect.right = min(rect.right, accRect.right);\n accRect.bottom = min(rect.bottom, accRect.bottom);\n accRect.left = max(rect.left, accRect.left);\n return accRect;\n }, getClientRectFromMixedType(element, firstClippingParent, strategy));\n clippingRect.width = clippingRect.right - clippingRect.left;\n clippingRect.height = clippingRect.bottom - clippingRect.top;\n clippingRect.x = clippingRect.left;\n clippingRect.y = clippingRect.top;\n return clippingRect;\n}","import getWindow from \"./getWindow.js\";\nimport getDocumentElement from \"./getDocumentElement.js\";\nimport getWindowScrollBarX from \"./getWindowScrollBarX.js\";\nimport isLayoutViewport from \"./isLayoutViewport.js\";\nexport default function getViewportRect(element, strategy) {\n var win = getWindow(element);\n var html = getDocumentElement(element);\n var visualViewport = win.visualViewport;\n var width = html.clientWidth;\n var height = html.clientHeight;\n var x = 0;\n var y = 0;\n\n if (visualViewport) {\n width = visualViewport.width;\n height = visualViewport.height;\n var layoutViewport = isLayoutViewport();\n\n if (layoutViewport || !layoutViewport && strategy === 'fixed') {\n x = visualViewport.offsetLeft;\n y = visualViewport.offsetTop;\n }\n }\n\n return {\n width: width,\n height: height,\n x: x + getWindowScrollBarX(element),\n y: y\n };\n}","import getDocumentElement from \"./getDocumentElement.js\";\nimport getComputedStyle from \"./getComputedStyle.js\";\nimport getWindowScrollBarX from \"./getWindowScrollBarX.js\";\nimport getWindowScroll from \"./getWindowScroll.js\";\nimport { max } from \"../utils/math.js\"; // Gets the entire size of the scrollable document area, even extending outside\n// of the `<html>` and `<body>` rect bounds if horizontally scrollable\n\nexport default function getDocumentRect(element) {\n var _element$ownerDocumen;\n\n var html = getDocumentElement(element);\n var winScroll = getWindowScroll(element);\n var body = (_element$ownerDocumen = element.ownerDocument) == null ? void 0 : _element$ownerDocumen.body;\n var width = max(html.scrollWidth, html.clientWidth, body ? body.scrollWidth : 0, body ? body.clientWidth : 0);\n var height = max(html.scrollHeight, html.clientHeight, body ? body.scrollHeight : 0, body ? body.clientHeight : 0);\n var x = -winScroll.scrollLeft + getWindowScrollBarX(element);\n var y = -winScroll.scrollTop;\n\n if (getComputedStyle(body || html).direction === 'rtl') {\n x += max(html.clientWidth, body ? body.clientWidth : 0) - width;\n }\n\n return {\n width: width,\n height: height,\n x: x,\n y: y\n };\n}","import getBasePlacement from \"./getBasePlacement.js\";\nimport getVariation from \"./getVariation.js\";\nimport getMainAxisFromPlacement from \"./getMainAxisFromPlacement.js\";\nimport { top, right, bottom, left, start, end } from \"../enums.js\";\nexport default function computeOffsets(_ref) {\n var reference = _ref.reference,\n element = _ref.element,\n placement = _ref.placement;\n var basePlacement = placement ? getBasePlacement(placement) : null;\n var variation = placement ? getVariation(placement) : null;\n var commonX = reference.x + reference.width / 2 - element.width / 2;\n var commonY = reference.y + reference.height / 2 - element.height / 2;\n var offsets;\n\n switch (basePlacement) {\n case top:\n offsets = {\n x: commonX,\n y: reference.y - element.height\n };\n break;\n\n case bottom:\n offsets = {\n x: commonX,\n y: reference.y + reference.height\n };\n break;\n\n case right:\n offsets = {\n x: reference.x + reference.width,\n y: commonY\n };\n break;\n\n case left:\n offsets = {\n x: reference.x - element.width,\n y: commonY\n };\n break;\n\n default:\n offsets = {\n x: reference.x,\n y: reference.y\n };\n }\n\n var mainAxis = basePlacement ? getMainAxisFromPlacement(basePlacement) : null;\n\n if (mainAxis != null) {\n var len = mainAxis === 'y' ? 'height' : 'width';\n\n switch (variation) {\n case start:\n offsets[mainAxis] = offsets[mainAxis] - (reference[len] / 2 - element[len] / 2);\n break;\n\n case end:\n offsets[mainAxis] = offsets[mainAxis] + (reference[len] / 2 - element[len] / 2);\n break;\n\n default:\n }\n }\n\n return offsets;\n}","import getClippingRect from \"../dom-utils/getClippingRect.js\";\nimport getDocumentElement from \"../dom-utils/getDocumentElement.js\";\nimport getBoundingClientRect from \"../dom-utils/getBoundingClientRect.js\";\nimport computeOffsets from \"./computeOffsets.js\";\nimport rectToClientRect from \"./rectToClientRect.js\";\nimport { clippingParents, reference, popper, bottom, top, right, basePlacements, viewport } from \"../enums.js\";\nimport { isElement } from \"../dom-utils/instanceOf.js\";\nimport mergePaddingObject from \"./mergePaddingObject.js\";\nimport expandToHashMap from \"./expandToHashMap.js\"; // eslint-disable-next-line import/no-unused-modules\n\nexport default function detectOverflow(state, options) {\n if (options === void 0) {\n options = {};\n }\n\n var _options = options,\n _options$placement = _options.placement,\n placement = _options$placement === void 0 ? state.placement : _options$placement,\n _options$strategy = _options.strategy,\n strategy = _options$strategy === void 0 ? state.strategy : _options$strategy,\n _options$boundary = _options.boundary,\n boundary = _options$boundary === void 0 ? clippingParents : _options$boundary,\n _options$rootBoundary = _options.rootBoundary,\n rootBoundary = _options$rootBoundary === void 0 ? viewport : _options$rootBoundary,\n _options$elementConte = _options.elementContext,\n elementContext = _options$elementConte === void 0 ? popper : _options$elementConte,\n _options$altBoundary = _options.altBoundary,\n altBoundary = _options$altBoundary === void 0 ? false : _options$altBoundary,\n _options$padding = _options.padding,\n padding = _options$padding === void 0 ? 0 : _options$padding;\n var paddingObject = mergePaddingObject(typeof padding !== 'number' ? padding : expandToHashMap(padding, basePlacements));\n var altContext = elementContext === popper ? reference : popper;\n var popperRect = state.rects.popper;\n var element = state.elements[altBoundary ? altContext : elementContext];\n var clippingClientRect = getClippingRect(isElement(element) ? element : element.contextElement || getDocumentElement(state.elements.popper), boundary, rootBoundary, strategy);\n var referenceClientRect = getBoundingClientRect(state.elements.reference);\n var popperOffsets = computeOffsets({\n reference: referenceClientRect,\n element: popperRect,\n strategy: 'absolute',\n placement: placement\n });\n var popperClientRect = rectToClientRect(Object.assign({}, popperRect, popperOffsets));\n var elementClientRect = elementContext === popper ? popperClientRect : referenceClientRect; // positive = overflowing the clipping rect\n // 0 or negative = within the clipping rect\n\n var overflowOffsets = {\n top: clippingClientRect.top - elementClientRect.top + paddingObject.top,\n bottom: elementClientRect.bottom - clippingClientRect.bottom + paddingObject.bottom,\n left: clippingClientRect.left - elementClientRect.left + paddingObject.left,\n right: elementClientRect.right - clippingClientRect.right + paddingObject.right\n };\n var offsetData = state.modifiersData.offset; // Offsets can be applied only to the popper element\n\n if (elementContext === popper && offsetData) {\n var offset = offsetData[placement];\n Object.keys(overflowOffsets).forEach(function (key) {\n var multiply = [right, bottom].indexOf(key) >= 0 ? 1 : -1;\n var axis = [top, bottom].indexOf(key) >= 0 ? 'y' : 'x';\n overflowOffsets[key] += offset[axis] * multiply;\n });\n }\n\n return overflowOffsets;\n}","import getVariation from \"./getVariation.js\";\nimport { variationPlacements, basePlacements, placements as allPlacements } from \"../enums.js\";\nimport detectOverflow from \"./detectOverflow.js\";\nimport getBasePlacement from \"./getBasePlacement.js\";\nexport default function computeAutoPlacement(state, options) {\n if (options === void 0) {\n options = {};\n }\n\n var _options = options,\n placement = _options.placement,\n boundary = _options.boundary,\n rootBoundary = _options.rootBoundary,\n padding = _options.padding,\n flipVariations = _options.flipVariations,\n _options$allowedAutoP = _options.allowedAutoPlacements,\n allowedAutoPlacements = _options$allowedAutoP === void 0 ? allPlacements : _options$allowedAutoP;\n var variation = getVariation(placement);\n var placements = variation ? flipVariations ? variationPlacements : variationPlacements.filter(function (placement) {\n return getVariation(placement) === variation;\n }) : basePlacements;\n var allowedPlacements = placements.filter(function (placement) {\n return allowedAutoPlacements.indexOf(placement) >= 0;\n });\n\n if (allowedPlacements.length === 0) {\n allowedPlacements = placements;\n\n if (process.env.NODE_ENV !== \"production\") {\n console.error(['Popper: The `allowedAutoPlacements` option did not allow any', 'placements. Ensure the `placement` option matches the variation', 'of the allowed placements.', 'For example, \"auto\" cannot be used to allow \"bottom-start\".', 'Use \"auto-start\" instead.'].join(' '));\n }\n } // $FlowFixMe[incompatible-type]: Flow seems to have problems with two array unions...\n\n\n var overflows = allowedPlacements.reduce(function (acc, placement) {\n acc[placement] = detectOverflow(state, {\n placement: placement,\n boundary: boundary,\n rootBoundary: rootBoundary,\n padding: padding\n })[getBasePlacement(placement)];\n return acc;\n }, {});\n return Object.keys(overflows).sort(function (a, b) {\n return overflows[a] - overflows[b];\n });\n}","import getOppositePlacement from \"../utils/getOppositePlacement.js\";\nimport getBasePlacement from \"../utils/getBasePlacement.js\";\nimport getOppositeVariationPlacement from \"../utils/getOppositeVariationPlacement.js\";\nimport detectOverflow from \"../utils/detectOverflow.js\";\nimport computeAutoPlacement from \"../utils/computeAutoPlacement.js\";\nimport { bottom, top, start, right, left, auto } from \"../enums.js\";\nimport getVariation from \"../utils/getVariation.js\"; // eslint-disable-next-line import/no-unused-modules\n\nfunction getExpandedFallbackPlacements(placement) {\n if (getBasePlacement(placement) === auto) {\n return [];\n }\n\n var oppositePlacement = getOppositePlacement(placement);\n return [getOppositeVariationPlacement(placement), oppositePlacement, getOppositeVariationPlacement(oppositePlacement)];\n}\n\nfunction flip(_ref) {\n var state = _ref.state,\n options = _ref.options,\n name = _ref.name;\n\n if (state.modifiersData[name]._skip) {\n return;\n }\n\n var _options$mainAxis = options.mainAxis,\n checkMainAxis = _options$mainAxis === void 0 ? true : _options$mainAxis,\n _options$altAxis = options.altAxis,\n checkAltAxis = _options$altAxis === void 0 ? true : _options$altAxis,\n specifiedFallbackPlacements = options.fallbackPlacements,\n padding = options.padding,\n boundary = options.boundary,\n rootBoundary = options.rootBoundary,\n altBoundary = options.altBoundary,\n _options$flipVariatio = options.flipVariations,\n flipVariations = _options$flipVariatio === void 0 ? true : _options$flipVariatio,\n allowedAutoPlacements = options.allowedAutoPlacements;\n var preferredPlacement = state.options.placement;\n var basePlacement = getBasePlacement(preferredPlacement);\n var isBasePlacement = basePlacement === preferredPlacement;\n var fallbackPlacements = specifiedFallbackPlacements || (isBasePlacement || !flipVariations ? [getOppositePlacement(preferredPlacement)] : getExpandedFallbackPlacements(preferredPlacement));\n var placements = [preferredPlacement].concat(fallbackPlacements).reduce(function (acc, placement) {\n return acc.concat(getBasePlacement(placement) === auto ? computeAutoPlacement(state, {\n placement: placement,\n boundary: boundary,\n rootBoundary: rootBoundary,\n padding: padding,\n flipVariations: flipVariations,\n allowedAutoPlacements: allowedAutoPlacements\n }) : placement);\n }, []);\n var referenceRect = state.rects.reference;\n var popperRect = state.rects.popper;\n var checksMap = new Map();\n var makeFallbackChecks = true;\n var firstFittingPlacement = placements[0];\n\n for (var i = 0; i < placements.length; i++) {\n var placement = placements[i];\n\n var _basePlacement = getBasePlacement(placement);\n\n var isStartVariation = getVariation(placement) === start;\n var isVertical = [top, bottom].indexOf(_basePlacement) >= 0;\n var len = isVertical ? 'width' : 'height';\n var overflow = detectOverflow(state, {\n placement: placement,\n boundary: boundary,\n rootBoundary: rootBoundary,\n altBoundary: altBoundary,\n padding: padding\n });\n var mainVariationSide = isVertical ? isStartVariation ? right : left : isStartVariation ? bottom : top;\n\n if (referenceRect[len] > popperRect[len]) {\n mainVariationSide = getOppositePlacement(mainVariationSide);\n }\n\n var altVariationSide = getOppositePlacement(mainVariationSide);\n var checks = [];\n\n if (checkMainAxis) {\n checks.push(overflow[_basePlacement] <= 0);\n }\n\n if (checkAltAxis) {\n checks.push(overflow[mainVariationSide] <= 0, overflow[altVariationSide] <= 0);\n }\n\n if (checks.every(function (check) {\n return check;\n })) {\n firstFittingPlacement = placement;\n makeFallbackChecks = false;\n break;\n }\n\n checksMap.set(placement, checks);\n }\n\n if (makeFallbackChecks) {\n // `2` may be desired in some cases – research later\n var numberOfChecks = flipVariations ? 3 : 1;\n\n var _loop = function _loop(_i) {\n var fittingPlacement = placements.find(function (placement) {\n var checks = checksMap.get(placement);\n\n if (checks) {\n return checks.slice(0, _i).every(function (check) {\n return check;\n });\n }\n });\n\n if (fittingPlacement) {\n firstFittingPlacement = fittingPlacement;\n return \"break\";\n }\n };\n\n for (var _i = numberOfChecks; _i > 0; _i--) {\n var _ret = _loop(_i);\n\n if (_ret === \"break\") break;\n }\n }\n\n if (state.placement !== firstFittingPlacement) {\n state.modifiersData[name]._skip = true;\n state.placement = firstFittingPlacement;\n state.reset = true;\n }\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n name: 'flip',\n enabled: true,\n phase: 'main',\n fn: flip,\n requiresIfExists: ['offset'],\n data: {\n _skip: false\n }\n};","import { top, bottom, left, right } from \"../enums.js\";\nimport detectOverflow from \"../utils/detectOverflow.js\";\n\nfunction getSideOffsets(overflow, rect, preventedOffsets) {\n if (preventedOffsets === void 0) {\n preventedOffsets = {\n x: 0,\n y: 0\n };\n }\n\n return {\n top: overflow.top - rect.height - preventedOffsets.y,\n right: overflow.right - rect.width + preventedOffsets.x,\n bottom: overflow.bottom - rect.height + preventedOffsets.y,\n left: overflow.left - rect.width - preventedOffsets.x\n };\n}\n\nfunction isAnySideFullyClipped(overflow) {\n return [top, right, bottom, left].some(function (side) {\n return overflow[side] >= 0;\n });\n}\n\nfunction hide(_ref) {\n var state = _ref.state,\n name = _ref.name;\n var referenceRect = state.rects.reference;\n var popperRect = state.rects.popper;\n var preventedOffsets = state.modifiersData.preventOverflow;\n var referenceOverflow = detectOverflow(state, {\n elementContext: 'reference'\n });\n var popperAltOverflow = detectOverflow(state, {\n altBoundary: true\n });\n var referenceClippingOffsets = getSideOffsets(referenceOverflow, referenceRect);\n var popperEscapeOffsets = getSideOffsets(popperAltOverflow, popperRect, preventedOffsets);\n var isReferenceHidden = isAnySideFullyClipped(referenceClippingOffsets);\n var hasPopperEscaped = isAnySideFullyClipped(popperEscapeOffsets);\n state.modifiersData[name] = {\n referenceClippingOffsets: referenceClippingOffsets,\n popperEscapeOffsets: popperEscapeOffsets,\n isReferenceHidden: isReferenceHidden,\n hasPopperEscaped: hasPopperEscaped\n };\n state.attributes.popper = Object.assign({}, state.attributes.popper, {\n 'data-popper-reference-hidden': isReferenceHidden,\n 'data-popper-escaped': hasPopperEscaped\n });\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n name: 'hide',\n enabled: true,\n phase: 'main',\n requiresIfExists: ['preventOverflow'],\n fn: hide\n};","import getBasePlacement from \"../utils/getBasePlacement.js\";\nimport { top, left, right, placements } from \"../enums.js\"; // eslint-disable-next-line import/no-unused-modules\n\nexport function distanceAndSkiddingToXY(placement, rects, offset) {\n var basePlacement = getBasePlacement(placement);\n var invertDistance = [left, top].indexOf(basePlacement) >= 0 ? -1 : 1;\n\n var _ref = typeof offset === 'function' ? offset(Object.assign({}, rects, {\n placement: placement\n })) : offset,\n skidding = _ref[0],\n distance = _ref[1];\n\n skidding = skidding || 0;\n distance = (distance || 0) * invertDistance;\n return [left, right].indexOf(basePlacement) >= 0 ? {\n x: distance,\n y: skidding\n } : {\n x: skidding,\n y: distance\n };\n}\n\nfunction offset(_ref2) {\n var state = _ref2.state,\n options = _ref2.options,\n name = _ref2.name;\n var _options$offset = options.offset,\n offset = _options$offset === void 0 ? [0, 0] : _options$offset;\n var data = placements.reduce(function (acc, placement) {\n acc[placement] = distanceAndSkiddingToXY(placement, state.rects, offset);\n return acc;\n }, {});\n var _data$state$placement = data[state.placement],\n x = _data$state$placement.x,\n y = _data$state$placement.y;\n\n if (state.modifiersData.popperOffsets != null) {\n state.modifiersData.popperOffsets.x += x;\n state.modifiersData.popperOffsets.y += y;\n }\n\n state.modifiersData[name] = data;\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n name: 'offset',\n enabled: true,\n phase: 'main',\n requires: ['popperOffsets'],\n fn: offset\n};","import computeOffsets from \"../utils/computeOffsets.js\";\n\nfunction popperOffsets(_ref) {\n var state = _ref.state,\n name = _ref.name;\n // Offsets are the actual position the popper needs to have to be\n // properly positioned near its reference element\n // This is the most basic placement, and will be adjusted by\n // the modifiers in the next step\n state.modifiersData[name] = computeOffsets({\n reference: state.rects.reference,\n element: state.rects.popper,\n strategy: 'absolute',\n placement: state.placement\n });\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n name: 'popperOffsets',\n enabled: true,\n phase: 'read',\n fn: popperOffsets,\n data: {}\n};","import { top, left, right, bottom, start } from \"../enums.js\";\nimport getBasePlacement from \"../utils/getBasePlacement.js\";\nimport getMainAxisFromPlacement from \"../utils/getMainAxisFromPlacement.js\";\nimport getAltAxis from \"../utils/getAltAxis.js\";\nimport { within, withinMaxClamp } from \"../utils/within.js\";\nimport getLayoutRect from \"../dom-utils/getLayoutRect.js\";\nimport getOffsetParent from \"../dom-utils/getOffsetParent.js\";\nimport detectOverflow from \"../utils/detectOverflow.js\";\nimport getVariation from \"../utils/getVariation.js\";\nimport getFreshSideObject from \"../utils/getFreshSideObject.js\";\nimport { min as mathMin, max as mathMax } from \"../utils/math.js\";\n\nfunction preventOverflow(_ref) {\n var state = _ref.state,\n options = _ref.options,\n name = _ref.name;\n var _options$mainAxis = options.mainAxis,\n checkMainAxis = _options$mainAxis === void 0 ? true : _options$mainAxis,\n _options$altAxis = options.altAxis,\n checkAltAxis = _options$altAxis === void 0 ? false : _options$altAxis,\n boundary = options.boundary,\n rootBoundary = options.rootBoundary,\n altBoundary = options.altBoundary,\n padding = options.padding,\n _options$tether = options.tether,\n tether = _options$tether === void 0 ? true : _options$tether,\n _options$tetherOffset = options.tetherOffset,\n tetherOffset = _options$tetherOffset === void 0 ? 0 : _options$tetherOffset;\n var overflow = detectOverflow(state, {\n boundary: boundary,\n rootBoundary: rootBoundary,\n padding: padding,\n altBoundary: altBoundary\n });\n var basePlacement = getBasePlacement(state.placement);\n var variation = getVariation(state.placement);\n var isBasePlacement = !variation;\n var mainAxis = getMainAxisFromPlacement(basePlacement);\n var altAxis = getAltAxis(mainAxis);\n var popperOffsets = state.modifiersData.popperOffsets;\n var referenceRect = state.rects.reference;\n var popperRect = state.rects.popper;\n var tetherOffsetValue = typeof tetherOffset === 'function' ? tetherOffset(Object.assign({}, state.rects, {\n placement: state.placement\n })) : tetherOffset;\n var normalizedTetherOffsetValue = typeof tetherOffsetValue === 'number' ? {\n mainAxis: tetherOffsetValue,\n altAxis: tetherOffsetValue\n } : Object.assign({\n mainAxis: 0,\n altAxis: 0\n }, tetherOffsetValue);\n var offsetModifierState = state.modifiersData.offset ? state.modifiersData.offset[state.placement] : null;\n var data = {\n x: 0,\n y: 0\n };\n\n if (!popperOffsets) {\n return;\n }\n\n if (checkMainAxis) {\n var _offsetModifierState$;\n\n var mainSide = mainAxis === 'y' ? top : left;\n var altSide = mainAxis === 'y' ? bottom : right;\n var len = mainAxis === 'y' ? 'height' : 'width';\n var offset = popperOffsets[mainAxis];\n var min = offset + overflow[mainSide];\n var max = offset - overflow[altSide];\n var additive = tether ? -popperRect[len] / 2 : 0;\n var minLen = variation === start ? referenceRect[len] : popperRect[len];\n var maxLen = variation === start ? -popperRect[len] : -referenceRect[len]; // We need to include the arrow in the calculation so the arrow doesn't go\n // outside the reference bounds\n\n var arrowElement = state.elements.arrow;\n var arrowRect = tether && arrowElement ? getLayoutRect(arrowElement) : {\n width: 0,\n height: 0\n };\n var arrowPaddingObject = state.modifiersData['arrow#persistent'] ? state.modifiersData['arrow#persistent'].padding : getFreshSideObject();\n var arrowPaddingMin = arrowPaddingObject[mainSide];\n var arrowPaddingMax = arrowPaddingObject[altSide]; // If the reference length is smaller than the arrow length, we don't want\n // to include its full size in the calculation. If the reference is small\n // and near the edge of a boundary, the popper can overflow even if the\n // reference is not overflowing as well (e.g. virtual elements with no\n // width or height)\n\n var arrowLen = within(0, referenceRect[len], arrowRect[len]);\n var minOffset = isBasePlacement ? referenceRect[len] / 2 - additive - arrowLen - arrowPaddingMin - normalizedTetherOffsetValue.mainAxis : minLen - arrowLen - arrowPaddingMin - normalizedTetherOffsetValue.mainAxis;\n var maxOffset = isBasePlacement ? -referenceRect[len] / 2 + additive + arrowLen + arrowPaddingMax + normalizedTetherOffsetValue.mainAxis : maxLen + arrowLen + arrowPaddingMax + normalizedTetherOffsetValue.mainAxis;\n var arrowOffsetParent = state.elements.arrow && getOffsetParent(state.elements.arrow);\n var clientOffset = arrowOffsetParent ? mainAxis === 'y' ? arrowOffsetParent.clientTop || 0 : arrowOffsetParent.clientLeft || 0 : 0;\n var offsetModifierValue = (_offsetModifierState$ = offsetModifierState == null ? void 0 : offsetModifierState[mainAxis]) != null ? _offsetModifierState$ : 0;\n var tetherMin = offset + minOffset - offsetModifierValue - clientOffset;\n var tetherMax = offset + maxOffset - offsetModifierValue;\n var preventedOffset = within(tether ? mathMin(min, tetherMin) : min, offset, tether ? mathMax(max, tetherMax) : max);\n popperOffsets[mainAxis] = preventedOffset;\n data[mainAxis] = preventedOffset - offset;\n }\n\n if (checkAltAxis) {\n var _offsetModifierState$2;\n\n var _mainSide = mainAxis === 'x' ? top : left;\n\n var _altSide = mainAxis === 'x' ? bottom : right;\n\n var _offset = popperOffsets[altAxis];\n\n var _len = altAxis === 'y' ? 'height' : 'width';\n\n var _min = _offset + overflow[_mainSide];\n\n var _max = _offset - overflow[_altSide];\n\n var isOriginSide = [top, left].indexOf(basePlacement) !== -1;\n\n var _offsetModifierValue = (_offsetModifierState$2 = offsetModifierState == null ? void 0 : offsetModifierState[altAxis]) != null ? _offsetModifierState$2 : 0;\n\n var _tetherMin = isOriginSide ? _min : _offset - referenceRect[_len] - popperRect[_len] - _offsetModifierValue + normalizedTetherOffsetValue.altAxis;\n\n var _tetherMax = isOriginSide ? _offset + referenceRect[_len] + popperRect[_len] - _offsetModifierValue - normalizedTetherOffsetValue.altAxis : _max;\n\n var _preventedOffset = tether && isOriginSide ? withinMaxClamp(_tetherMin, _offset, _tetherMax) : within(tether ? _tetherMin : _min, _offset, tether ? _tetherMax : _max);\n\n popperOffsets[altAxis] = _preventedOffset;\n data[altAxis] = _preventedOffset - _offset;\n }\n\n state.modifiersData[name] = data;\n} // eslint-disable-next-line import/no-unused-modules\n\n\nexport default {\n name: 'preventOverflow',\n enabled: true,\n phase: 'main',\n fn: preventOverflow,\n requiresIfExists: ['offset']\n};","export default function getAltAxis(axis) {\n return axis === 'x' ? 'y' : 'x';\n}","import getBoundingClientRect from \"./getBoundingClientRect.js\";\nimport getNodeScroll from \"./getNodeScroll.js\";\nimport getNodeName from \"./getNodeName.js\";\nimport { isHTMLElement } from \"./instanceOf.js\";\nimport getWindowScrollBarX from \"./getWindowScrollBarX.js\";\nimport getDocumentElement from \"./getDocumentElement.js\";\nimport isScrollParent from \"./isScrollParent.js\";\nimport { round } from \"../utils/math.js\";\n\nfunction isElementScaled(element) {\n var rect = element.getBoundingClientRect();\n var scaleX = round(rect.width) / element.offsetWidth || 1;\n var scaleY = round(rect.height) / element.offsetHeight || 1;\n return scaleX !== 1 || scaleY !== 1;\n} // Returns the composite rect of an element relative to its offsetParent.\n// Composite means it takes into account transforms as well as layout.\n\n\nexport default function getCompositeRect(elementOrVirtualElement, offsetParent, isFixed) {\n if (isFixed === void 0) {\n isFixed = false;\n }\n\n var isOffsetParentAnElement = isHTMLElement(offsetParent);\n var offsetParentIsScaled = isHTMLElement(offsetParent) && isElementScaled(offsetParent);\n var documentElement = getDocumentElement(offsetParent);\n var rect = getBoundingClientRect(elementOrVirtualElement, offsetParentIsScaled, isFixed);\n var scroll = {\n scrollLeft: 0,\n scrollTop: 0\n };\n var offsets = {\n x: 0,\n y: 0\n };\n\n if (isOffsetParentAnElement || !isOffsetParentAnElement && !isFixed) {\n if (getNodeName(offsetParent) !== 'body' || // https://github.com/popperjs/popper-core/issues/1078\n isScrollParent(documentElement)) {\n scroll = getNodeScroll(offsetParent);\n }\n\n if (isHTMLElement(offsetParent)) {\n offsets = getBoundingClientRect(offsetParent, true);\n offsets.x += offsetParent.clientLeft;\n offsets.y += offsetParent.clientTop;\n } else if (documentElement) {\n offsets.x = getWindowScrollBarX(documentElement);\n }\n }\n\n return {\n x: rect.left + scroll.scrollLeft - offsets.x,\n y: rect.top + scroll.scrollTop - offsets.y,\n width: rect.width,\n height: rect.height\n };\n}","import getWindowScroll from \"./getWindowScroll.js\";\nimport getWindow from \"./getWindow.js\";\nimport { isHTMLElement } from \"./instanceOf.js\";\nimport getHTMLElementScroll from \"./getHTMLElementScroll.js\";\nexport default function getNodeScroll(node) {\n if (node === getWindow(node) || !isHTMLElement(node)) {\n return getWindowScroll(node);\n } else {\n return getHTMLElementScroll(node);\n }\n}","export default function getHTMLElementScroll(element) {\n return {\n scrollLeft: element.scrollLeft,\n scrollTop: element.scrollTop\n };\n}","import { modifierPhases } from \"../enums.js\"; // source: https://stackoverflow.com/questions/49875255\n\nfunction order(modifiers) {\n var map = new Map();\n var visited = new Set();\n var result = [];\n modifiers.forEach(function (modifier) {\n map.set(modifier.name, modifier);\n }); // On visiting object, check for its dependencies and visit them recursively\n\n function sort(modifier) {\n visited.add(modifier.name);\n var requires = [].concat(modifier.requires || [], modifier.requiresIfExists || []);\n requires.forEach(function (dep) {\n if (!visited.has(dep)) {\n var depModifier = map.get(dep);\n\n if (depModifier) {\n sort(depModifier);\n }\n }\n });\n result.push(modifier);\n }\n\n modifiers.forEach(function (modifier) {\n if (!visited.has(modifier.name)) {\n // check for visited object\n sort(modifier);\n }\n });\n return result;\n}\n\nexport default function orderModifiers(modifiers) {\n // order based on dependencies\n var orderedModifiers = order(modifiers); // order based on phase\n\n return modifierPhases.reduce(function (acc, phase) {\n return acc.concat(orderedModifiers.filter(function (modifier) {\n return modifier.phase === phase;\n }));\n }, []);\n}","import getCompositeRect from \"./dom-utils/getCompositeRect.js\";\nimport getLayoutRect from \"./dom-utils/getLayoutRect.js\";\nimport listScrollParents from \"./dom-utils/listScrollParents.js\";\nimport getOffsetParent from \"./dom-utils/getOffsetParent.js\";\nimport getComputedStyle from \"./dom-utils/getComputedStyle.js\";\nimport orderModifiers from \"./utils/orderModifiers.js\";\nimport debounce from \"./utils/debounce.js\";\nimport validateModifiers from \"./utils/validateModifiers.js\";\nimport uniqueBy from \"./utils/uniqueBy.js\";\nimport getBasePlacement from \"./utils/getBasePlacement.js\";\nimport mergeByName from \"./utils/mergeByName.js\";\nimport detectOverflow from \"./utils/detectOverflow.js\";\nimport { isElement } from \"./dom-utils/instanceOf.js\";\nimport { auto } from \"./enums.js\";\nvar INVALID_ELEMENT_ERROR = 'Popper: Invalid reference or popper argument provided. They must be either a DOM element or virtual element.';\nvar INFINITE_LOOP_ERROR = 'Popper: An infinite loop in the modifiers cycle has been detected! The cycle has been interrupted to prevent a browser crash.';\nvar DEFAULT_OPTIONS = {\n placement: 'bottom',\n modifiers: [],\n strategy: 'absolute'\n};\n\nfunction areValidElements() {\n for (var _len = arguments.length, args = new Array(_len), _key = 0; _key < _len; _key++) {\n args[_key] = arguments[_key];\n }\n\n return !args.some(function (element) {\n return !(element && typeof element.getBoundingClientRect === 'function');\n });\n}\n\nexport function popperGenerator(generatorOptions) {\n if (generatorOptions === void 0) {\n generatorOptions = {};\n }\n\n var _generatorOptions = generatorOptions,\n _generatorOptions$def = _generatorOptions.defaultModifiers,\n defaultModifiers = _generatorOptions$def === void 0 ? [] : _generatorOptions$def,\n _generatorOptions$def2 = _generatorOptions.defaultOptions,\n defaultOptions = _generatorOptions$def2 === void 0 ? DEFAULT_OPTIONS : _generatorOptions$def2;\n return function createPopper(reference, popper, options) {\n if (options === void 0) {\n options = defaultOptions;\n }\n\n var state = {\n placement: 'bottom',\n orderedModifiers: [],\n options: Object.assign({}, DEFAULT_OPTIONS, defaultOptions),\n modifiersData: {},\n elements: {\n reference: reference,\n popper: popper\n },\n attributes: {},\n styles: {}\n };\n var effectCleanupFns = [];\n var isDestroyed = false;\n var instance = {\n state: state,\n setOptions: function setOptions(setOptionsAction) {\n var options = typeof setOptionsAction === 'function' ? setOptionsAction(state.options) : setOptionsAction;\n cleanupModifierEffects();\n state.options = Object.assign({}, defaultOptions, state.options, options);\n state.scrollParents = {\n reference: isElement(reference) ? listScrollParents(reference) : reference.contextElement ? listScrollParents(reference.contextElement) : [],\n popper: listScrollParents(popper)\n }; // Orders the modifiers based on their dependencies and `phase`\n // properties\n\n var orderedModifiers = orderModifiers(mergeByName([].concat(defaultModifiers, state.options.modifiers))); // Strip out disabled modifiers\n\n state.orderedModifiers = orderedModifiers.filter(function (m) {\n return m.enabled;\n }); // Validate the provided modifiers so that the consumer will get warned\n // if one of the modifiers is invalid for any reason\n\n if (process.env.NODE_ENV !== \"production\") {\n var modifiers = uniqueBy([].concat(orderedModifiers, state.options.modifiers), function (_ref) {\n var name = _ref.name;\n return name;\n });\n validateModifiers(modifiers);\n\n if (getBasePlacement(state.options.placement) === auto) {\n var flipModifier = state.orderedModifiers.find(function (_ref2) {\n var name = _ref2.name;\n return name === 'flip';\n });\n\n if (!flipModifier) {\n console.error(['Popper: \"auto\" placements require the \"flip\" modifier be', 'present and enabled to work.'].join(' '));\n }\n }\n\n var _getComputedStyle = getComputedStyle(popper),\n marginTop = _getComputedStyle.marginTop,\n marginRight = _getComputedStyle.marginRight,\n marginBottom = _getComputedStyle.marginBottom,\n marginLeft = _getComputedStyle.marginLeft; // We no longer take into account `margins` on the popper, and it can\n // cause bugs with positioning, so we'll warn the consumer\n\n\n if ([marginTop, marginRight, marginBottom, marginLeft].some(function (margin) {\n return parseFloat(margin);\n })) {\n console.warn(['Popper: CSS \"margin\" styles cannot be used to apply padding', 'between the popper and its reference element or boundary.', 'To replicate margin, use the `offset` modifier, as well as', 'the `padding` option in the `preventOverflow` and `flip`', 'modifiers.'].join(' '));\n }\n }\n\n runModifierEffects();\n return instance.update();\n },\n // Sync update – it will always be executed, even if not necessary. This\n // is useful for low frequency updates where sync behavior simplifies the\n // logic.\n // For high frequency updates (e.g. `resize` and `scroll` events), always\n // prefer the async Popper#update method\n forceUpdate: function forceUpdate() {\n if (isDestroyed) {\n return;\n }\n\n var _state$elements = state.elements,\n reference = _state$elements.reference,\n popper = _state$elements.popper; // Don't proceed if `reference` or `popper` are not valid elements\n // anymore\n\n if (!areValidElements(reference, popper)) {\n if (process.env.NODE_ENV !== \"production\") {\n console.error(INVALID_ELEMENT_ERROR);\n }\n\n return;\n } // Store the reference and popper rects to be read by modifiers\n\n\n state.rects = {\n reference: getCompositeRect(reference, getOffsetParent(popper), state.options.strategy === 'fixed'),\n popper: getLayoutRect(popper)\n }; // Modifiers have the ability to reset the current update cycle. The\n // most common use case for this is the `flip` modifier changing the\n // placement, which then needs to re-run all the modifiers, because the\n // logic was previously ran for the previous placement and is therefore\n // stale/incorrect\n\n state.reset = false;\n state.placement = state.options.placement; // On each update cycle, the `modifiersData` property for each modifier\n // is filled with the initial data specified by the modifier. This means\n // it doesn't persist and is fresh on each update.\n // To ensure persistent data, use `${name}#persistent`\n\n state.orderedModifiers.forEach(function (modifier) {\n return state.modifiersData[modifier.name] = Object.assign({}, modifier.data);\n });\n var __debug_loops__ = 0;\n\n for (var index = 0; index < state.orderedModifiers.length; index++) {\n if (process.env.NODE_ENV !== \"production\") {\n __debug_loops__ += 1;\n\n if (__debug_loops__ > 100) {\n console.error(INFINITE_LOOP_ERROR);\n break;\n }\n }\n\n if (state.reset === true) {\n state.reset = false;\n index = -1;\n continue;\n }\n\n var _state$orderedModifie = state.orderedModifiers[index],\n fn = _state$orderedModifie.fn,\n _state$orderedModifie2 = _state$orderedModifie.options,\n _options = _state$orderedModifie2 === void 0 ? {} : _state$orderedModifie2,\n name = _state$orderedModifie.name;\n\n if (typeof fn === 'function') {\n state = fn({\n state: state,\n options: _options,\n name: name,\n instance: instance\n }) || state;\n }\n }\n },\n // Async and optimistically optimized update – it will not be executed if\n // not necessary (debounced to run at most once-per-tick)\n update: debounce(function () {\n return new Promise(function (resolve) {\n instance.forceUpdate();\n resolve(state);\n });\n }),\n destroy: function destroy() {\n cleanupModifierEffects();\n isDestroyed = true;\n }\n };\n\n if (!areValidElements(reference, popper)) {\n if (process.env.NODE_ENV !== \"production\") {\n console.error(INVALID_ELEMENT_ERROR);\n }\n\n return instance;\n }\n\n instance.setOptions(options).then(function (state) {\n if (!isDestroyed && options.onFirstUpdate) {\n options.onFirstUpdate(state);\n }\n }); // Modifiers have the ability to execute arbitrary code before the first\n // update cycle runs. They will be executed in the same order as the update\n // cycle. This is useful when a modifier adds some persistent data that\n // other modifiers need to use, but the modifier is run after the dependent\n // one.\n\n function runModifierEffects() {\n state.orderedModifiers.forEach(function (_ref3) {\n var name = _ref3.name,\n _ref3$options = _ref3.options,\n options = _ref3$options === void 0 ? {} : _ref3$options,\n effect = _ref3.effect;\n\n if (typeof effect === 'function') {\n var cleanupFn = effect({\n state: state,\n name: name,\n instance: instance,\n options: options\n });\n\n var noopFn = function noopFn() {};\n\n effectCleanupFns.push(cleanupFn || noopFn);\n }\n });\n }\n\n function cleanupModifierEffects() {\n effectCleanupFns.forEach(function (fn) {\n return fn();\n });\n effectCleanupFns = [];\n }\n\n return instance;\n };\n}\nexport var createPopper = /*#__PURE__*/popperGenerator(); // eslint-disable-next-line import/no-unused-modules\n\nexport { detectOverflow };","export default function debounce(fn) {\n var pending;\n return function () {\n if (!pending) {\n pending = new Promise(function (resolve) {\n Promise.resolve().then(function () {\n pending = undefined;\n resolve(fn());\n });\n });\n }\n\n return pending;\n };\n}","export default function mergeByName(modifiers) {\n var merged = modifiers.reduce(function (merged, current) {\n var existing = merged[current.name];\n merged[current.name] = existing ? Object.assign({}, existing, current, {\n options: Object.assign({}, existing.options, current.options),\n data: Object.assign({}, existing.data, current.data)\n }) : current;\n return merged;\n }, {}); // IE11 does not support Object.values\n\n return Object.keys(merged).map(function (key) {\n return merged[key];\n });\n}","import { popperGenerator, detectOverflow } from \"./createPopper.js\";\nimport eventListeners from \"./modifiers/eventListeners.js\";\nimport popperOffsets from \"./modifiers/popperOffsets.js\";\nimport computeStyles from \"./modifiers/computeStyles.js\";\nimport applyStyles from \"./modifiers/applyStyles.js\";\nvar defaultModifiers = [eventListeners, popperOffsets, computeStyles, applyStyles];\nvar createPopper = /*#__PURE__*/popperGenerator({\n defaultModifiers: defaultModifiers\n}); // eslint-disable-next-line import/no-unused-modules\n\nexport { createPopper, popperGenerator, defaultModifiers, detectOverflow };","import { popperGenerator, detectOverflow } from \"./createPopper.js\";\nimport eventListeners from \"./modifiers/eventListeners.js\";\nimport popperOffsets from \"./modifiers/popperOffsets.js\";\nimport computeStyles from \"./modifiers/computeStyles.js\";\nimport applyStyles from \"./modifiers/applyStyles.js\";\nimport offset from \"./modifiers/offset.js\";\nimport flip from \"./modifiers/flip.js\";\nimport preventOverflow from \"./modifiers/preventOverflow.js\";\nimport arrow from \"./modifiers/arrow.js\";\nimport hide from \"./modifiers/hide.js\";\nvar defaultModifiers = [eventListeners, popperOffsets, computeStyles, applyStyles, offset, flip, preventOverflow, arrow, hide];\nvar createPopper = /*#__PURE__*/popperGenerator({\n defaultModifiers: defaultModifiers\n}); // eslint-disable-next-line import/no-unused-modules\n\nexport { createPopper, popperGenerator, defaultModifiers, detectOverflow }; // eslint-disable-next-line import/no-unused-modules\n\nexport { createPopper as createPopperLite } from \"./popper-lite.js\"; // eslint-disable-next-line import/no-unused-modules\n\nexport * from \"./modifiers/index.js\";","/**\n * --------------------------------------------------------------------------\n * Bootstrap (v5.2.2): dropdown.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport * as Popper from '@popperjs/core'\nimport {\n defineJQueryPlugin,\n getElement,\n getNextActiveElement,\n isDisabled,\n isElement,\n isRTL,\n isVisible,\n noop\n} from './util/index'\nimport EventHandler from './dom/event-handler'\nimport Manipulator from './dom/manipulator'\nimport SelectorEngine from './dom/selector-engine'\nimport BaseComponent from './base-component'\n\n/**\n * Constants\n */\n\nconst NAME = 'dropdown'\nconst DATA_KEY = 'bs.dropdown'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst DATA_API_KEY = '.data-api'\n\nconst ESCAPE_KEY = 'Escape'\nconst TAB_KEY = 'Tab'\nconst ARROW_UP_KEY = 'ArrowUp'\nconst ARROW_DOWN_KEY = 'ArrowDown'\nconst RIGHT_MOUSE_BUTTON = 2 // MouseEvent.button value for the secondary button, usually the right button\n\nconst EVENT_HIDE = `hide${EVENT_KEY}`\nconst EVENT_HIDDEN = `hidden${EVENT_KEY}`\nconst EVENT_SHOW = `show${EVENT_KEY}`\nconst EVENT_SHOWN = `shown${EVENT_KEY}`\nconst EVENT_CLICK_DATA_API = `click${EVENT_KEY}${DATA_API_KEY}`\nconst EVENT_KEYDOWN_DATA_API = `keydown${EVENT_KEY}${DATA_API_KEY}`\nconst EVENT_KEYUP_DATA_API = `keyup${EVENT_KEY}${DATA_API_KEY}`\n\nconst CLASS_NAME_SHOW = 'show'\nconst CLASS_NAME_DROPUP = 'dropup'\nconst CLASS_NAME_DROPEND = 'dropend'\nconst CLASS_NAME_DROPSTART = 'dropstart'\nconst CLASS_NAME_DROPUP_CENTER = 'dropup-center'\nconst CLASS_NAME_DROPDOWN_CENTER = 'dropdown-center'\n\nconst SELECTOR_DATA_TOGGLE = '[data-bs-toggle=\"dropdown\"]:not(.disabled):not(:disabled)'\nconst SELECTOR_DATA_TOGGLE_SHOWN = `${SELECTOR_DATA_TOGGLE}.${CLASS_NAME_SHOW}`\nconst SELECTOR_MENU = '.dropdown-menu'\nconst SELECTOR_NAVBAR = '.navbar'\nconst SELECTOR_NAVBAR_NAV = '.navbar-nav'\nconst SELECTOR_VISIBLE_ITEMS = '.dropdown-menu .dropdown-item:not(.disabled):not(:disabled)'\n\nconst PLACEMENT_TOP = isRTL() ? 'top-end' : 'top-start'\nconst PLACEMENT_TOPEND = isRTL() ? 'top-start' : 'top-end'\nconst PLACEMENT_BOTTOM = isRTL() ? 'bottom-end' : 'bottom-start'\nconst PLACEMENT_BOTTOMEND = isRTL() ? 'bottom-start' : 'bottom-end'\nconst PLACEMENT_RIGHT = isRTL() ? 'left-start' : 'right-start'\nconst PLACEMENT_LEFT = isRTL() ? 'right-start' : 'left-start'\nconst PLACEMENT_TOPCENTER = 'top'\nconst PLACEMENT_BOTTOMCENTER = 'bottom'\n\nconst Default = {\n autoClose: true,\n boundary: 'clippingParents',\n display: 'dynamic',\n offset: [0, 2],\n popperConfig: null,\n reference: 'toggle'\n}\n\nconst DefaultType = {\n autoClose: '(boolean|string)',\n boundary: '(string|element)',\n display: 'string',\n offset: '(array|string|function)',\n popperConfig: '(null|object|function)',\n reference: '(string|element|object)'\n}\n\n/**\n * Class definition\n */\n\nclass Dropdown extends BaseComponent {\n constructor(element, config) {\n super(element, config)\n\n this._popper = null\n this._parent = this._element.parentNode // dropdown wrapper\n // todo: v6 revert #37011 & change markup https://getbootstrap.com/docs/5.2/forms/input-group/\n this._menu = SelectorEngine.next(this._element, SELECTOR_MENU)[0] ||\n SelectorEngine.prev(this._element, SELECTOR_MENU)[0] ||\n SelectorEngine.findOne(SELECTOR_MENU, this._parent)\n this._inNavbar = this._detectNavbar()\n }\n\n // Getters\n static get Default() {\n return Default\n }\n\n static get DefaultType() {\n return DefaultType\n }\n\n static get NAME() {\n return NAME\n }\n\n // Public\n toggle() {\n return this._isShown() ? this.hide() : this.show()\n }\n\n show() {\n if (isDisabled(this._element) || this._isShown()) {\n return\n }\n\n const relatedTarget = {\n relatedTarget: this._element\n }\n\n const showEvent = EventHandler.trigger(this._element, EVENT_SHOW, relatedTarget)\n\n if (showEvent.defaultPrevented) {\n return\n }\n\n this._createPopper()\n\n // If this is a touch-enabled device we add extra\n // empty mouseover listeners to the body's immediate children;\n // only needed because of broken event delegation on iOS\n // https://www.quirksmode.org/blog/archives/2014/02/mouse_event_bub.html\n if ('ontouchstart' in document.documentElement && !this._parent.closest(SELECTOR_NAVBAR_NAV)) {\n for (const element of [].concat(...document.body.children)) {\n EventHandler.on(element, 'mouseover', noop)\n }\n }\n\n this._element.focus()\n this._element.setAttribute('aria-expanded', true)\n\n this._menu.classList.add(CLASS_NAME_SHOW)\n this._element.classList.add(CLASS_NAME_SHOW)\n EventHandler.trigger(this._element, EVENT_SHOWN, relatedTarget)\n }\n\n hide() {\n if (isDisabled(this._element) || !this._isShown()) {\n return\n }\n\n const relatedTarget = {\n relatedTarget: this._element\n }\n\n this._completeHide(relatedTarget)\n }\n\n dispose() {\n if (this._popper) {\n this._popper.destroy()\n }\n\n super.dispose()\n }\n\n update() {\n this._inNavbar = this._detectNavbar()\n if (this._popper) {\n this._popper.update()\n }\n }\n\n // Private\n _completeHide(relatedTarget) {\n const hideEvent = EventHandler.trigger(this._element, EVENT_HIDE, relatedTarget)\n if (hideEvent.defaultPrevented) {\n return\n }\n\n // If this is a touch-enabled device we remove the extra\n // empty mouseover listeners we added for iOS support\n if ('ontouchstart' in document.documentElement) {\n for (const element of [].concat(...document.body.children)) {\n EventHandler.off(element, 'mouseover', noop)\n }\n }\n\n if (this._popper) {\n this._popper.destroy()\n }\n\n this._menu.classList.remove(CLASS_NAME_SHOW)\n this._element.classList.remove(CLASS_NAME_SHOW)\n this._element.setAttribute('aria-expanded', 'false')\n Manipulator.removeDataAttribute(this._menu, 'popper')\n EventHandler.trigger(this._element, EVENT_HIDDEN, relatedTarget)\n }\n\n _getConfig(config) {\n config = super._getConfig(config)\n\n if (typeof config.reference === 'object' && !isElement(config.reference) &&\n typeof config.reference.getBoundingClientRect !== 'function'\n ) {\n // Popper virtual elements require a getBoundingClientRect method\n throw new TypeError(`${NAME.toUpperCase()}: Option \"reference\" provided type \"object\" without a required \"getBoundingClientRect\" method.`)\n }\n\n return config\n }\n\n _createPopper() {\n if (typeof Popper === 'undefined') {\n throw new TypeError('Bootstrap\\'s dropdowns require Popper (https://popper.js.org)')\n }\n\n let referenceElement = this._element\n\n if (this._config.reference === 'parent') {\n referenceElement = this._parent\n } else if (isElement(this._config.reference)) {\n referenceElement = getElement(this._config.reference)\n } else if (typeof this._config.reference === 'object') {\n referenceElement = this._config.reference\n }\n\n const popperConfig = this._getPopperConfig()\n this._popper = Popper.createPopper(referenceElement, this._menu, popperConfig)\n }\n\n _isShown() {\n return this._menu.classList.contains(CLASS_NAME_SHOW)\n }\n\n _getPlacement() {\n const parentDropdown = this._parent\n\n if (parentDropdown.classList.contains(CLASS_NAME_DROPEND)) {\n return PLACEMENT_RIGHT\n }\n\n if (parentDropdown.classList.contains(CLASS_NAME_DROPSTART)) {\n return PLACEMENT_LEFT\n }\n\n if (parentDropdown.classList.contains(CLASS_NAME_DROPUP_CENTER)) {\n return PLACEMENT_TOPCENTER\n }\n\n if (parentDropdown.classList.contains(CLASS_NAME_DROPDOWN_CENTER)) {\n return PLACEMENT_BOTTOMCENTER\n }\n\n // We need to trim the value because custom properties can also include spaces\n const isEnd = getComputedStyle(this._menu).getPropertyValue('--bs-position').trim() === 'end'\n\n if (parentDropdown.classList.contains(CLASS_NAME_DROPUP)) {\n return isEnd ? PLACEMENT_TOPEND : PLACEMENT_TOP\n }\n\n return isEnd ? PLACEMENT_BOTTOMEND : PLACEMENT_BOTTOM\n }\n\n _detectNavbar() {\n return this._element.closest(SELECTOR_NAVBAR) !== null\n }\n\n _getOffset() {\n const { offset } = this._config\n\n if (typeof offset === 'string') {\n return offset.split(',').map(value => Number.parseInt(value, 10))\n }\n\n if (typeof offset === 'function') {\n return popperData => offset(popperData, this._element)\n }\n\n return offset\n }\n\n _getPopperConfig() {\n const defaultBsPopperConfig = {\n placement: this._getPlacement(),\n modifiers: [{\n name: 'preventOverflow',\n options: {\n boundary: this._config.boundary\n }\n },\n {\n name: 'offset',\n options: {\n offset: this._getOffset()\n }\n }]\n }\n\n // Disable Popper if we have a static display or Dropdown is in Navbar\n if (this._inNavbar || this._config.display === 'static') {\n Manipulator.setDataAttribute(this._menu, 'popper', 'static') // todo:v6 remove\n defaultBsPopperConfig.modifiers = [{\n name: 'applyStyles',\n enabled: false\n }]\n }\n\n return {\n ...defaultBsPopperConfig,\n ...(typeof this._config.popperConfig === 'function' ? this._config.popperConfig(defaultBsPopperConfig) : this._config.popperConfig)\n }\n }\n\n _selectMenuItem({ key, target }) {\n const items = SelectorEngine.find(SELECTOR_VISIBLE_ITEMS, this._menu).filter(element => isVisible(element))\n\n if (!items.length) {\n return\n }\n\n // if target isn't included in items (e.g. when expanding the dropdown)\n // allow cycling to get the last item in case key equals ARROW_UP_KEY\n getNextActiveElement(items, target, key === ARROW_DOWN_KEY, !items.includes(target)).focus()\n }\n\n // Static\n static jQueryInterface(config) {\n return this.each(function () {\n const data = Dropdown.getOrCreateInstance(this, config)\n\n if (typeof config !== 'string') {\n return\n }\n\n if (typeof data[config] === 'undefined') {\n throw new TypeError(`No method named \"${config}\"`)\n }\n\n data[config]()\n })\n }\n\n static clearMenus(event) {\n if (event.button === RIGHT_MOUSE_BUTTON || (event.type === 'keyup' && event.key !== TAB_KEY)) {\n return\n }\n\n const openToggles = SelectorEngine.find(SELECTOR_DATA_TOGGLE_SHOWN)\n\n for (const toggle of openToggles) {\n const context = Dropdown.getInstance(toggle)\n if (!context || context._config.autoClose === false) {\n continue\n }\n\n const composedPath = event.composedPath()\n const isMenuTarget = composedPath.includes(context._menu)\n if (\n composedPath.includes(context._element) ||\n (context._config.autoClose === 'inside' && !isMenuTarget) ||\n (context._config.autoClose === 'outside' && isMenuTarget)\n ) {\n continue\n }\n\n // Tab navigation through the dropdown menu or events from contained inputs shouldn't close the menu\n if (context._menu.contains(event.target) && ((event.type === 'keyup' && event.key === TAB_KEY) || /input|select|option|textarea|form/i.test(event.target.tagName))) {\n continue\n }\n\n const relatedTarget = { relatedTarget: context._element }\n\n if (event.type === 'click') {\n relatedTarget.clickEvent = event\n }\n\n context._completeHide(relatedTarget)\n }\n }\n\n static dataApiKeydownHandler(event) {\n // If not an UP | DOWN | ESCAPE key => not a dropdown command\n // If input/textarea && if key is other than ESCAPE => not a dropdown command\n\n const isInput = /input|textarea/i.test(event.target.tagName)\n const isEscapeEvent = event.key === ESCAPE_KEY\n const isUpOrDownEvent = [ARROW_UP_KEY, ARROW_DOWN_KEY].includes(event.key)\n\n if (!isUpOrDownEvent && !isEscapeEvent) {\n return\n }\n\n if (isInput && !isEscapeEvent) {\n return\n }\n\n event.preventDefault()\n\n // todo: v6 revert #37011 & change markup https://getbootstrap.com/docs/5.2/forms/input-group/\n const getToggleButton = this.matches(SELECTOR_DATA_TOGGLE) ?\n this :\n (SelectorEngine.prev(this, SELECTOR_DATA_TOGGLE)[0] ||\n SelectorEngine.next(this, SELECTOR_DATA_TOGGLE)[0] ||\n SelectorEngine.findOne(SELECTOR_DATA_TOGGLE, event.delegateTarget.parentNode))\n\n const instance = Dropdown.getOrCreateInstance(getToggleButton)\n\n if (isUpOrDownEvent) {\n event.stopPropagation()\n instance.show()\n instance._selectMenuItem(event)\n return\n }\n\n if (instance._isShown()) { // else is escape and we check if it is shown\n event.stopPropagation()\n instance.hide()\n getToggleButton.focus()\n }\n }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(document, EVENT_KEYDOWN_DATA_API, SELECTOR_DATA_TOGGLE, Dropdown.dataApiKeydownHandler)\nEventHandler.on(document, EVENT_KEYDOWN_DATA_API, SELECTOR_MENU, Dropdown.dataApiKeydownHandler)\nEventHandler.on(document, EVENT_CLICK_DATA_API, Dropdown.clearMenus)\nEventHandler.on(document, EVENT_KEYUP_DATA_API, Dropdown.clearMenus)\nEventHandler.on(document, EVENT_CLICK_DATA_API, SELECTOR_DATA_TOGGLE, function (event) {\n event.preventDefault()\n Dropdown.getOrCreateInstance(this).toggle()\n})\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Dropdown)\n\nexport default Dropdown\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap (v5.2.2): util/scrollBar.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport SelectorEngine from '../dom/selector-engine'\nimport Manipulator from '../dom/manipulator'\nimport { isElement } from './index'\n\n/**\n * Constants\n */\n\nconst SELECTOR_FIXED_CONTENT = '.fixed-top, .fixed-bottom, .is-fixed, .sticky-top'\nconst SELECTOR_STICKY_CONTENT = '.sticky-top'\nconst PROPERTY_PADDING = 'padding-right'\nconst PROPERTY_MARGIN = 'margin-right'\n\n/**\n * Class definition\n */\n\nclass ScrollBarHelper {\n constructor() {\n this._element = document.body\n }\n\n // Public\n getWidth() {\n // https://developer.mozilla.org/en-US/docs/Web/API/Window/innerWidth#usage_notes\n const documentWidth = document.documentElement.clientWidth\n return Math.abs(window.innerWidth - documentWidth)\n }\n\n hide() {\n const width = this.getWidth()\n this._disableOverFlow()\n // give padding to element to balance the hidden scrollbar width\n this._setElementAttributes(this._element, PROPERTY_PADDING, calculatedValue => calculatedValue + width)\n // trick: We adjust positive paddingRight and negative marginRight to sticky-top elements to keep showing fullwidth\n this._setElementAttributes(SELECTOR_FIXED_CONTENT, PROPERTY_PADDING, calculatedValue => calculatedValue + width)\n this._setElementAttributes(SELECTOR_STICKY_CONTENT, PROPERTY_MARGIN, calculatedValue => calculatedValue - width)\n }\n\n reset() {\n this._resetElementAttributes(this._element, 'overflow')\n this._resetElementAttributes(this._element, PROPERTY_PADDING)\n this._resetElementAttributes(SELECTOR_FIXED_CONTENT, PROPERTY_PADDING)\n this._resetElementAttributes(SELECTOR_STICKY_CONTENT, PROPERTY_MARGIN)\n }\n\n isOverflowing() {\n return this.getWidth() > 0\n }\n\n // Private\n _disableOverFlow() {\n this._saveInitialAttribute(this._element, 'overflow')\n this._element.style.overflow = 'hidden'\n }\n\n _setElementAttributes(selector, styleProperty, callback) {\n const scrollbarWidth = this.getWidth()\n const manipulationCallBack = element => {\n if (element !== this._element && window.innerWidth > element.clientWidth + scrollbarWidth) {\n return\n }\n\n this._saveInitialAttribute(element, styleProperty)\n const calculatedValue = window.getComputedStyle(element).getPropertyValue(styleProperty)\n element.style.setProperty(styleProperty, `${callback(Number.parseFloat(calculatedValue))}px`)\n }\n\n this._applyManipulationCallback(selector, manipulationCallBack)\n }\n\n _saveInitialAttribute(element, styleProperty) {\n const actualValue = element.style.getPropertyValue(styleProperty)\n if (actualValue) {\n Manipulator.setDataAttribute(element, styleProperty, actualValue)\n }\n }\n\n _resetElementAttributes(selector, styleProperty) {\n const manipulationCallBack = element => {\n const value = Manipulator.getDataAttribute(element, styleProperty)\n // We only want to remove the property if the value is `null`; the value can also be zero\n if (value === null) {\n element.style.removeProperty(styleProperty)\n return\n }\n\n Manipulator.removeDataAttribute(element, styleProperty)\n element.style.setProperty(styleProperty, value)\n }\n\n this._applyManipulationCallback(selector, manipulationCallBack)\n }\n\n _applyManipulationCallback(selector, callBack) {\n if (isElement(selector)) {\n callBack(selector)\n return\n }\n\n for (const sel of SelectorEngine.find(selector, this._element)) {\n callBack(sel)\n }\n }\n}\n\nexport default ScrollBarHelper\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap (v5.2.2): util/backdrop.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport EventHandler from '../dom/event-handler'\nimport { execute, executeAfterTransition, getElement, reflow } from './index'\nimport Config from './config'\n\n/**\n * Constants\n */\n\nconst NAME = 'backdrop'\nconst CLASS_NAME_FADE = 'fade'\nconst CLASS_NAME_SHOW = 'show'\nconst EVENT_MOUSEDOWN = `mousedown.bs.${NAME}`\n\nconst Default = {\n className: 'modal-backdrop',\n clickCallback: null,\n isAnimated: false,\n isVisible: true, // if false, we use the backdrop helper without adding any element to the dom\n rootElement: 'body' // give the choice to place backdrop under different elements\n}\n\nconst DefaultType = {\n className: 'string',\n clickCallback: '(function|null)',\n isAnimated: 'boolean',\n isVisible: 'boolean',\n rootElement: '(element|string)'\n}\n\n/**\n * Class definition\n */\n\nclass Backdrop extends Config {\n constructor(config) {\n super()\n this._config = this._getConfig(config)\n this._isAppended = false\n this._element = null\n }\n\n // Getters\n static get Default() {\n return Default\n }\n\n static get DefaultType() {\n return DefaultType\n }\n\n static get NAME() {\n return NAME\n }\n\n // Public\n show(callback) {\n if (!this._config.isVisible) {\n execute(callback)\n return\n }\n\n this._append()\n\n const element = this._getElement()\n if (this._config.isAnimated) {\n reflow(element)\n }\n\n element.classList.add(CLASS_NAME_SHOW)\n\n this._emulateAnimation(() => {\n execute(callback)\n })\n }\n\n hide(callback) {\n if (!this._config.isVisible) {\n execute(callback)\n return\n }\n\n this._getElement().classList.remove(CLASS_NAME_SHOW)\n\n this._emulateAnimation(() => {\n this.dispose()\n execute(callback)\n })\n }\n\n dispose() {\n if (!this._isAppended) {\n return\n }\n\n EventHandler.off(this._element, EVENT_MOUSEDOWN)\n\n this._element.remove()\n this._isAppended = false\n }\n\n // Private\n _getElement() {\n if (!this._element) {\n const backdrop = document.createElement('div')\n backdrop.className = this._config.className\n if (this._config.isAnimated) {\n backdrop.classList.add(CLASS_NAME_FADE)\n }\n\n this._element = backdrop\n }\n\n return this._element\n }\n\n _configAfterMerge(config) {\n // use getElement() with the default \"body\" to get a fresh Element on each instantiation\n config.rootElement = getElement(config.rootElement)\n return config\n }\n\n _append() {\n if (this._isAppended) {\n return\n }\n\n const element = this._getElement()\n this._config.rootElement.append(element)\n\n EventHandler.on(element, EVENT_MOUSEDOWN, () => {\n execute(this._config.clickCallback)\n })\n\n this._isAppended = true\n }\n\n _emulateAnimation(callback) {\n executeAfterTransition(callback, this._getElement(), this._config.isAnimated)\n }\n}\n\nexport default Backdrop\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap (v5.2.2): util/focustrap.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport EventHandler from '../dom/event-handler'\nimport SelectorEngine from '../dom/selector-engine'\nimport Config from './config'\n\n/**\n * Constants\n */\n\nconst NAME = 'focustrap'\nconst DATA_KEY = 'bs.focustrap'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst EVENT_FOCUSIN = `focusin${EVENT_KEY}`\nconst EVENT_KEYDOWN_TAB = `keydown.tab${EVENT_KEY}`\n\nconst TAB_KEY = 'Tab'\nconst TAB_NAV_FORWARD = 'forward'\nconst TAB_NAV_BACKWARD = 'backward'\n\nconst Default = {\n autofocus: true,\n trapElement: null // The element to trap focus inside of\n}\n\nconst DefaultType = {\n autofocus: 'boolean',\n trapElement: 'element'\n}\n\n/**\n * Class definition\n */\n\nclass FocusTrap extends Config {\n constructor(config) {\n super()\n this._config = this._getConfig(config)\n this._isActive = false\n this._lastTabNavDirection = null\n }\n\n // Getters\n static get Default() {\n return Default\n }\n\n static get DefaultType() {\n return DefaultType\n }\n\n static get NAME() {\n return NAME\n }\n\n // Public\n activate() {\n if (this._isActive) {\n return\n }\n\n if (this._config.autofocus) {\n this._config.trapElement.focus()\n }\n\n EventHandler.off(document, EVENT_KEY) // guard against infinite focus loop\n EventHandler.on(document, EVENT_FOCUSIN, event => this._handleFocusin(event))\n EventHandler.on(document, EVENT_KEYDOWN_TAB, event => this._handleKeydown(event))\n\n this._isActive = true\n }\n\n deactivate() {\n if (!this._isActive) {\n return\n }\n\n this._isActive = false\n EventHandler.off(document, EVENT_KEY)\n }\n\n // Private\n _handleFocusin(event) {\n const { trapElement } = this._config\n\n if (event.target === document || event.target === trapElement || trapElement.contains(event.target)) {\n return\n }\n\n const elements = SelectorEngine.focusableChildren(trapElement)\n\n if (elements.length === 0) {\n trapElement.focus()\n } else if (this._lastTabNavDirection === TAB_NAV_BACKWARD) {\n elements[elements.length - 1].focus()\n } else {\n elements[0].focus()\n }\n }\n\n _handleKeydown(event) {\n if (event.key !== TAB_KEY) {\n return\n }\n\n this._lastTabNavDirection = event.shiftKey ? TAB_NAV_BACKWARD : TAB_NAV_FORWARD\n }\n}\n\nexport default FocusTrap\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap (v5.2.2): modal.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport { defineJQueryPlugin, getElementFromSelector, isRTL, isVisible, reflow } from './util/index'\nimport EventHandler from './dom/event-handler'\nimport SelectorEngine from './dom/selector-engine'\nimport ScrollBarHelper from './util/scrollbar'\nimport BaseComponent from './base-component'\nimport Backdrop from './util/backdrop'\nimport FocusTrap from './util/focustrap'\nimport { enableDismissTrigger } from './util/component-functions'\n\n/**\n * Constants\n */\n\nconst NAME = 'modal'\nconst DATA_KEY = 'bs.modal'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst DATA_API_KEY = '.data-api'\nconst ESCAPE_KEY = 'Escape'\n\nconst EVENT_HIDE = `hide${EVENT_KEY}`\nconst EVENT_HIDE_PREVENTED = `hidePrevented${EVENT_KEY}`\nconst EVENT_HIDDEN = `hidden${EVENT_KEY}`\nconst EVENT_SHOW = `show${EVENT_KEY}`\nconst EVENT_SHOWN = `shown${EVENT_KEY}`\nconst EVENT_RESIZE = `resize${EVENT_KEY}`\nconst EVENT_CLICK_DISMISS = `click.dismiss${EVENT_KEY}`\nconst EVENT_MOUSEDOWN_DISMISS = `mousedown.dismiss${EVENT_KEY}`\nconst EVENT_KEYDOWN_DISMISS = `keydown.dismiss${EVENT_KEY}`\nconst EVENT_CLICK_DATA_API = `click${EVENT_KEY}${DATA_API_KEY}`\n\nconst CLASS_NAME_OPEN = 'modal-open'\nconst CLASS_NAME_FADE = 'fade'\nconst CLASS_NAME_SHOW = 'show'\nconst CLASS_NAME_STATIC = 'modal-static'\n\nconst OPEN_SELECTOR = '.modal.show'\nconst SELECTOR_DIALOG = '.modal-dialog'\nconst SELECTOR_MODAL_BODY = '.modal-body'\nconst SELECTOR_DATA_TOGGLE = '[data-bs-toggle=\"modal\"]'\n\nconst Default = {\n backdrop: true,\n focus: true,\n keyboard: true\n}\n\nconst DefaultType = {\n backdrop: '(boolean|string)',\n focus: 'boolean',\n keyboard: 'boolean'\n}\n\n/**\n * Class definition\n */\n\nclass Modal extends BaseComponent {\n constructor(element, config) {\n super(element, config)\n\n this._dialog = SelectorEngine.findOne(SELECTOR_DIALOG, this._element)\n this._backdrop = this._initializeBackDrop()\n this._focustrap = this._initializeFocusTrap()\n this._isShown = false\n this._isTransitioning = false\n this._scrollBar = new ScrollBarHelper()\n\n this._addEventListeners()\n }\n\n // Getters\n static get Default() {\n return Default\n }\n\n static get DefaultType() {\n return DefaultType\n }\n\n static get NAME() {\n return NAME\n }\n\n // Public\n toggle(relatedTarget) {\n return this._isShown ? this.hide() : this.show(relatedTarget)\n }\n\n show(relatedTarget) {\n if (this._isShown || this._isTransitioning) {\n return\n }\n\n const showEvent = EventHandler.trigger(this._element, EVENT_SHOW, {\n relatedTarget\n })\n\n if (showEvent.defaultPrevented) {\n return\n }\n\n this._isShown = true\n this._isTransitioning = true\n\n this._scrollBar.hide()\n\n document.body.classList.add(CLASS_NAME_OPEN)\n\n this._adjustDialog()\n\n this._backdrop.show(() => this._showElement(relatedTarget))\n }\n\n hide() {\n if (!this._isShown || this._isTransitioning) {\n return\n }\n\n const hideEvent = EventHandler.trigger(this._element, EVENT_HIDE)\n\n if (hideEvent.defaultPrevented) {\n return\n }\n\n this._isShown = false\n this._isTransitioning = true\n this._focustrap.deactivate()\n\n this._element.classList.remove(CLASS_NAME_SHOW)\n\n this._queueCallback(() => this._hideModal(), this._element, this._isAnimated())\n }\n\n dispose() {\n for (const htmlElement of [window, this._dialog]) {\n EventHandler.off(htmlElement, EVENT_KEY)\n }\n\n this._backdrop.dispose()\n this._focustrap.deactivate()\n super.dispose()\n }\n\n handleUpdate() {\n this._adjustDialog()\n }\n\n // Private\n _initializeBackDrop() {\n return new Backdrop({\n isVisible: Boolean(this._config.backdrop), // 'static' option will be translated to true, and booleans will keep their value,\n isAnimated: this._isAnimated()\n })\n }\n\n _initializeFocusTrap() {\n return new FocusTrap({\n trapElement: this._element\n })\n }\n\n _showElement(relatedTarget) {\n // try to append dynamic modal\n if (!document.body.contains(this._element)) {\n document.body.append(this._element)\n }\n\n this._element.style.display = 'block'\n this._element.removeAttribute('aria-hidden')\n this._element.setAttribute('aria-modal', true)\n this._element.setAttribute('role', 'dialog')\n this._element.scrollTop = 0\n\n const modalBody = SelectorEngine.findOne(SELECTOR_MODAL_BODY, this._dialog)\n if (modalBody) {\n modalBody.scrollTop = 0\n }\n\n reflow(this._element)\n\n this._element.classList.add(CLASS_NAME_SHOW)\n\n const transitionComplete = () => {\n if (this._config.focus) {\n this._focustrap.activate()\n }\n\n this._isTransitioning = false\n EventHandler.trigger(this._element, EVENT_SHOWN, {\n relatedTarget\n })\n }\n\n this._queueCallback(transitionComplete, this._dialog, this._isAnimated())\n }\n\n _addEventListeners() {\n EventHandler.on(this._element, EVENT_KEYDOWN_DISMISS, event => {\n if (event.key !== ESCAPE_KEY) {\n return\n }\n\n if (this._config.keyboard) {\n event.preventDefault()\n this.hide()\n return\n }\n\n this._triggerBackdropTransition()\n })\n\n EventHandler.on(window, EVENT_RESIZE, () => {\n if (this._isShown && !this._isTransitioning) {\n this._adjustDialog()\n }\n })\n\n EventHandler.on(this._element, EVENT_MOUSEDOWN_DISMISS, event => {\n // a bad trick to segregate clicks that may start inside dialog but end outside, and avoid listen to scrollbar clicks\n EventHandler.one(this._element, EVENT_CLICK_DISMISS, event2 => {\n if (this._element !== event.target || this._element !== event2.target) {\n return\n }\n\n if (this._config.backdrop === 'static') {\n this._triggerBackdropTransition()\n return\n }\n\n if (this._config.backdrop) {\n this.hide()\n }\n })\n })\n }\n\n _hideModal() {\n this._element.style.display = 'none'\n this._element.setAttribute('aria-hidden', true)\n this._element.removeAttribute('aria-modal')\n this._element.removeAttribute('role')\n this._isTransitioning = false\n\n this._backdrop.hide(() => {\n document.body.classList.remove(CLASS_NAME_OPEN)\n this._resetAdjustments()\n this._scrollBar.reset()\n EventHandler.trigger(this._element, EVENT_HIDDEN)\n })\n }\n\n _isAnimated() {\n return this._element.classList.contains(CLASS_NAME_FADE)\n }\n\n _triggerBackdropTransition() {\n const hideEvent = EventHandler.trigger(this._element, EVENT_HIDE_PREVENTED)\n if (hideEvent.defaultPrevented) {\n return\n }\n\n const isModalOverflowing = this._element.scrollHeight > document.documentElement.clientHeight\n const initialOverflowY = this._element.style.overflowY\n // return if the following background transition hasn't yet completed\n if (initialOverflowY === 'hidden' || this._element.classList.contains(CLASS_NAME_STATIC)) {\n return\n }\n\n if (!isModalOverflowing) {\n this._element.style.overflowY = 'hidden'\n }\n\n this._element.classList.add(CLASS_NAME_STATIC)\n this._queueCallback(() => {\n this._element.classList.remove(CLASS_NAME_STATIC)\n this._queueCallback(() => {\n this._element.style.overflowY = initialOverflowY\n }, this._dialog)\n }, this._dialog)\n\n this._element.focus()\n }\n\n /**\n * The following methods are used to handle overflowing modals\n */\n\n _adjustDialog() {\n const isModalOverflowing = this._element.scrollHeight > document.documentElement.clientHeight\n const scrollbarWidth = this._scrollBar.getWidth()\n const isBodyOverflowing = scrollbarWidth > 0\n\n if (isBodyOverflowing && !isModalOverflowing) {\n const property = isRTL() ? 'paddingLeft' : 'paddingRight'\n this._element.style[property] = `${scrollbarWidth}px`\n }\n\n if (!isBodyOverflowing && isModalOverflowing) {\n const property = isRTL() ? 'paddingRight' : 'paddingLeft'\n this._element.style[property] = `${scrollbarWidth}px`\n }\n }\n\n _resetAdjustments() {\n this._element.style.paddingLeft = ''\n this._element.style.paddingRight = ''\n }\n\n // Static\n static jQueryInterface(config, relatedTarget) {\n return this.each(function () {\n const data = Modal.getOrCreateInstance(this, config)\n\n if (typeof config !== 'string') {\n return\n }\n\n if (typeof data[config] === 'undefined') {\n throw new TypeError(`No method named \"${config}\"`)\n }\n\n data[config](relatedTarget)\n })\n }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(document, EVENT_CLICK_DATA_API, SELECTOR_DATA_TOGGLE, function (event) {\n const target = getElementFromSelector(this)\n\n if (['A', 'AREA'].includes(this.tagName)) {\n event.preventDefault()\n }\n\n EventHandler.one(target, EVENT_SHOW, showEvent => {\n if (showEvent.defaultPrevented) {\n // only register focus restorer if modal will actually get shown\n return\n }\n\n EventHandler.one(target, EVENT_HIDDEN, () => {\n if (isVisible(this)) {\n this.focus()\n }\n })\n })\n\n // avoid conflict when clicking modal toggler while another one is open\n const alreadyOpen = SelectorEngine.findOne(OPEN_SELECTOR)\n if (alreadyOpen) {\n Modal.getInstance(alreadyOpen).hide()\n }\n\n const data = Modal.getOrCreateInstance(target)\n\n data.toggle(this)\n})\n\nenableDismissTrigger(Modal)\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Modal)\n\nexport default Modal\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap (v5.2.2): offcanvas.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport {\n defineJQueryPlugin,\n getElementFromSelector,\n isDisabled,\n isVisible\n} from './util/index'\nimport ScrollBarHelper from './util/scrollbar'\nimport EventHandler from './dom/event-handler'\nimport BaseComponent from './base-component'\nimport SelectorEngine from './dom/selector-engine'\nimport Backdrop from './util/backdrop'\nimport FocusTrap from './util/focustrap'\nimport { enableDismissTrigger } from './util/component-functions'\n\n/**\n * Constants\n */\n\nconst NAME = 'offcanvas'\nconst DATA_KEY = 'bs.offcanvas'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst DATA_API_KEY = '.data-api'\nconst EVENT_LOAD_DATA_API = `load${EVENT_KEY}${DATA_API_KEY}`\nconst ESCAPE_KEY = 'Escape'\n\nconst CLASS_NAME_SHOW = 'show'\nconst CLASS_NAME_SHOWING = 'showing'\nconst CLASS_NAME_HIDING = 'hiding'\nconst CLASS_NAME_BACKDROP = 'offcanvas-backdrop'\nconst OPEN_SELECTOR = '.offcanvas.show'\n\nconst EVENT_SHOW = `show${EVENT_KEY}`\nconst EVENT_SHOWN = `shown${EVENT_KEY}`\nconst EVENT_HIDE = `hide${EVENT_KEY}`\nconst EVENT_HIDE_PREVENTED = `hidePrevented${EVENT_KEY}`\nconst EVENT_HIDDEN = `hidden${EVENT_KEY}`\nconst EVENT_RESIZE = `resize${EVENT_KEY}`\nconst EVENT_CLICK_DATA_API = `click${EVENT_KEY}${DATA_API_KEY}`\nconst EVENT_KEYDOWN_DISMISS = `keydown.dismiss${EVENT_KEY}`\n\nconst SELECTOR_DATA_TOGGLE = '[data-bs-toggle=\"offcanvas\"]'\n\nconst Default = {\n backdrop: true,\n keyboard: true,\n scroll: false\n}\n\nconst DefaultType = {\n backdrop: '(boolean|string)',\n keyboard: 'boolean',\n scroll: 'boolean'\n}\n\n/**\n * Class definition\n */\n\nclass Offcanvas extends BaseComponent {\n constructor(element, config) {\n super(element, config)\n\n this._isShown = false\n this._backdrop = this._initializeBackDrop()\n this._focustrap = this._initializeFocusTrap()\n this._addEventListeners()\n }\n\n // Getters\n static get Default() {\n return Default\n }\n\n static get DefaultType() {\n return DefaultType\n }\n\n static get NAME() {\n return NAME\n }\n\n // Public\n toggle(relatedTarget) {\n return this._isShown ? this.hide() : this.show(relatedTarget)\n }\n\n show(relatedTarget) {\n if (this._isShown) {\n return\n }\n\n const showEvent = EventHandler.trigger(this._element, EVENT_SHOW, { relatedTarget })\n\n if (showEvent.defaultPrevented) {\n return\n }\n\n this._isShown = true\n this._backdrop.show()\n\n if (!this._config.scroll) {\n new ScrollBarHelper().hide()\n }\n\n this._element.setAttribute('aria-modal', true)\n this._element.setAttribute('role', 'dialog')\n this._element.classList.add(CLASS_NAME_SHOWING)\n\n const completeCallBack = () => {\n if (!this._config.scroll || this._config.backdrop) {\n this._focustrap.activate()\n }\n\n this._element.classList.add(CLASS_NAME_SHOW)\n this._element.classList.remove(CLASS_NAME_SHOWING)\n EventHandler.trigger(this._element, EVENT_SHOWN, { relatedTarget })\n }\n\n this._queueCallback(completeCallBack, this._element, true)\n }\n\n hide() {\n if (!this._isShown) {\n return\n }\n\n const hideEvent = EventHandler.trigger(this._element, EVENT_HIDE)\n\n if (hideEvent.defaultPrevented) {\n return\n }\n\n this._focustrap.deactivate()\n this._element.blur()\n this._isShown = false\n this._element.classList.add(CLASS_NAME_HIDING)\n this._backdrop.hide()\n\n const completeCallback = () => {\n this._element.classList.remove(CLASS_NAME_SHOW, CLASS_NAME_HIDING)\n this._element.removeAttribute('aria-modal')\n this._element.removeAttribute('role')\n\n if (!this._config.scroll) {\n new ScrollBarHelper().reset()\n }\n\n EventHandler.trigger(this._element, EVENT_HIDDEN)\n }\n\n this._queueCallback(completeCallback, this._element, true)\n }\n\n dispose() {\n this._backdrop.dispose()\n this._focustrap.deactivate()\n super.dispose()\n }\n\n // Private\n _initializeBackDrop() {\n const clickCallback = () => {\n if (this._config.backdrop === 'static') {\n EventHandler.trigger(this._element, EVENT_HIDE_PREVENTED)\n return\n }\n\n this.hide()\n }\n\n // 'static' option will be translated to true, and booleans will keep their value\n const isVisible = Boolean(this._config.backdrop)\n\n return new Backdrop({\n className: CLASS_NAME_BACKDROP,\n isVisible,\n isAnimated: true,\n rootElement: this._element.parentNode,\n clickCallback: isVisible ? clickCallback : null\n })\n }\n\n _initializeFocusTrap() {\n return new FocusTrap({\n trapElement: this._element\n })\n }\n\n _addEventListeners() {\n EventHandler.on(this._element, EVENT_KEYDOWN_DISMISS, event => {\n if (event.key !== ESCAPE_KEY) {\n return\n }\n\n if (!this._config.keyboard) {\n EventHandler.trigger(this._element, EVENT_HIDE_PREVENTED)\n return\n }\n\n this.hide()\n })\n }\n\n // Static\n static jQueryInterface(config) {\n return this.each(function () {\n const data = Offcanvas.getOrCreateInstance(this, config)\n\n if (typeof config !== 'string') {\n return\n }\n\n if (data[config] === undefined || config.startsWith('_') || config === 'constructor') {\n throw new TypeError(`No method named \"${config}\"`)\n }\n\n data[config](this)\n })\n }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(document, EVENT_CLICK_DATA_API, SELECTOR_DATA_TOGGLE, function (event) {\n const target = getElementFromSelector(this)\n\n if (['A', 'AREA'].includes(this.tagName)) {\n event.preventDefault()\n }\n\n if (isDisabled(this)) {\n return\n }\n\n EventHandler.one(target, EVENT_HIDDEN, () => {\n // focus on trigger when it is closed\n if (isVisible(this)) {\n this.focus()\n }\n })\n\n // avoid conflict when clicking a toggler of an offcanvas, while another is open\n const alreadyOpen = SelectorEngine.findOne(OPEN_SELECTOR)\n if (alreadyOpen && alreadyOpen !== target) {\n Offcanvas.getInstance(alreadyOpen).hide()\n }\n\n const data = Offcanvas.getOrCreateInstance(target)\n data.toggle(this)\n})\n\nEventHandler.on(window, EVENT_LOAD_DATA_API, () => {\n for (const selector of SelectorEngine.find(OPEN_SELECTOR)) {\n Offcanvas.getOrCreateInstance(selector).show()\n }\n})\n\nEventHandler.on(window, EVENT_RESIZE, () => {\n for (const element of SelectorEngine.find('[aria-modal][class*=show][class*=offcanvas-]')) {\n if (getComputedStyle(element).position !== 'fixed') {\n Offcanvas.getOrCreateInstance(element).hide()\n }\n }\n})\n\nenableDismissTrigger(Offcanvas)\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Offcanvas)\n\nexport default Offcanvas\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap (v5.2.2): util/sanitizer.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nconst uriAttributes = new Set([\n 'background',\n 'cite',\n 'href',\n 'itemtype',\n 'longdesc',\n 'poster',\n 'src',\n 'xlink:href'\n])\n\nconst ARIA_ATTRIBUTE_PATTERN = /^aria-[\\w-]*$/i\n\n/**\n * A pattern that recognizes a commonly useful subset of URLs that are safe.\n *\n * Shout-out to Angular https://github.com/angular/angular/blob/12.2.x/packages/core/src/sanitization/url_sanitizer.ts\n */\nconst SAFE_URL_PATTERN = /^(?:(?:https?|mailto|ftp|tel|file|sms):|[^#&/:?]*(?:[#/?]|$))/i\n\n/**\n * A pattern that matches safe data URLs. Only matches image, video and audio types.\n *\n * Shout-out to Angular https://github.com/angular/angular/blob/12.2.x/packages/core/src/sanitization/url_sanitizer.ts\n */\nconst DATA_URL_PATTERN = /^data:(?:image\\/(?:bmp|gif|jpeg|jpg|png|tiff|webp)|video\\/(?:mpeg|mp4|ogg|webm)|audio\\/(?:mp3|oga|ogg|opus));base64,[\\d+/a-z]+=*$/i\n\nconst allowedAttribute = (attribute, allowedAttributeList) => {\n const attributeName = attribute.nodeName.toLowerCase()\n\n if (allowedAttributeList.includes(attributeName)) {\n if (uriAttributes.has(attributeName)) {\n return Boolean(SAFE_URL_PATTERN.test(attribute.nodeValue) || DATA_URL_PATTERN.test(attribute.nodeValue))\n }\n\n return true\n }\n\n // Check if a regular expression validates the attribute.\n return allowedAttributeList.filter(attributeRegex => attributeRegex instanceof RegExp)\n .some(regex => regex.test(attributeName))\n}\n\nexport const DefaultAllowlist = {\n // Global attributes allowed on any supplied element below.\n '*': ['class', 'dir', 'id', 'lang', 'role', ARIA_ATTRIBUTE_PATTERN],\n a: ['target', 'href', 'title', 'rel'],\n area: [],\n b: [],\n br: [],\n col: [],\n code: [],\n div: [],\n em: [],\n hr: [],\n h1: [],\n h2: [],\n h3: [],\n h4: [],\n h5: [],\n h6: [],\n i: [],\n img: ['src', 'srcset', 'alt', 'title', 'width', 'height'],\n li: [],\n ol: [],\n p: [],\n pre: [],\n s: [],\n small: [],\n span: [],\n sub: [],\n sup: [],\n strong: [],\n u: [],\n ul: []\n}\n\nexport function sanitizeHtml(unsafeHtml, allowList, sanitizeFunction) {\n if (!unsafeHtml.length) {\n return unsafeHtml\n }\n\n if (sanitizeFunction && typeof sanitizeFunction === 'function') {\n return sanitizeFunction(unsafeHtml)\n }\n\n const domParser = new window.DOMParser()\n const createdDocument = domParser.parseFromString(unsafeHtml, 'text/html')\n const elements = [].concat(...createdDocument.body.querySelectorAll('*'))\n\n for (const element of elements) {\n const elementName = element.nodeName.toLowerCase()\n\n if (!Object.keys(allowList).includes(elementName)) {\n element.remove()\n\n continue\n }\n\n const attributeList = [].concat(...element.attributes)\n const allowedAttributes = [].concat(allowList['*'] || [], allowList[elementName] || [])\n\n for (const attribute of attributeList) {\n if (!allowedAttribute(attribute, allowedAttributes)) {\n element.removeAttribute(attribute.nodeName)\n }\n }\n }\n\n return createdDocument.body.innerHTML\n}\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap (v5.2.2): util/template-factory.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport { DefaultAllowlist, sanitizeHtml } from './sanitizer'\nimport { getElement, isElement } from '../util/index'\nimport SelectorEngine from '../dom/selector-engine'\nimport Config from './config'\n\n/**\n * Constants\n */\n\nconst NAME = 'TemplateFactory'\n\nconst Default = {\n allowList: DefaultAllowlist,\n content: {}, // { selector : text , selector2 : text2 , }\n extraClass: '',\n html: false,\n sanitize: true,\n sanitizeFn: null,\n template: '<div></div>'\n}\n\nconst DefaultType = {\n allowList: 'object',\n content: 'object',\n extraClass: '(string|function)',\n html: 'boolean',\n sanitize: 'boolean',\n sanitizeFn: '(null|function)',\n template: 'string'\n}\n\nconst DefaultContentType = {\n entry: '(string|element|function|null)',\n selector: '(string|element)'\n}\n\n/**\n * Class definition\n */\n\nclass TemplateFactory extends Config {\n constructor(config) {\n super()\n this._config = this._getConfig(config)\n }\n\n // Getters\n static get Default() {\n return Default\n }\n\n static get DefaultType() {\n return DefaultType\n }\n\n static get NAME() {\n return NAME\n }\n\n // Public\n getContent() {\n return Object.values(this._config.content)\n .map(config => this._resolvePossibleFunction(config))\n .filter(Boolean)\n }\n\n hasContent() {\n return this.getContent().length > 0\n }\n\n changeContent(content) {\n this._checkContent(content)\n this._config.content = { ...this._config.content, ...content }\n return this\n }\n\n toHtml() {\n const templateWrapper = document.createElement('div')\n templateWrapper.innerHTML = this._maybeSanitize(this._config.template)\n\n for (const [selector, text] of Object.entries(this._config.content)) {\n this._setContent(templateWrapper, text, selector)\n }\n\n const template = templateWrapper.children[0]\n const extraClass = this._resolvePossibleFunction(this._config.extraClass)\n\n if (extraClass) {\n template.classList.add(...extraClass.split(' '))\n }\n\n return template\n }\n\n // Private\n _typeCheckConfig(config) {\n super._typeCheckConfig(config)\n this._checkContent(config.content)\n }\n\n _checkContent(arg) {\n for (const [selector, content] of Object.entries(arg)) {\n super._typeCheckConfig({ selector, entry: content }, DefaultContentType)\n }\n }\n\n _setContent(template, content, selector) {\n const templateElement = SelectorEngine.findOne(selector, template)\n\n if (!templateElement) {\n return\n }\n\n content = this._resolvePossibleFunction(content)\n\n if (!content) {\n templateElement.remove()\n return\n }\n\n if (isElement(content)) {\n this._putElementInTemplate(getElement(content), templateElement)\n return\n }\n\n if (this._config.html) {\n templateElement.innerHTML = this._maybeSanitize(content)\n return\n }\n\n templateElement.textContent = content\n }\n\n _maybeSanitize(arg) {\n return this._config.sanitize ? sanitizeHtml(arg, this._config.allowList, this._config.sanitizeFn) : arg\n }\n\n _resolvePossibleFunction(arg) {\n return typeof arg === 'function' ? arg(this) : arg\n }\n\n _putElementInTemplate(element, templateElement) {\n if (this._config.html) {\n templateElement.innerHTML = ''\n templateElement.append(element)\n return\n }\n\n templateElement.textContent = element.textContent\n }\n}\n\nexport default TemplateFactory\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap (v5.2.2): tooltip.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport * as Popper from '@popperjs/core'\nimport { defineJQueryPlugin, findShadowRoot, getElement, getUID, isRTL, noop } from './util/index'\nimport { DefaultAllowlist } from './util/sanitizer'\nimport EventHandler from './dom/event-handler'\nimport Manipulator from './dom/manipulator'\nimport BaseComponent from './base-component'\nimport TemplateFactory from './util/template-factory'\n\n/**\n * Constants\n */\n\nconst NAME = 'tooltip'\nconst DISALLOWED_ATTRIBUTES = new Set(['sanitize', 'allowList', 'sanitizeFn'])\n\nconst CLASS_NAME_FADE = 'fade'\nconst CLASS_NAME_MODAL = 'modal'\nconst CLASS_NAME_SHOW = 'show'\n\nconst SELECTOR_TOOLTIP_INNER = '.tooltip-inner'\nconst SELECTOR_MODAL = `.${CLASS_NAME_MODAL}`\n\nconst EVENT_MODAL_HIDE = 'hide.bs.modal'\n\nconst TRIGGER_HOVER = 'hover'\nconst TRIGGER_FOCUS = 'focus'\nconst TRIGGER_CLICK = 'click'\nconst TRIGGER_MANUAL = 'manual'\n\nconst EVENT_HIDE = 'hide'\nconst EVENT_HIDDEN = 'hidden'\nconst EVENT_SHOW = 'show'\nconst EVENT_SHOWN = 'shown'\nconst EVENT_INSERTED = 'inserted'\nconst EVENT_CLICK = 'click'\nconst EVENT_FOCUSIN = 'focusin'\nconst EVENT_FOCUSOUT = 'focusout'\nconst EVENT_MOUSEENTER = 'mouseenter'\nconst EVENT_MOUSELEAVE = 'mouseleave'\n\nconst AttachmentMap = {\n AUTO: 'auto',\n TOP: 'top',\n RIGHT: isRTL() ? 'left' : 'right',\n BOTTOM: 'bottom',\n LEFT: isRTL() ? 'right' : 'left'\n}\n\nconst Default = {\n allowList: DefaultAllowlist,\n animation: true,\n boundary: 'clippingParents',\n container: false,\n customClass: '',\n delay: 0,\n fallbackPlacements: ['top', 'right', 'bottom', 'left'],\n html: false,\n offset: [0, 0],\n placement: 'top',\n popperConfig: null,\n sanitize: true,\n sanitizeFn: null,\n selector: false,\n template: '<div class=\"tooltip\" role=\"tooltip\">' +\n '<div class=\"tooltip-arrow\"></div>' +\n '<div class=\"tooltip-inner\"></div>' +\n '</div>',\n title: '',\n trigger: 'hover focus'\n}\n\nconst DefaultType = {\n allowList: 'object',\n animation: 'boolean',\n boundary: '(string|element)',\n container: '(string|element|boolean)',\n customClass: '(string|function)',\n delay: '(number|object)',\n fallbackPlacements: 'array',\n html: 'boolean',\n offset: '(array|string|function)',\n placement: '(string|function)',\n popperConfig: '(null|object|function)',\n sanitize: 'boolean',\n sanitizeFn: '(null|function)',\n selector: '(string|boolean)',\n template: 'string',\n title: '(string|element|function)',\n trigger: 'string'\n}\n\n/**\n * Class definition\n */\n\nclass Tooltip extends BaseComponent {\n constructor(element, config) {\n if (typeof Popper === 'undefined') {\n throw new TypeError('Bootstrap\\'s tooltips require Popper (https://popper.js.org)')\n }\n\n super(element, config)\n\n // Private\n this._isEnabled = true\n this._timeout = 0\n this._isHovered = null\n this._activeTrigger = {}\n this._popper = null\n this._templateFactory = null\n this._newContent = null\n\n // Protected\n this.tip = null\n\n this._setListeners()\n\n if (!this._config.selector) {\n this._fixTitle()\n }\n }\n\n // Getters\n static get Default() {\n return Default\n }\n\n static get DefaultType() {\n return DefaultType\n }\n\n static get NAME() {\n return NAME\n }\n\n // Public\n enable() {\n this._isEnabled = true\n }\n\n disable() {\n this._isEnabled = false\n }\n\n toggleEnabled() {\n this._isEnabled = !this._isEnabled\n }\n\n toggle() {\n if (!this._isEnabled) {\n return\n }\n\n this._activeTrigger.click = !this._activeTrigger.click\n if (this._isShown()) {\n this._leave()\n return\n }\n\n this._enter()\n }\n\n dispose() {\n clearTimeout(this._timeout)\n\n EventHandler.off(this._element.closest(SELECTOR_MODAL), EVENT_MODAL_HIDE, this._hideModalHandler)\n\n if (this.tip) {\n this.tip.remove()\n }\n\n if (this._element.getAttribute('data-bs-original-title')) {\n this._element.setAttribute('title', this._element.getAttribute('data-bs-original-title'))\n }\n\n this._disposePopper()\n super.dispose()\n }\n\n show() {\n if (this._element.style.display === 'none') {\n throw new Error('Please use show on visible elements')\n }\n\n if (!(this._isWithContent() && this._isEnabled)) {\n return\n }\n\n const showEvent = EventHandler.trigger(this._element, this.constructor.eventName(EVENT_SHOW))\n const shadowRoot = findShadowRoot(this._element)\n const isInTheDom = (shadowRoot || this._element.ownerDocument.documentElement).contains(this._element)\n\n if (showEvent.defaultPrevented || !isInTheDom) {\n return\n }\n\n // todo v6 remove this OR make it optional\n if (this.tip) {\n this.tip.remove()\n this.tip = null\n }\n\n const tip = this._getTipElement()\n\n this._element.setAttribute('aria-describedby', tip.getAttribute('id'))\n\n const { container } = this._config\n\n if (!this._element.ownerDocument.documentElement.contains(this.tip)) {\n container.append(tip)\n EventHandler.trigger(this._element, this.constructor.eventName(EVENT_INSERTED))\n }\n\n if (this._popper) {\n this._popper.update()\n } else {\n this._popper = this._createPopper(tip)\n }\n\n tip.classList.add(CLASS_NAME_SHOW)\n\n // If this is a touch-enabled device we add extra\n // empty mouseover listeners to the body's immediate children;\n // only needed because of broken event delegation on iOS\n // https://www.quirksmode.org/blog/archives/2014/02/mouse_event_bub.html\n if ('ontouchstart' in document.documentElement) {\n for (const element of [].concat(...document.body.children)) {\n EventHandler.on(element, 'mouseover', noop)\n }\n }\n\n const complete = () => {\n EventHandler.trigger(this._element, this.constructor.eventName(EVENT_SHOWN))\n\n if (this._isHovered === false) {\n this._leave()\n }\n\n this._isHovered = false\n }\n\n this._queueCallback(complete, this.tip, this._isAnimated())\n }\n\n hide() {\n if (!this._isShown()) {\n return\n }\n\n const hideEvent = EventHandler.trigger(this._element, this.constructor.eventName(EVENT_HIDE))\n if (hideEvent.defaultPrevented) {\n return\n }\n\n const tip = this._getTipElement()\n tip.classList.remove(CLASS_NAME_SHOW)\n\n // If this is a touch-enabled device we remove the extra\n // empty mouseover listeners we added for iOS support\n if ('ontouchstart' in document.documentElement) {\n for (const element of [].concat(...document.body.children)) {\n EventHandler.off(element, 'mouseover', noop)\n }\n }\n\n this._activeTrigger[TRIGGER_CLICK] = false\n this._activeTrigger[TRIGGER_FOCUS] = false\n this._activeTrigger[TRIGGER_HOVER] = false\n this._isHovered = null // it is a trick to support manual triggering\n\n const complete = () => {\n if (this._isWithActiveTrigger()) {\n return\n }\n\n if (!this._isHovered) {\n tip.remove()\n }\n\n this._element.removeAttribute('aria-describedby')\n EventHandler.trigger(this._element, this.constructor.eventName(EVENT_HIDDEN))\n\n this._disposePopper()\n }\n\n this._queueCallback(complete, this.tip, this._isAnimated())\n }\n\n update() {\n if (this._popper) {\n this._popper.update()\n }\n }\n\n // Protected\n _isWithContent() {\n return Boolean(this._getTitle())\n }\n\n _getTipElement() {\n if (!this.tip) {\n this.tip = this._createTipElement(this._newContent || this._getContentForTemplate())\n }\n\n return this.tip\n }\n\n _createTipElement(content) {\n const tip = this._getTemplateFactory(content).toHtml()\n\n // todo: remove this check on v6\n if (!tip) {\n return null\n }\n\n tip.classList.remove(CLASS_NAME_FADE, CLASS_NAME_SHOW)\n // todo: on v6 the following can be achieved with CSS only\n tip.classList.add(`bs-${this.constructor.NAME}-auto`)\n\n const tipId = getUID(this.constructor.NAME).toString()\n\n tip.setAttribute('id', tipId)\n\n if (this._isAnimated()) {\n tip.classList.add(CLASS_NAME_FADE)\n }\n\n return tip\n }\n\n setContent(content) {\n this._newContent = content\n if (this._isShown()) {\n this._disposePopper()\n this.show()\n }\n }\n\n _getTemplateFactory(content) {\n if (this._templateFactory) {\n this._templateFactory.changeContent(content)\n } else {\n this._templateFactory = new TemplateFactory({\n ...this._config,\n // the `content` var has to be after `this._config`\n // to override config.content in case of popover\n content,\n extraClass: this._resolvePossibleFunction(this._config.customClass)\n })\n }\n\n return this._templateFactory\n }\n\n _getContentForTemplate() {\n return {\n [SELECTOR_TOOLTIP_INNER]: this._getTitle()\n }\n }\n\n _getTitle() {\n return this._resolvePossibleFunction(this._config.title) || this._element.getAttribute('data-bs-original-title')\n }\n\n // Private\n _initializeOnDelegatedTarget(event) {\n return this.constructor.getOrCreateInstance(event.delegateTarget, this._getDelegateConfig())\n }\n\n _isAnimated() {\n return this._config.animation || (this.tip && this.tip.classList.contains(CLASS_NAME_FADE))\n }\n\n _isShown() {\n return this.tip && this.tip.classList.contains(CLASS_NAME_SHOW)\n }\n\n _createPopper(tip) {\n const placement = typeof this._config.placement === 'function' ?\n this._config.placement.call(this, tip, this._element) :\n this._config.placement\n const attachment = AttachmentMap[placement.toUpperCase()]\n return Popper.createPopper(this._element, tip, this._getPopperConfig(attachment))\n }\n\n _getOffset() {\n const { offset } = this._config\n\n if (typeof offset === 'string') {\n return offset.split(',').map(value => Number.parseInt(value, 10))\n }\n\n if (typeof offset === 'function') {\n return popperData => offset(popperData, this._element)\n }\n\n return offset\n }\n\n _resolvePossibleFunction(arg) {\n return typeof arg === 'function' ? arg.call(this._element) : arg\n }\n\n _getPopperConfig(attachment) {\n const defaultBsPopperConfig = {\n placement: attachment,\n modifiers: [\n {\n name: 'flip',\n options: {\n fallbackPlacements: this._config.fallbackPlacements\n }\n },\n {\n name: 'offset',\n options: {\n offset: this._getOffset()\n }\n },\n {\n name: 'preventOverflow',\n options: {\n boundary: this._config.boundary\n }\n },\n {\n name: 'arrow',\n options: {\n element: `.${this.constructor.NAME}-arrow`\n }\n },\n {\n name: 'preSetPlacement',\n enabled: true,\n phase: 'beforeMain',\n fn: data => {\n // Pre-set Popper's placement attribute in order to read the arrow sizes properly.\n // Otherwise, Popper mixes up the width and height dimensions since the initial arrow style is for top placement\n this._getTipElement().setAttribute('data-popper-placement', data.state.placement)\n }\n }\n ]\n }\n\n return {\n ...defaultBsPopperConfig,\n ...(typeof this._config.popperConfig === 'function' ? this._config.popperConfig(defaultBsPopperConfig) : this._config.popperConfig)\n }\n }\n\n _setListeners() {\n const triggers = this._config.trigger.split(' ')\n\n for (const trigger of triggers) {\n if (trigger === 'click') {\n EventHandler.on(this._element, this.constructor.eventName(EVENT_CLICK), this._config.selector, event => {\n const context = this._initializeOnDelegatedTarget(event)\n context.toggle()\n })\n } else if (trigger !== TRIGGER_MANUAL) {\n const eventIn = trigger === TRIGGER_HOVER ?\n this.constructor.eventName(EVENT_MOUSEENTER) :\n this.constructor.eventName(EVENT_FOCUSIN)\n const eventOut = trigger === TRIGGER_HOVER ?\n this.constructor.eventName(EVENT_MOUSELEAVE) :\n this.constructor.eventName(EVENT_FOCUSOUT)\n\n EventHandler.on(this._element, eventIn, this._config.selector, event => {\n const context = this._initializeOnDelegatedTarget(event)\n context._activeTrigger[event.type === 'focusin' ? TRIGGER_FOCUS : TRIGGER_HOVER] = true\n context._enter()\n })\n EventHandler.on(this._element, eventOut, this._config.selector, event => {\n const context = this._initializeOnDelegatedTarget(event)\n context._activeTrigger[event.type === 'focusout' ? TRIGGER_FOCUS : TRIGGER_HOVER] =\n context._element.contains(event.relatedTarget)\n\n context._leave()\n })\n }\n }\n\n this._hideModalHandler = () => {\n if (this._element) {\n this.hide()\n }\n }\n\n EventHandler.on(this._element.closest(SELECTOR_MODAL), EVENT_MODAL_HIDE, this._hideModalHandler)\n }\n\n _fixTitle() {\n const title = this._element.getAttribute('title')\n\n if (!title) {\n return\n }\n\n if (!this._element.getAttribute('aria-label') && !this._element.textContent.trim()) {\n this._element.setAttribute('aria-label', title)\n }\n\n this._element.setAttribute('data-bs-original-title', title) // DO NOT USE IT. Is only for backwards compatibility\n this._element.removeAttribute('title')\n }\n\n _enter() {\n if (this._isShown() || this._isHovered) {\n this._isHovered = true\n return\n }\n\n this._isHovered = true\n\n this._setTimeout(() => {\n if (this._isHovered) {\n this.show()\n }\n }, this._config.delay.show)\n }\n\n _leave() {\n if (this._isWithActiveTrigger()) {\n return\n }\n\n this._isHovered = false\n\n this._setTimeout(() => {\n if (!this._isHovered) {\n this.hide()\n }\n }, this._config.delay.hide)\n }\n\n _setTimeout(handler, timeout) {\n clearTimeout(this._timeout)\n this._timeout = setTimeout(handler, timeout)\n }\n\n _isWithActiveTrigger() {\n return Object.values(this._activeTrigger).includes(true)\n }\n\n _getConfig(config) {\n const dataAttributes = Manipulator.getDataAttributes(this._element)\n\n for (const dataAttribute of Object.keys(dataAttributes)) {\n if (DISALLOWED_ATTRIBUTES.has(dataAttribute)) {\n delete dataAttributes[dataAttribute]\n }\n }\n\n config = {\n ...dataAttributes,\n ...(typeof config === 'object' && config ? config : {})\n }\n config = this._mergeConfigObj(config)\n config = this._configAfterMerge(config)\n this._typeCheckConfig(config)\n return config\n }\n\n _configAfterMerge(config) {\n config.container = config.container === false ? document.body : getElement(config.container)\n\n if (typeof config.delay === 'number') {\n config.delay = {\n show: config.delay,\n hide: config.delay\n }\n }\n\n if (typeof config.title === 'number') {\n config.title = config.title.toString()\n }\n\n if (typeof config.content === 'number') {\n config.content = config.content.toString()\n }\n\n return config\n }\n\n _getDelegateConfig() {\n const config = {}\n\n for (const key in this._config) {\n if (this.constructor.Default[key] !== this._config[key]) {\n config[key] = this._config[key]\n }\n }\n\n config.selector = false\n config.trigger = 'manual'\n\n // In the future can be replaced with:\n // const keysWithDifferentValues = Object.entries(this._config).filter(entry => this.constructor.Default[entry[0]] !== this._config[entry[0]])\n // `Object.fromEntries(keysWithDifferentValues)`\n return config\n }\n\n _disposePopper() {\n if (this._popper) {\n this._popper.destroy()\n this._popper = null\n }\n }\n\n // Static\n static jQueryInterface(config) {\n return this.each(function () {\n const data = Tooltip.getOrCreateInstance(this, config)\n\n if (typeof config !== 'string') {\n return\n }\n\n if (typeof data[config] === 'undefined') {\n throw new TypeError(`No method named \"${config}\"`)\n }\n\n data[config]()\n })\n }\n}\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Tooltip)\n\nexport default Tooltip\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap (v5.2.2): popover.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport { defineJQueryPlugin } from './util/index'\nimport Tooltip from './tooltip'\n\n/**\n * Constants\n */\n\nconst NAME = 'popover'\n\nconst SELECTOR_TITLE = '.popover-header'\nconst SELECTOR_CONTENT = '.popover-body'\n\nconst Default = {\n ...Tooltip.Default,\n content: '',\n offset: [0, 8],\n placement: 'right',\n template: '<div class=\"popover\" role=\"tooltip\">' +\n '<div class=\"popover-arrow\"></div>' +\n '<h3 class=\"popover-header\"></h3>' +\n '<div class=\"popover-body\"></div>' +\n '</div>',\n trigger: 'click'\n}\n\nconst DefaultType = {\n ...Tooltip.DefaultType,\n content: '(null|string|element|function)'\n}\n\n/**\n * Class definition\n */\n\nclass Popover extends Tooltip {\n // Getters\n static get Default() {\n return Default\n }\n\n static get DefaultType() {\n return DefaultType\n }\n\n static get NAME() {\n return NAME\n }\n\n // Overrides\n _isWithContent() {\n return this._getTitle() || this._getContent()\n }\n\n // Private\n _getContentForTemplate() {\n return {\n [SELECTOR_TITLE]: this._getTitle(),\n [SELECTOR_CONTENT]: this._getContent()\n }\n }\n\n _getContent() {\n return this._resolvePossibleFunction(this._config.content)\n }\n\n // Static\n static jQueryInterface(config) {\n return this.each(function () {\n const data = Popover.getOrCreateInstance(this, config)\n\n if (typeof config !== 'string') {\n return\n }\n\n if (typeof data[config] === 'undefined') {\n throw new TypeError(`No method named \"${config}\"`)\n }\n\n data[config]()\n })\n }\n}\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Popover)\n\nexport default Popover\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap (v5.2.2): scrollspy.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport { defineJQueryPlugin, getElement, isDisabled, isVisible } from './util/index'\nimport EventHandler from './dom/event-handler'\nimport SelectorEngine from './dom/selector-engine'\nimport BaseComponent from './base-component'\n\n/**\n * Constants\n */\n\nconst NAME = 'scrollspy'\nconst DATA_KEY = 'bs.scrollspy'\nconst EVENT_KEY = `.${DATA_KEY}`\nconst DATA_API_KEY = '.data-api'\n\nconst EVENT_ACTIVATE = `activate${EVENT_KEY}`\nconst EVENT_CLICK = `click${EVENT_KEY}`\nconst EVENT_LOAD_DATA_API = `load${EVENT_KEY}${DATA_API_KEY}`\n\nconst CLASS_NAME_DROPDOWN_ITEM = 'dropdown-item'\nconst CLASS_NAME_ACTIVE = 'active'\n\nconst SELECTOR_DATA_SPY = '[data-bs-spy=\"scroll\"]'\nconst SELECTOR_TARGET_LINKS = '[href]'\nconst SELECTOR_NAV_LIST_GROUP = '.nav, .list-group'\nconst SELECTOR_NAV_LINKS = '.nav-link'\nconst SELECTOR_NAV_ITEMS = '.nav-item'\nconst SELECTOR_LIST_ITEMS = '.list-group-item'\nconst SELECTOR_LINK_ITEMS = `${SELECTOR_NAV_LINKS}, ${SELECTOR_NAV_ITEMS} > ${SELECTOR_NAV_LINKS}, ${SELECTOR_LIST_ITEMS}`\nconst SELECTOR_DROPDOWN = '.dropdown'\nconst SELECTOR_DROPDOWN_TOGGLE = '.dropdown-toggle'\n\nconst Default = {\n offset: null, // TODO: v6 @deprecated, keep it for backwards compatibility reasons\n rootMargin: '0px 0px -25%',\n smoothScroll: false,\n target: null,\n threshold: [0.1, 0.5, 1]\n}\n\nconst DefaultType = {\n offset: '(number|null)', // TODO v6 @deprecated, keep it for backwards compatibility reasons\n rootMargin: 'string',\n smoothScroll: 'boolean',\n target: 'element',\n threshold: 'array'\n}\n\n/**\n * Class definition\n */\n\nclass ScrollSpy extends BaseComponent {\n constructor(element, config) {\n super(element, config)\n\n // this._element is the observablesContainer and config.target the menu links wrapper\n this._targetLinks = new Map()\n this._observableSections = new Map()\n this._rootElement = getComputedStyle(this._element).overflowY === 'visible' ? null : this._element\n this._activeTarget = null\n this._observer = null\n this._previousScrollData = {\n visibleEntryTop: 0,\n parentScrollTop: 0\n }\n this.refresh() // initialize\n }\n\n // Getters\n static get Default() {\n return Default\n }\n\n static get DefaultType() {\n return DefaultType\n }\n\n static get NAME() {\n return NAME\n }\n\n // Public\n refresh() {\n this._initializeTargetsAndObservables()\n this._maybeEnableSmoothScroll()\n\n if (this._observer) {\n this._observer.disconnect()\n } else {\n this._observer = this._getNewObserver()\n }\n\n for (const section of this._observableSections.values()) {\n this._observer.observe(section)\n }\n }\n\n dispose() {\n this._observer.disconnect()\n super.dispose()\n }\n\n // Private\n _configAfterMerge(config) {\n // TODO: on v6 target should be given explicitly & remove the {target: 'ss-target'} case\n config.target = getElement(config.target) || document.body\n\n // TODO: v6 Only for backwards compatibility reasons. Use rootMargin only\n config.rootMargin = config.offset ? `${config.offset}px 0px -30%` : config.rootMargin\n\n if (typeof config.threshold === 'string') {\n config.threshold = config.threshold.split(',').map(value => Number.parseFloat(value))\n }\n\n return config\n }\n\n _maybeEnableSmoothScroll() {\n if (!this._config.smoothScroll) {\n return\n }\n\n // unregister any previous listeners\n EventHandler.off(this._config.target, EVENT_CLICK)\n\n EventHandler.on(this._config.target, EVENT_CLICK, SELECTOR_TARGET_LINKS, event => {\n const observableSection = this._observableSections.get(event.target.hash)\n if (observableSection) {\n event.preventDefault()\n const root = this._rootElement || window\n const height = observableSection.offsetTop - this._element.offsetTop\n if (root.scrollTo) {\n root.scrollTo({ top: height, behavior: 'smooth' })\n return\n }\n\n // Chrome 60 doesn't support `scrollTo`\n root.scrollTop = height\n }\n })\n }\n\n _getNewObserver() {\n const options = {\n root: this._rootElement,\n threshold: this._config.threshold,\n rootMargin: this._config.rootMargin\n }\n\n return new IntersectionObserver(entries => this._observerCallback(entries), options)\n }\n\n // The logic of selection\n _observerCallback(entries) {\n const targetElement = entry => this._targetLinks.get(`#${entry.target.id}`)\n const activate = entry => {\n this._previousScrollData.visibleEntryTop = entry.target.offsetTop\n this._process(targetElement(entry))\n }\n\n const parentScrollTop = (this._rootElement || document.documentElement).scrollTop\n const userScrollsDown = parentScrollTop >= this._previousScrollData.parentScrollTop\n this._previousScrollData.parentScrollTop = parentScrollTop\n\n for (const entry of entries) {\n if (!entry.isIntersecting) {\n this._activeTarget = null\n this._clearActiveClass(targetElement(entry))\n\n continue\n }\n\n const entryIsLowerThanPrevious = entry.target.offsetTop >= this._previousScrollData.visibleEntryTop\n // if we are scrolling down, pick the bigger offsetTop\n if (userScrollsDown && entryIsLowerThanPrevious) {\n activate(entry)\n // if parent isn't scrolled, let's keep the first visible item, breaking the iteration\n if (!parentScrollTop) {\n return\n }\n\n continue\n }\n\n // if we are scrolling up, pick the smallest offsetTop\n if (!userScrollsDown && !entryIsLowerThanPrevious) {\n activate(entry)\n }\n }\n }\n\n _initializeTargetsAndObservables() {\n this._targetLinks = new Map()\n this._observableSections = new Map()\n\n const targetLinks = SelectorEngine.find(SELECTOR_TARGET_LINKS, this._config.target)\n\n for (const anchor of targetLinks) {\n // ensure that the anchor has an id and is not disabled\n if (!anchor.hash || isDisabled(anchor)) {\n continue\n }\n\n const observableSection = SelectorEngine.findOne(anchor.hash, this._element)\n\n // ensure that the observableSection exists & is visible\n if (isVisible(observableSection)) {\n this._targetLinks.set(anchor.hash, anchor)\n this._observableSections.set(anchor.hash, observableSection)\n }\n }\n }\n\n _process(target) {\n if (this._activeTarget === target) {\n return\n }\n\n this._clearActiveClass(this._config.target)\n this._activeTarget = target\n target.classList.add(CLASS_NAME_ACTIVE)\n this._activateParents(target)\n\n EventHandler.trigger(this._element, EVENT_ACTIVATE, { relatedTarget: target })\n }\n\n _activateParents(target) {\n // Activate dropdown parents\n if (target.classList.contains(CLASS_NAME_DROPDOWN_ITEM)) {\n SelectorEngine.findOne(SELECTOR_DROPDOWN_TOGGLE, target.closest(SELECTOR_DROPDOWN))\n .classList.add(CLASS_NAME_ACTIVE)\n return\n }\n\n for (const listGroup of SelectorEngine.parents(target, SELECTOR_NAV_LIST_GROUP)) {\n // Set triggered links parents as active\n // With both <ul> and <nav> markup a parent is the previous sibling of any nav ancestor\n for (const item of SelectorEngine.prev(listGroup, SELECTOR_LINK_ITEMS)) {\n item.classList.add(CLASS_NAME_ACTIVE)\n }\n }\n }\n\n _clearActiveClass(parent) {\n parent.classList.remove(CLASS_NAME_ACTIVE)\n\n const activeNodes = SelectorEngine.find(`${SELECTOR_TARGET_LINKS}.${CLASS_NAME_ACTIVE}`, parent)\n for (const node of activeNodes) {\n node.classList.remove(CLASS_NAME_ACTIVE)\n }\n }\n\n // Static\n static jQueryInterface(config) {\n return this.each(function () {\n const data = ScrollSpy.getOrCreateInstance(this, config)\n\n if (typeof config !== 'string') {\n return\n }\n\n if (data[config] === undefined || config.startsWith('_') || config === 'constructor') {\n throw new TypeError(`No method named \"${config}\"`)\n }\n\n data[config]()\n })\n }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(window, EVENT_LOAD_DATA_API, () => {\n for (const spy of SelectorEngine.find(SELECTOR_DATA_SPY)) {\n ScrollSpy.getOrCreateInstance(spy)\n }\n})\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(ScrollSpy)\n\nexport default ScrollSpy\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap (v5.2.2): tab.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport { defineJQueryPlugin, getElementFromSelector, getNextActiveElement, isDisabled } from './util/index'\nimport EventHandler from './dom/event-handler'\nimport SelectorEngine from './dom/selector-engine'\nimport BaseComponent from './base-component'\n\n/**\n * Constants\n */\n\nconst NAME = 'tab'\nconst DATA_KEY = 'bs.tab'\nconst EVENT_KEY = `.${DATA_KEY}`\n\nconst EVENT_HIDE = `hide${EVENT_KEY}`\nconst EVENT_HIDDEN = `hidden${EVENT_KEY}`\nconst EVENT_SHOW = `show${EVENT_KEY}`\nconst EVENT_SHOWN = `shown${EVENT_KEY}`\nconst EVENT_CLICK_DATA_API = `click${EVENT_KEY}`\nconst EVENT_KEYDOWN = `keydown${EVENT_KEY}`\nconst EVENT_LOAD_DATA_API = `load${EVENT_KEY}`\n\nconst ARROW_LEFT_KEY = 'ArrowLeft'\nconst ARROW_RIGHT_KEY = 'ArrowRight'\nconst ARROW_UP_KEY = 'ArrowUp'\nconst ARROW_DOWN_KEY = 'ArrowDown'\n\nconst CLASS_NAME_ACTIVE = 'active'\nconst CLASS_NAME_FADE = 'fade'\nconst CLASS_NAME_SHOW = 'show'\nconst CLASS_DROPDOWN = 'dropdown'\n\nconst SELECTOR_DROPDOWN_TOGGLE = '.dropdown-toggle'\nconst SELECTOR_DROPDOWN_MENU = '.dropdown-menu'\nconst NOT_SELECTOR_DROPDOWN_TOGGLE = ':not(.dropdown-toggle)'\n\nconst SELECTOR_TAB_PANEL = '.list-group, .nav, [role=\"tablist\"]'\nconst SELECTOR_OUTER = '.nav-item, .list-group-item'\nconst SELECTOR_INNER = `.nav-link${NOT_SELECTOR_DROPDOWN_TOGGLE}, .list-group-item${NOT_SELECTOR_DROPDOWN_TOGGLE}, [role=\"tab\"]${NOT_SELECTOR_DROPDOWN_TOGGLE}`\nconst SELECTOR_DATA_TOGGLE = '[data-bs-toggle=\"tab\"], [data-bs-toggle=\"pill\"], [data-bs-toggle=\"list\"]' // todo:v6: could be only `tab`\nconst SELECTOR_INNER_ELEM = `${SELECTOR_INNER}, ${SELECTOR_DATA_TOGGLE}`\n\nconst SELECTOR_DATA_TOGGLE_ACTIVE = `.${CLASS_NAME_ACTIVE}[data-bs-toggle=\"tab\"], .${CLASS_NAME_ACTIVE}[data-bs-toggle=\"pill\"], .${CLASS_NAME_ACTIVE}[data-bs-toggle=\"list\"]`\n\n/**\n * Class definition\n */\n\nclass Tab extends BaseComponent {\n constructor(element) {\n super(element)\n this._parent = this._element.closest(SELECTOR_TAB_PANEL)\n\n if (!this._parent) {\n return\n // todo: should Throw exception on v6\n // throw new TypeError(`${element.outerHTML} has not a valid parent ${SELECTOR_INNER_ELEM}`)\n }\n\n // Set up initial aria attributes\n this._setInitialAttributes(this._parent, this._getChildren())\n\n EventHandler.on(this._element, EVENT_KEYDOWN, event => this._keydown(event))\n }\n\n // Getters\n static get NAME() {\n return NAME\n }\n\n // Public\n show() { // Shows this elem and deactivate the active sibling if exists\n const innerElem = this._element\n if (this._elemIsActive(innerElem)) {\n return\n }\n\n // Search for active tab on same parent to deactivate it\n const active = this._getActiveElem()\n\n const hideEvent = active ?\n EventHandler.trigger(active, EVENT_HIDE, { relatedTarget: innerElem }) :\n null\n\n const showEvent = EventHandler.trigger(innerElem, EVENT_SHOW, { relatedTarget: active })\n\n if (showEvent.defaultPrevented || (hideEvent && hideEvent.defaultPrevented)) {\n return\n }\n\n this._deactivate(active, innerElem)\n this._activate(innerElem, active)\n }\n\n // Private\n _activate(element, relatedElem) {\n if (!element) {\n return\n }\n\n element.classList.add(CLASS_NAME_ACTIVE)\n\n this._activate(getElementFromSelector(element)) // Search and activate/show the proper section\n\n const complete = () => {\n if (element.getAttribute('role') !== 'tab') {\n element.classList.add(CLASS_NAME_SHOW)\n return\n }\n\n element.removeAttribute('tabindex')\n element.setAttribute('aria-selected', true)\n this._toggleDropDown(element, true)\n EventHandler.trigger(element, EVENT_SHOWN, {\n relatedTarget: relatedElem\n })\n }\n\n this._queueCallback(complete, element, element.classList.contains(CLASS_NAME_FADE))\n }\n\n _deactivate(element, relatedElem) {\n if (!element) {\n return\n }\n\n element.classList.remove(CLASS_NAME_ACTIVE)\n element.blur()\n\n this._deactivate(getElementFromSelector(element)) // Search and deactivate the shown section too\n\n const complete = () => {\n if (element.getAttribute('role') !== 'tab') {\n element.classList.remove(CLASS_NAME_SHOW)\n return\n }\n\n element.setAttribute('aria-selected', false)\n element.setAttribute('tabindex', '-1')\n this._toggleDropDown(element, false)\n EventHandler.trigger(element, EVENT_HIDDEN, { relatedTarget: relatedElem })\n }\n\n this._queueCallback(complete, element, element.classList.contains(CLASS_NAME_FADE))\n }\n\n _keydown(event) {\n if (!([ARROW_LEFT_KEY, ARROW_RIGHT_KEY, ARROW_UP_KEY, ARROW_DOWN_KEY].includes(event.key))) {\n return\n }\n\n event.stopPropagation()// stopPropagation/preventDefault both added to support up/down keys without scrolling the page\n event.preventDefault()\n const isNext = [ARROW_RIGHT_KEY, ARROW_DOWN_KEY].includes(event.key)\n const nextActiveElement = getNextActiveElement(this._getChildren().filter(element => !isDisabled(element)), event.target, isNext, true)\n\n if (nextActiveElement) {\n nextActiveElement.focus({ preventScroll: true })\n Tab.getOrCreateInstance(nextActiveElement).show()\n }\n }\n\n _getChildren() { // collection of inner elements\n return SelectorEngine.find(SELECTOR_INNER_ELEM, this._parent)\n }\n\n _getActiveElem() {\n return this._getChildren().find(child => this._elemIsActive(child)) || null\n }\n\n _setInitialAttributes(parent, children) {\n this._setAttributeIfNotExists(parent, 'role', 'tablist')\n\n for (const child of children) {\n this._setInitialAttributesOnChild(child)\n }\n }\n\n _setInitialAttributesOnChild(child) {\n child = this._getInnerElement(child)\n const isActive = this._elemIsActive(child)\n const outerElem = this._getOuterElement(child)\n child.setAttribute('aria-selected', isActive)\n\n if (outerElem !== child) {\n this._setAttributeIfNotExists(outerElem, 'role', 'presentation')\n }\n\n if (!isActive) {\n child.setAttribute('tabindex', '-1')\n }\n\n this._setAttributeIfNotExists(child, 'role', 'tab')\n\n // set attributes to the related panel too\n this._setInitialAttributesOnTargetPanel(child)\n }\n\n _setInitialAttributesOnTargetPanel(child) {\n const target = getElementFromSelector(child)\n\n if (!target) {\n return\n }\n\n this._setAttributeIfNotExists(target, 'role', 'tabpanel')\n\n if (child.id) {\n this._setAttributeIfNotExists(target, 'aria-labelledby', `#${child.id}`)\n }\n }\n\n _toggleDropDown(element, open) {\n const outerElem = this._getOuterElement(element)\n if (!outerElem.classList.contains(CLASS_DROPDOWN)) {\n return\n }\n\n const toggle = (selector, className) => {\n const element = SelectorEngine.findOne(selector, outerElem)\n if (element) {\n element.classList.toggle(className, open)\n }\n }\n\n toggle(SELECTOR_DROPDOWN_TOGGLE, CLASS_NAME_ACTIVE)\n toggle(SELECTOR_DROPDOWN_MENU, CLASS_NAME_SHOW)\n outerElem.setAttribute('aria-expanded', open)\n }\n\n _setAttributeIfNotExists(element, attribute, value) {\n if (!element.hasAttribute(attribute)) {\n element.setAttribute(attribute, value)\n }\n }\n\n _elemIsActive(elem) {\n return elem.classList.contains(CLASS_NAME_ACTIVE)\n }\n\n // Try to get the inner element (usually the .nav-link)\n _getInnerElement(elem) {\n return elem.matches(SELECTOR_INNER_ELEM) ? elem : SelectorEngine.findOne(SELECTOR_INNER_ELEM, elem)\n }\n\n // Try to get the outer element (usually the .nav-item)\n _getOuterElement(elem) {\n return elem.closest(SELECTOR_OUTER) || elem\n }\n\n // Static\n static jQueryInterface(config) {\n return this.each(function () {\n const data = Tab.getOrCreateInstance(this)\n\n if (typeof config !== 'string') {\n return\n }\n\n if (data[config] === undefined || config.startsWith('_') || config === 'constructor') {\n throw new TypeError(`No method named \"${config}\"`)\n }\n\n data[config]()\n })\n }\n}\n\n/**\n * Data API implementation\n */\n\nEventHandler.on(document, EVENT_CLICK_DATA_API, SELECTOR_DATA_TOGGLE, function (event) {\n if (['A', 'AREA'].includes(this.tagName)) {\n event.preventDefault()\n }\n\n if (isDisabled(this)) {\n return\n }\n\n Tab.getOrCreateInstance(this).show()\n})\n\n/**\n * Initialize on focus\n */\nEventHandler.on(window, EVENT_LOAD_DATA_API, () => {\n for (const element of SelectorEngine.find(SELECTOR_DATA_TOGGLE_ACTIVE)) {\n Tab.getOrCreateInstance(element)\n }\n})\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Tab)\n\nexport default Tab\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap (v5.2.2): toast.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport { defineJQueryPlugin, reflow } from './util/index'\nimport EventHandler from './dom/event-handler'\nimport BaseComponent from './base-component'\nimport { enableDismissTrigger } from './util/component-functions'\n\n/**\n * Constants\n */\n\nconst NAME = 'toast'\nconst DATA_KEY = 'bs.toast'\nconst EVENT_KEY = `.${DATA_KEY}`\n\nconst EVENT_MOUSEOVER = `mouseover${EVENT_KEY}`\nconst EVENT_MOUSEOUT = `mouseout${EVENT_KEY}`\nconst EVENT_FOCUSIN = `focusin${EVENT_KEY}`\nconst EVENT_FOCUSOUT = `focusout${EVENT_KEY}`\nconst EVENT_HIDE = `hide${EVENT_KEY}`\nconst EVENT_HIDDEN = `hidden${EVENT_KEY}`\nconst EVENT_SHOW = `show${EVENT_KEY}`\nconst EVENT_SHOWN = `shown${EVENT_KEY}`\n\nconst CLASS_NAME_FADE = 'fade'\nconst CLASS_NAME_HIDE = 'hide' // @deprecated - kept here only for backwards compatibility\nconst CLASS_NAME_SHOW = 'show'\nconst CLASS_NAME_SHOWING = 'showing'\n\nconst DefaultType = {\n animation: 'boolean',\n autohide: 'boolean',\n delay: 'number'\n}\n\nconst Default = {\n animation: true,\n autohide: true,\n delay: 5000\n}\n\n/**\n * Class definition\n */\n\nclass Toast extends BaseComponent {\n constructor(element, config) {\n super(element, config)\n\n this._timeout = null\n this._hasMouseInteraction = false\n this._hasKeyboardInteraction = false\n this._setListeners()\n }\n\n // Getters\n static get Default() {\n return Default\n }\n\n static get DefaultType() {\n return DefaultType\n }\n\n static get NAME() {\n return NAME\n }\n\n // Public\n show() {\n const showEvent = EventHandler.trigger(this._element, EVENT_SHOW)\n\n if (showEvent.defaultPrevented) {\n return\n }\n\n this._clearTimeout()\n\n if (this._config.animation) {\n this._element.classList.add(CLASS_NAME_FADE)\n }\n\n const complete = () => {\n this._element.classList.remove(CLASS_NAME_SHOWING)\n EventHandler.trigger(this._element, EVENT_SHOWN)\n\n this._maybeScheduleHide()\n }\n\n this._element.classList.remove(CLASS_NAME_HIDE) // @deprecated\n reflow(this._element)\n this._element.classList.add(CLASS_NAME_SHOW, CLASS_NAME_SHOWING)\n\n this._queueCallback(complete, this._element, this._config.animation)\n }\n\n hide() {\n if (!this.isShown()) {\n return\n }\n\n const hideEvent = EventHandler.trigger(this._element, EVENT_HIDE)\n\n if (hideEvent.defaultPrevented) {\n return\n }\n\n const complete = () => {\n this._element.classList.add(CLASS_NAME_HIDE) // @deprecated\n this._element.classList.remove(CLASS_NAME_SHOWING, CLASS_NAME_SHOW)\n EventHandler.trigger(this._element, EVENT_HIDDEN)\n }\n\n this._element.classList.add(CLASS_NAME_SHOWING)\n this._queueCallback(complete, this._element, this._config.animation)\n }\n\n dispose() {\n this._clearTimeout()\n\n if (this.isShown()) {\n this._element.classList.remove(CLASS_NAME_SHOW)\n }\n\n super.dispose()\n }\n\n isShown() {\n return this._element.classList.contains(CLASS_NAME_SHOW)\n }\n\n // Private\n\n _maybeScheduleHide() {\n if (!this._config.autohide) {\n return\n }\n\n if (this._hasMouseInteraction || this._hasKeyboardInteraction) {\n return\n }\n\n this._timeout = setTimeout(() => {\n this.hide()\n }, this._config.delay)\n }\n\n _onInteraction(event, isInteracting) {\n switch (event.type) {\n case 'mouseover':\n case 'mouseout': {\n this._hasMouseInteraction = isInteracting\n break\n }\n\n case 'focusin':\n case 'focusout': {\n this._hasKeyboardInteraction = isInteracting\n break\n }\n\n default: {\n break\n }\n }\n\n if (isInteracting) {\n this._clearTimeout()\n return\n }\n\n const nextElement = event.relatedTarget\n if (this._element === nextElement || this._element.contains(nextElement)) {\n return\n }\n\n this._maybeScheduleHide()\n }\n\n _setListeners() {\n EventHandler.on(this._element, EVENT_MOUSEOVER, event => this._onInteraction(event, true))\n EventHandler.on(this._element, EVENT_MOUSEOUT, event => this._onInteraction(event, false))\n EventHandler.on(this._element, EVENT_FOCUSIN, event => this._onInteraction(event, true))\n EventHandler.on(this._element, EVENT_FOCUSOUT, event => this._onInteraction(event, false))\n }\n\n _clearTimeout() {\n clearTimeout(this._timeout)\n this._timeout = null\n }\n\n // Static\n static jQueryInterface(config) {\n return this.each(function () {\n const data = Toast.getOrCreateInstance(this, config)\n\n if (typeof config === 'string') {\n if (typeof data[config] === 'undefined') {\n throw new TypeError(`No method named \"${config}\"`)\n }\n\n data[config](this)\n }\n })\n }\n}\n\n/**\n * Data API implementation\n */\n\nenableDismissTrigger(Toast)\n\n/**\n * jQuery\n */\n\ndefineJQueryPlugin(Toast)\n\nexport default Toast\n","/**\n * --------------------------------------------------------------------------\n * Bootstrap (v5.2.2): index.umd.js\n * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)\n * --------------------------------------------------------------------------\n */\n\nimport Alert from './src/alert'\nimport Button from './src/button'\nimport Carousel from './src/carousel'\nimport Collapse from './src/collapse'\nimport Dropdown from './src/dropdown'\nimport Modal from './src/modal'\nimport Offcanvas from './src/offcanvas'\nimport Popover from './src/popover'\nimport ScrollSpy from './src/scrollspy'\nimport Tab from './src/tab'\nimport Toast from './src/toast'\nimport Tooltip from './src/tooltip'\n\nexport default {\n Alert,\n Button,\n Carousel,\n Collapse,\n Dropdown,\n Modal,\n Offcanvas,\n Popover,\n ScrollSpy,\n Tab,\n Toast,\n 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992px){.navbar-expand-lg{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand-lg .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand-lg .navbar-nav .dropdown-menu{position:absolute}.navbar-expand-lg .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand-lg .navbar-nav-scroll{overflow:visible}.navbar-expand-lg .navbar-collapse{display:flex !important;display:-webkit-flex !important;flex-basis:auto;-webkit-flex-basis:auto}.navbar-expand-lg .navbar-toggler{display:none}.navbar-expand-lg .offcanvas{position:static;z-index:auto;flex-grow:1;-webkit-flex-grow:1;width:auto !important;height:auto !important;visibility:visible !important;background-color:transparent !important;border:0 !important;transform:none !important;transition:none}.navbar-expand-lg .offcanvas .offcanvas-header{display:none}.navbar-expand-lg .offcanvas 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!important;transform:none !important;transition:none}.navbar-expand-xl .offcanvas .offcanvas-header{display:none}.navbar-expand-xl .offcanvas .offcanvas-body{display:flex;display:-webkit-flex;flex-grow:0;-webkit-flex-grow:0;padding:0;overflow-y:visible}}@media (min-width: 1400px){.navbar-expand-xxl{flex-wrap:nowrap;-webkit-flex-wrap:nowrap;justify-content:flex-start;-webkit-justify-content:flex-start}.navbar-expand-xxl .navbar-nav{flex-direction:row;-webkit-flex-direction:row}.navbar-expand-xxl .navbar-nav .dropdown-menu{position:absolute}.navbar-expand-xxl .navbar-nav .nav-link{padding-right:var(--bs-navbar-nav-link-padding-x);padding-left:var(--bs-navbar-nav-link-padding-x)}.navbar-expand-xxl .navbar-nav-scroll{overflow:visible}.navbar-expand-xxl .navbar-collapse{display:flex !important;display:-webkit-flex !important;flex-basis:auto;-webkit-flex-basis:auto}.navbar-expand-xxl .navbar-toggler{display:none}.navbar-expand-xxl 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viewBox='0 0 30 30'%3e%3cpath stroke='rgba%28255,255,255,0.75%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e")}.card{--bs-card-spacer-y: 1rem;--bs-card-spacer-x: 1rem;--bs-card-title-spacer-y: .5rem;--bs-card-border-width: 1px;--bs-card-border-color: var(--bs-border-color-translucent);--bs-card-border-radius: .375rem;--bs-card-box-shadow: ;--bs-card-inner-border-radius: calc(.375rem - 1px);--bs-card-cap-padding-y: .5rem;--bs-card-cap-padding-x: 1rem;--bs-card-cap-bg: rgba(0,0,0,0.03);--bs-card-cap-color: ;--bs-card-height: ;--bs-card-color: ;--bs-card-bg: #fff;--bs-card-img-overlay-padding: 1rem;--bs-card-group-margin: .75rem;position:relative;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;min-width:0;height:var(--bs-card-height);word-wrap:break-word;background-color:var(--bs-card-bg);background-clip:border-box;border:var(--bs-card-border-width) solid 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var(--bs-accordion-border-width)) 0 var(--bs-accordion-border-color)}.accordion-button:not(.collapsed)::after{background-image:var(--bs-accordion-btn-active-icon);transform:var(--bs-accordion-btn-icon-transform)}.accordion-button::after{flex-shrink:0;-webkit-flex-shrink:0;width:var(--bs-accordion-btn-icon-width);height:var(--bs-accordion-btn-icon-width);margin-left:auto;content:"";background-image:var(--bs-accordion-btn-icon);background-repeat:no-repeat;background-size:var(--bs-accordion-btn-icon-width);transition:var(--bs-accordion-btn-icon-transition)}@media (prefers-reduced-motion: reduce){.accordion-button::after{transition:none}}.accordion-button:hover{z-index:2}.accordion-button:focus{z-index:3;border-color:var(--bs-accordion-btn-focus-border-color);outline:0;box-shadow:var(--bs-accordion-btn-focus-box-shadow)}.accordion-header{margin-bottom:0}.accordion-item{color:var(--bs-accordion-color);background-color:var(--bs-accordion-bg);border:var(--bs-accordion-border-width) solid var(--bs-accordion-border-color)}.accordion-item:first-of-type{border-top-left-radius:var(--bs-accordion-border-radius);border-top-right-radius:var(--bs-accordion-border-radius)}.accordion-item:first-of-type .accordion-button{border-top-left-radius:var(--bs-accordion-inner-border-radius);border-top-right-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:not(:first-of-type){border-top:0}.accordion-item:last-of-type{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-item:last-of-type .accordion-button.collapsed{border-bottom-right-radius:var(--bs-accordion-inner-border-radius);border-bottom-left-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:last-of-type .accordion-collapse{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-body{padding:var(--bs-accordion-body-padding-y) var(--bs-accordion-body-padding-x)}.accordion-flush .accordion-collapse{border-width:0}.accordion-flush .accordion-item{border-right:0;border-left:0;border-radius:0}.accordion-flush .accordion-item:first-child{border-top:0}.accordion-flush .accordion-item:last-child{border-bottom:0}.accordion-flush .accordion-item .accordion-button,.accordion-flush .accordion-item .accordion-button.collapsed{border-radius:0}.breadcrumb{--bs-breadcrumb-padding-x: 0;--bs-breadcrumb-padding-y: 0;--bs-breadcrumb-margin-bottom: 1rem;--bs-breadcrumb-bg: ;--bs-breadcrumb-border-radius: ;--bs-breadcrumb-divider-color: #777;--bs-breadcrumb-item-padding-x: .5rem;--bs-breadcrumb-item-active-color: #777;display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding:var(--bs-breadcrumb-padding-y) var(--bs-breadcrumb-padding-x);margin-bottom:var(--bs-breadcrumb-margin-bottom);font-size:var(--bs-breadcrumb-font-size);list-style:none;background-color:var(--bs-breadcrumb-bg);border-radius:var(--bs-breadcrumb-border-radius)}.breadcrumb-item+.breadcrumb-item{padding-left:var(--bs-breadcrumb-item-padding-x)}.breadcrumb-item+.breadcrumb-item::before{float:left;padding-right:var(--bs-breadcrumb-item-padding-x);color:var(--bs-breadcrumb-divider-color);content:var(--bs-breadcrumb-divider, "/") /* rtl: var(--bs-breadcrumb-divider, "/") */}.breadcrumb-item.active{color:var(--bs-breadcrumb-item-active-color)}.pagination{--bs-pagination-padding-x: .75rem;--bs-pagination-padding-y: .375rem;--bs-pagination-font-size:1rem;--bs-pagination-color: var(--bs-link-color);--bs-pagination-bg: #fff;--bs-pagination-border-width: 1px;--bs-pagination-border-color: #dee2e6;--bs-pagination-border-radius: .375rem;--bs-pagination-hover-color: var(--bs-link-hover-color);--bs-pagination-hover-bg: #eee;--bs-pagination-hover-border-color: #dee2e6;--bs-pagination-focus-color: var(--bs-link-hover-color);--bs-pagination-focus-bg: #eee;--bs-pagination-focus-box-shadow: 0 0 0 .25rem rgba(68,110,155,0.25);--bs-pagination-active-color: #fff;--bs-pagination-active-bg: #446e9b;--bs-pagination-active-border-color: #446e9b;--bs-pagination-disabled-color: #777;--bs-pagination-disabled-bg: #fff;--bs-pagination-disabled-border-color: #dee2e6;display:flex;display:-webkit-flex;padding-left:0;list-style:none}.page-link{position:relative;display:block;padding:var(--bs-pagination-padding-y) var(--bs-pagination-padding-x);font-size:var(--bs-pagination-font-size);color:var(--bs-pagination-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-pagination-bg);border:var(--bs-pagination-border-width) solid var(--bs-pagination-border-color);transition:color 0.15s ease-in-out,background-color 0.15s ease-in-out,border-color 0.15s ease-in-out,box-shadow 0.15s ease-in-out}@media (prefers-reduced-motion: reduce){.page-link{transition:none}}.page-link:hover{z-index:2;color:var(--bs-pagination-hover-color);background-color:var(--bs-pagination-hover-bg);border-color:var(--bs-pagination-hover-border-color)}.page-link:focus{z-index:3;color:var(--bs-pagination-focus-color);background-color:var(--bs-pagination-focus-bg);outline:0;box-shadow:var(--bs-pagination-focus-box-shadow)}.page-link.active,.active>.page-link{z-index:3;color:var(--bs-pagination-active-color);background-color:var(--bs-pagination-active-bg);border-color:var(--bs-pagination-active-border-color)}.page-link.disabled,.disabled>.page-link{color:var(--bs-pagination-disabled-color);pointer-events:none;background-color:var(--bs-pagination-disabled-bg);border-color:var(--bs-pagination-disabled-border-color)}.page-item:not(:first-child) .page-link{margin-left:-1px}.page-item:first-child .page-link{border-top-left-radius:var(--bs-pagination-border-radius);border-bottom-left-radius:var(--bs-pagination-border-radius)}.page-item:last-child .page-link{border-top-right-radius:var(--bs-pagination-border-radius);border-bottom-right-radius:var(--bs-pagination-border-radius)}.pagination-lg{--bs-pagination-padding-x: 1.5rem;--bs-pagination-padding-y: .75rem;--bs-pagination-font-size:1.25rem;--bs-pagination-border-radius: .5rem}.pagination-sm{--bs-pagination-padding-x: .5rem;--bs-pagination-padding-y: .25rem;--bs-pagination-font-size:.875rem;--bs-pagination-border-radius: .25rem}.badge{--bs-badge-padding-x: .65em;--bs-badge-padding-y: .35em;--bs-badge-font-size:.75em;--bs-badge-font-weight: 700;--bs-badge-color: #fff;--bs-badge-border-radius: .375rem;display:inline-block;padding:var(--bs-badge-padding-y) var(--bs-badge-padding-x);font-size:var(--bs-badge-font-size);font-weight:var(--bs-badge-font-weight);line-height:1;color:var(--bs-badge-color);text-align:center;white-space:nowrap;vertical-align:baseline;border-radius:var(--bs-badge-border-radius)}.badge:empty{display:none}.btn .badge{position:relative;top:-1px}.alert{--bs-alert-bg: transparent;--bs-alert-padding-x: 1rem;--bs-alert-padding-y: 1rem;--bs-alert-margin-bottom: 1rem;--bs-alert-color: inherit;--bs-alert-border-color: transparent;--bs-alert-border: 1px solid var(--bs-alert-border-color);--bs-alert-border-radius: .375rem;position:relative;padding:var(--bs-alert-padding-y) var(--bs-alert-padding-x);margin-bottom:var(--bs-alert-margin-bottom);color:var(--bs-alert-color);background-color:var(--bs-alert-bg);border:var(--bs-alert-border);border-radius:var(--bs-alert-border-radius)}.alert-heading{color:inherit}.alert-link{font-weight:700}.alert-dismissible{padding-right:3rem}.alert-dismissible .btn-close{position:absolute;top:0;right:0;z-index:2;padding:1.25rem 1rem}.alert-default{--bs-alert-color: #5c5c5c;--bs-alert-bg: #ebebeb;--bs-alert-border-color: #e0e0e0}.alert-default .alert-link{color:#4a4a4a}.alert-primary{--bs-alert-color: #29425d;--bs-alert-bg: #dae2eb;--bs-alert-border-color: #c7d4e1}.alert-primary .alert-link{color:#21354a}.alert-secondary{--bs-alert-color: #5c5c5c;--bs-alert-bg: #ebebeb;--bs-alert-border-color: #e0e0e0}.alert-secondary .alert-link{color:#4a4a4a}.alert-success{--bs-alert-color: #246d14;--bs-alert-bg: #d8f0d3;--bs-alert-border-color: #c5e9bc}.alert-success .alert-link{color:#1d5710}.alert-info{--bs-alert-color: #1f5c92;--bs-alert-bg: #d6ebfd;--bs-alert-border-color: #c2e0fb}.alert-info .alert-link{color:#194a75}.alert-warning{--bs-alert-color: #7f4600;--bs-alert-bg: #f6e3cc;--bs-alert-border-color: #f2d6b3}.alert-warning .alert-link{color:#663800}.alert-danger{--bs-alert-color: #7b0100;--bs-alert-bg: #f5cccc;--bs-alert-border-color: #f0b3b3}.alert-danger .alert-link{color:#620100}.alert-light{--bs-alert-color: #8f8f8f;--bs-alert-bg: #fcfcfc;--bs-alert-border-color: #fafafa}.alert-light .alert-link{color:#727272}.alert-dark{--bs-alert-color: #1f1f1f;--bs-alert-bg: #d6d6d6;--bs-alert-border-color: #c2c2c2}.alert-dark .alert-link{color:#191919}@keyframes progress-bar-stripes{0%{background-position-x:1rem}}.progress{--bs-progress-height: 1rem;--bs-progress-font-size:.75rem;--bs-progress-bg: #eee;--bs-progress-border-radius: .375rem;--bs-progress-box-shadow: inset 0 1px 2px rgba(0,0,0,0.075);--bs-progress-bar-color: #fff;--bs-progress-bar-bg: #446e9b;--bs-progress-bar-transition: width 0.6s ease;display:flex;display:-webkit-flex;height:var(--bs-progress-height);overflow:hidden;font-size:var(--bs-progress-font-size);background-color:var(--bs-progress-bg);border-radius:var(--bs-progress-border-radius)}.progress-bar{display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;justify-content:center;-webkit-justify-content:center;overflow:hidden;color:var(--bs-progress-bar-color);text-align:center;white-space:nowrap;background-color:var(--bs-progress-bar-bg);transition:var(--bs-progress-bar-transition)}@media (prefers-reduced-motion: reduce){.progress-bar{transition:none}}.progress-bar-striped{background-image:linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-size:var(--bs-progress-height) var(--bs-progress-height)}.progress-bar-animated{animation:1s linear infinite progress-bar-stripes}@media (prefers-reduced-motion: reduce){.progress-bar-animated{animation:none}}.list-group{--bs-list-group-color: #2d2d2d;--bs-list-group-bg: #fff;--bs-list-group-border-color: rgba(0,0,0,0.125);--bs-list-group-border-width: 1px;--bs-list-group-border-radius: .375rem;--bs-list-group-item-padding-x: 1rem;--bs-list-group-item-padding-y: .5rem;--bs-list-group-action-color: #495057;--bs-list-group-action-hover-color: #495057;--bs-list-group-action-hover-bg: #f8f9fa;--bs-list-group-action-active-color: #777;--bs-list-group-action-active-bg: #eee;--bs-list-group-disabled-color: #777;--bs-list-group-disabled-bg: #fff;--bs-list-group-active-color: #fff;--bs-list-group-active-bg: #446e9b;--bs-list-group-active-border-color: #446e9b;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;padding-left:0;margin-bottom:0;border-radius:var(--bs-list-group-border-radius)}.list-group-numbered{list-style-type:none;counter-reset:section}.list-group-numbered>.list-group-item::before{content:counters(section, ".") 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";counter-increment:section}.list-group-item-action{width:100%;color:var(--bs-list-group-action-color);text-align:inherit}.list-group-item-action:hover,.list-group-item-action:focus{z-index:1;color:var(--bs-list-group-action-hover-color);text-decoration:none;background-color:var(--bs-list-group-action-hover-bg)}.list-group-item-action:active{color:var(--bs-list-group-action-active-color);background-color:var(--bs-list-group-action-active-bg)}.list-group-item{position:relative;display:block;padding:var(--bs-list-group-item-padding-y) var(--bs-list-group-item-padding-x);color:var(--bs-list-group-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-list-group-bg);border:var(--bs-list-group-border-width) solid var(--bs-list-group-border-color)}.list-group-item:first-child{border-top-left-radius:inherit;border-top-right-radius:inherit}.list-group-item:last-child{border-bottom-right-radius:inherit;border-bottom-left-radius:inherit}.list-group-item.disabled,.list-group-item:disabled{color:var(--bs-list-group-disabled-color);pointer-events:none;background-color:var(--bs-list-group-disabled-bg)}.list-group-item.active{z-index:2;color:var(--bs-list-group-active-color);background-color:var(--bs-list-group-active-bg);border-color:var(--bs-list-group-active-border-color)}.list-group-item+.list-group-item{border-top-width:0}.list-group-item+.list-group-item.active{margin-top:calc(-1 * var(--bs-list-group-border-width));border-top-width:var(--bs-list-group-border-width)}.list-group-horizontal{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal>.list-group-item.active{margin-top:0}.list-group-horizontal>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}@media (min-width: 576px){.list-group-horizontal-sm{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-sm>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-sm>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-sm>.list-group-item.active{margin-top:0}.list-group-horizontal-sm>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-sm>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 768px){.list-group-horizontal-md{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-md>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-md>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-md>.list-group-item.active{margin-top:0}.list-group-horizontal-md>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-md>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 992px){.list-group-horizontal-lg{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-lg>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-lg>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-lg>.list-group-item.active{margin-top:0}.list-group-horizontal-lg>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-lg>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 1200px){.list-group-horizontal-xl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xl>.list-group-item.active{margin-top:0}.list-group-horizontal-xl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media (min-width: 1400px){.list-group-horizontal-xxl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xxl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xxl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xxl>.list-group-item.active{margin-top:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item.active{margin-left:calc(-1 * var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}.list-group-flush{border-radius:0}.list-group-flush>.list-group-item{border-width:0 0 var(--bs-list-group-border-width)}.list-group-flush>.list-group-item:last-child{border-bottom-width:0}.list-group-item-default{color:#5c5c5c;background-color:#ebebeb}.list-group-item-default.list-group-item-action:hover,.list-group-item-default.list-group-item-action:focus{color:#5c5c5c;background-color:#d4d4d4}.list-group-item-default.list-group-item-action.active{color:#fff;background-color:#5c5c5c;border-color:#5c5c5c}.list-group-item-primary{color:#29425d;background-color:#dae2eb}.list-group-item-primary.list-group-item-action:hover,.list-group-item-primary.list-group-item-action:focus{color:#29425d;background-color:#c4cbd4}.list-group-item-primary.list-group-item-action.active{color:#fff;background-color:#29425d;border-color:#29425d}.list-group-item-secondary{color:#5c5c5c;background-color:#ebebeb}.list-group-item-secondary.list-group-item-action:hover,.list-group-item-secondary.list-group-item-action:focus{color:#5c5c5c;background-color:#d4d4d4}.list-group-item-secondary.list-group-item-action.active{color:#fff;background-color:#5c5c5c;border-color:#5c5c5c}.list-group-item-success{color:#246d14;background-color:#d8f0d3}.list-group-item-success.list-group-item-action:hover,.list-group-item-success.list-group-item-action:focus{color:#246d14;background-color:#c2d8be}.list-group-item-success.list-group-item-action.active{color:#fff;background-color:#246d14;border-color:#246d14}.list-group-item-info{color:#1f5c92;background-color:#d6ebfd}.list-group-item-info.list-group-item-action:hover,.list-group-item-info.list-group-item-action:focus{color:#1f5c92;background-color:#c1d4e4}.list-group-item-info.list-group-item-action.active{color:#fff;background-color:#1f5c92;border-color:#1f5c92}.list-group-item-warning{color:#7f4600;background-color:#f6e3cc}.list-group-item-warning.list-group-item-action:hover,.list-group-item-warning.list-group-item-action:focus{color:#7f4600;background-color:#ddccb8}.list-group-item-warning.list-group-item-action.active{color:#fff;background-color:#7f4600;border-color:#7f4600}.list-group-item-danger{color:#7b0100;background-color:#f5cccc}.list-group-item-danger.list-group-item-action:hover,.list-group-item-danger.list-group-item-action:focus{color:#7b0100;background-color:#ddb8b8}.list-group-item-danger.list-group-item-action.active{color:#fff;background-color:#7b0100;border-color:#7b0100}.list-group-item-light{color:#8f8f8f;background-color:#fcfcfc}.list-group-item-light.list-group-item-action:hover,.list-group-item-light.list-group-item-action:focus{color:#8f8f8f;background-color:#e3e3e3}.list-group-item-light.list-group-item-action.active{color:#fff;background-color:#8f8f8f;border-color:#8f8f8f}.list-group-item-dark{color:#1f1f1f;background-color:#d6d6d6}.list-group-item-dark.list-group-item-action:hover,.list-group-item-dark.list-group-item-action:focus{color:#1f1f1f;background-color:#c1c1c1}.list-group-item-dark.list-group-item-action.active{color:#fff;background-color:#1f1f1f;border-color:#1f1f1f}.btn-close{box-sizing:content-box;width:1em;height:1em;padding:.25em .25em;color:#000;background:transparent url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23000'%3e%3cpath d='M.293.293a1 1 0 0 1 1.414 0L8 6.586 14.293.293a1 1 0 1 1 1.414 1.414L9.414 8l6.293 6.293a1 1 0 0 1-1.414 1.414L8 9.414l-6.293 6.293a1 1 0 0 1-1.414-1.414L6.586 8 .293 1.707a1 1 0 0 1 0-1.414z'/%3e%3c/svg%3e") center/1em auto no-repeat;border:0;border-radius:.375rem;opacity:.5}.btn-close:hover{color:#000;text-decoration:none;opacity:.75}.btn-close:focus{outline:0;box-shadow:0 0 0 .25rem rgba(68,110,155,0.25);opacity:1}.btn-close:disabled,.btn-close.disabled{pointer-events:none;user-select:none;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;opacity:.25}.btn-close-white{filter:invert(1) grayscale(100%) brightness(200%)}.toast{--bs-toast-zindex: 1090;--bs-toast-padding-x: .75rem;--bs-toast-padding-y: .5rem;--bs-toast-spacing: 1.5rem;--bs-toast-max-width: 350px;--bs-toast-font-size:.875rem;--bs-toast-color: ;--bs-toast-bg: rgba(255,255,255,0.85);--bs-toast-border-width: 1px;--bs-toast-border-color: var(--bs-border-color-translucent);--bs-toast-border-radius: .375rem;--bs-toast-box-shadow: 0 0.5rem 1rem rgba(0,0,0,0.15);--bs-toast-header-color: #777;--bs-toast-header-bg: rgba(255,255,255,0.85);--bs-toast-header-border-color: rgba(0,0,0,0.05);width:var(--bs-toast-max-width);max-width:100%;font-size:var(--bs-toast-font-size);color:var(--bs-toast-color);pointer-events:auto;background-color:var(--bs-toast-bg);background-clip:padding-box;border:var(--bs-toast-border-width) solid var(--bs-toast-border-color);box-shadow:var(--bs-toast-box-shadow);border-radius:var(--bs-toast-border-radius)}.toast.showing{opacity:0}.toast:not(.show){display:none}.toast-container{--bs-toast-zindex: 1090;position:absolute;z-index:var(--bs-toast-zindex);width:max-content;width:-webkit-max-content;width:-moz-max-content;width:-ms-max-content;width:-o-max-content;max-width:100%;pointer-events:none}.toast-container>:not(:last-child){margin-bottom:var(--bs-toast-spacing)}.toast-header{display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;padding:var(--bs-toast-padding-y) var(--bs-toast-padding-x);color:var(--bs-toast-header-color);background-color:var(--bs-toast-header-bg);background-clip:padding-box;border-bottom:var(--bs-toast-border-width) solid var(--bs-toast-header-border-color);border-top-left-radius:calc(var(--bs-toast-border-radius) - var(--bs-toast-border-width));border-top-right-radius:calc(var(--bs-toast-border-radius) - var(--bs-toast-border-width))}.toast-header .btn-close{margin-right:calc(-.5 * var(--bs-toast-padding-x));margin-left:var(--bs-toast-padding-x)}.toast-body{padding:var(--bs-toast-padding-x);word-wrap:break-word}.modal{--bs-modal-zindex: 1055;--bs-modal-width: 500px;--bs-modal-padding: 1rem;--bs-modal-margin: .5rem;--bs-modal-color: ;--bs-modal-bg: #fff;--bs-modal-border-color: var(--bs-border-color-translucent);--bs-modal-border-width: 1px;--bs-modal-border-radius: .5rem;--bs-modal-box-shadow: 0 0.125rem 0.25rem rgba(0,0,0,0.075);--bs-modal-inner-border-radius: calc(.5rem - 1px);--bs-modal-header-padding-x: 1rem;--bs-modal-header-padding-y: 1rem;--bs-modal-header-padding: 1rem 1rem;--bs-modal-header-border-color: var(--bs-border-color);--bs-modal-header-border-width: 1px;--bs-modal-title-line-height: 1.5;--bs-modal-footer-gap: .5rem;--bs-modal-footer-bg: ;--bs-modal-footer-border-color: var(--bs-border-color);--bs-modal-footer-border-width: 1px;position:fixed;top:0;left:0;z-index:var(--bs-modal-zindex);display:none;width:100%;height:100%;overflow-x:hidden;overflow-y:auto;outline:0}.modal-dialog{position:relative;width:auto;margin:var(--bs-modal-margin);pointer-events:none}.modal.fade .modal-dialog{transition:transform 0.3s ease-out;transform:translate(0, -50px)}@media (prefers-reduced-motion: reduce){.modal.fade .modal-dialog{transition:none}}.modal.show .modal-dialog{transform:none}.modal.modal-static .modal-dialog{transform:scale(1.02)}.modal-dialog-scrollable{height:calc(100% - var(--bs-modal-margin) * 2)}.modal-dialog-scrollable .modal-content{max-height:100%;overflow:hidden}.modal-dialog-scrollable .modal-body{overflow-y:auto}.modal-dialog-centered{display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;min-height:calc(100% - var(--bs-modal-margin) * 2)}.modal-content{position:relative;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;width:100%;color:var(--bs-modal-color);pointer-events:auto;background-color:var(--bs-modal-bg);background-clip:padding-box;border:var(--bs-modal-border-width) solid var(--bs-modal-border-color);border-radius:var(--bs-modal-border-radius);outline:0}.modal-backdrop{--bs-backdrop-zindex: 1050;--bs-backdrop-bg: #000;--bs-backdrop-opacity: .5;position:fixed;top:0;left:0;z-index:var(--bs-backdrop-zindex);width:100vw;height:100vh;background-color:var(--bs-backdrop-bg)}.modal-backdrop.fade{opacity:0}.modal-backdrop.show{opacity:var(--bs-backdrop-opacity)}.modal-header{display:flex;display:-webkit-flex;flex-shrink:0;-webkit-flex-shrink:0;align-items:center;-webkit-align-items:center;justify-content:space-between;-webkit-justify-content:space-between;padding:var(--bs-modal-header-padding);border-bottom:var(--bs-modal-header-border-width) solid 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{ + throw new Error( "jQuery requires a window with a document" ); + } + return factory( w ); + }; + } else { + factory( global ); + } + +// Pass this if window is not defined yet +} )( typeof window !== "undefined" ? window : this, function( window, noGlobal ) { + +// Edge <= 12 - 13+, Firefox <=18 - 45+, IE 10 - 11, Safari 5.1 - 9+, iOS 6 - 9.1 +// throw exceptions when non-strict code (e.g., ASP.NET 4.5) accesses strict mode +// arguments.callee.caller (trac-13335). But as of jQuery 3.0 (2016), strict mode should be common +// enough that all such attempts are guarded in a try block. +"use strict"; + +var arr = []; + +var getProto = Object.getPrototypeOf; + +var slice = arr.slice; + +var flat = arr.flat ? function( array ) { + return arr.flat.call( array ); +} : function( array ) { + return arr.concat.apply( [], array ); +}; + + +var push = arr.push; + +var indexOf = arr.indexOf; + +var class2type = {}; + +var toString = class2type.toString; + +var hasOwn = class2type.hasOwnProperty; + +var fnToString = hasOwn.toString; + +var ObjectFunctionString = fnToString.call( Object ); + +var support = {}; + +var isFunction = function isFunction( obj ) { + + // Support: Chrome <=57, Firefox <=52 + // In some browsers, typeof returns "function" for HTML <object> elements + // (i.e., `typeof document.createElement( "object" ) === "function"`). + // We don't want to classify *any* DOM node as a function. + // Support: QtWeb <=3.8.5, WebKit <=534.34, wkhtmltopdf tool <=0.12.5 + // Plus for old WebKit, typeof returns "function" for HTML collections + // (e.g., `typeof document.getElementsByTagName("div") === "function"`). (gh-4756) + return typeof obj === "function" && typeof obj.nodeType !== "number" && + typeof obj.item !== "function"; + }; + + +var isWindow = function isWindow( obj ) { + return obj != null && obj === obj.window; + }; + + +var document = window.document; + + + + var preservedScriptAttributes = { + type: true, + src: true, + nonce: true, + noModule: true + }; + + function DOMEval( code, node, doc ) { + doc = doc || document; + + var i, val, + script = doc.createElement( "script" ); + + script.text = code; + if ( node ) { + for ( i in preservedScriptAttributes ) { + + // Support: Firefox 64+, Edge 18+ + // Some browsers don't support the "nonce" property on scripts. + // On the other hand, just using `getAttribute` is not enough as + // the `nonce` attribute is reset to an empty string whenever it + // becomes browsing-context connected. + // See https://github.com/whatwg/html/issues/2369 + // See https://html.spec.whatwg.org/#nonce-attributes + // The `node.getAttribute` check was added for the sake of + // `jQuery.globalEval` so that it can fake a nonce-containing node + // via an object. + val = node[ i ] || node.getAttribute && node.getAttribute( i ); + if ( val ) { + script.setAttribute( i, val ); + } + } + } + doc.head.appendChild( script ).parentNode.removeChild( script ); + } + + +function toType( obj ) { + if ( obj == null ) { + return obj + ""; + } + + // Support: Android <=2.3 only (functionish RegExp) + return typeof obj === "object" || typeof obj === "function" ? + class2type[ toString.call( obj ) ] || "object" : + typeof obj; +} +/* global Symbol */ +// Defining this global in .eslintrc.json would create a danger of using the global +// unguarded in another place, it seems safer to define global only for this module + + + +var + version = "3.6.0", + + // Define a local copy of jQuery + jQuery = function( selector, context ) { + + // The jQuery object is actually just the init constructor 'enhanced' + // Need init if jQuery is called (just allow error to be thrown if not included) + return new jQuery.fn.init( selector, context ); + }; + +jQuery.fn = jQuery.prototype = { + + // The current version of jQuery being used + jquery: version, + + constructor: jQuery, + + // The default length of a jQuery object is 0 + length: 0, + + toArray: function() { + return slice.call( this ); + }, + + // Get the Nth element in the matched element set OR + // Get the whole matched element set as a clean array + get: function( num ) { + + // Return all the elements in a clean array + if ( num == null ) { + return slice.call( this ); + } + + // Return just the one element from the set + return num < 0 ? this[ num + this.length ] : this[ num ]; + }, + + // Take an array of elements and push it onto the stack + // (returning the new matched element set) + pushStack: function( elems ) { + + // Build a new jQuery matched element set + var ret = jQuery.merge( this.constructor(), elems ); + + // Add the old object onto the stack (as a reference) + ret.prevObject = this; + + // Return the newly-formed element set + return ret; + }, + + // Execute a callback for every element in the matched set. + each: function( callback ) { + return jQuery.each( this, callback ); + }, + + map: function( callback ) { + return this.pushStack( jQuery.map( this, function( elem, i ) { + return callback.call( elem, i, elem ); + } ) ); + }, + + slice: function() { + return this.pushStack( slice.apply( this, arguments ) ); + }, + + first: function() { + return this.eq( 0 ); + }, + + last: function() { + return this.eq( -1 ); + }, + + even: function() { + return this.pushStack( jQuery.grep( this, function( _elem, i ) { + return ( i + 1 ) % 2; + } ) ); + }, + + odd: function() { + return this.pushStack( jQuery.grep( this, function( _elem, i ) { + return i % 2; + } ) ); + }, + + eq: function( i ) { + var len = this.length, + j = +i + ( i < 0 ? len : 0 ); + return this.pushStack( j >= 0 && j < len ? [ this[ j ] ] : [] ); + }, + + end: function() { + return this.prevObject || this.constructor(); + }, + + // For internal use only. + // Behaves like an Array's method, not like a jQuery method. + push: push, + sort: arr.sort, + splice: arr.splice +}; + +jQuery.extend = jQuery.fn.extend = function() { + var options, name, src, copy, copyIsArray, clone, + target = arguments[ 0 ] || {}, + i = 1, + length = arguments.length, + deep = false; + + // Handle a deep copy situation + if ( typeof target === "boolean" ) { + deep = target; + + // Skip the boolean and the target + target = arguments[ i ] || {}; + i++; + } + + // Handle case when target is a string or something (possible in deep copy) + if ( typeof target !== "object" && !isFunction( target ) ) { + target = {}; + } + + // Extend jQuery itself if only one argument is passed + if ( i === length ) { + target = this; + i--; + } + + for ( ; i < length; i++ ) { + + // Only deal with non-null/undefined values + if ( ( options = arguments[ i ] ) != null ) { + + // Extend the base object + for ( name in options ) { + copy = options[ name ]; + + // Prevent Object.prototype pollution + // Prevent never-ending loop + if ( name === "__proto__" || target === copy ) { + continue; + } + + // Recurse if we're merging plain objects or arrays + if ( deep && copy && ( jQuery.isPlainObject( copy ) || + ( copyIsArray = Array.isArray( copy ) ) ) ) { + src = target[ name ]; + + // Ensure proper type for the source value + if ( copyIsArray && !Array.isArray( src ) ) { + clone = []; + } else if ( !copyIsArray && !jQuery.isPlainObject( src ) ) { + clone = {}; + } else { + clone = src; + } + copyIsArray = false; + + // Never move original objects, clone them + target[ name ] = jQuery.extend( deep, clone, copy ); + + // Don't bring in undefined values + } else if ( copy !== undefined ) { + target[ name ] = copy; + } + } + } + } + + // Return the modified object + return target; +}; + +jQuery.extend( { + + // Unique for each copy of jQuery on the page + expando: "jQuery" + ( version + Math.random() ).replace( /\D/g, "" ), + + // Assume jQuery is ready without the ready module + isReady: true, + + error: function( msg ) { + throw new Error( msg ); + }, + + noop: function() {}, + + isPlainObject: function( obj ) { + var proto, Ctor; + + // Detect obvious negatives + // Use toString instead of jQuery.type to catch host objects + if ( !obj || toString.call( obj ) !== "[object Object]" ) { + return false; + } + + proto = getProto( obj ); + + // Objects with no prototype (e.g., `Object.create( null )`) are plain + if ( !proto ) { + return true; + } + + // Objects with prototype are plain iff they were constructed by a global Object function + Ctor = hasOwn.call( proto, "constructor" ) && proto.constructor; + return typeof Ctor === "function" && fnToString.call( Ctor ) === ObjectFunctionString; + }, + + isEmptyObject: function( obj ) { + var name; + + for ( name in obj ) { + return false; + } + return true; + }, + + // Evaluates a script in a provided context; falls back to the global one + // if not specified. + globalEval: function( code, options, doc ) { + DOMEval( code, { nonce: options && options.nonce }, doc ); + }, + + each: function( obj, callback ) { + var length, i = 0; + + if ( isArrayLike( obj ) ) { + length = obj.length; + for ( ; i < length; i++ ) { + if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) { + break; + } + } + } else { + for ( i in obj ) { + if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) { + break; + } + } + } + + return obj; + }, + + // results is for internal usage only + makeArray: function( arr, results ) { + var ret = results || []; + + if ( arr != null ) { + if ( isArrayLike( Object( arr ) ) ) { + jQuery.merge( ret, + typeof arr === "string" ? + [ arr ] : arr + ); + } else { + push.call( ret, arr ); + } + } + + return ret; + }, + + inArray: function( elem, arr, i ) { + return arr == null ? -1 : indexOf.call( arr, elem, i ); + }, + + // Support: Android <=4.0 only, PhantomJS 1 only + // push.apply(_, arraylike) throws on ancient WebKit + merge: function( first, second ) { + var len = +second.length, + j = 0, + i = first.length; + + for ( ; j < len; j++ ) { + first[ i++ ] = second[ j ]; + } + + first.length = i; + + return first; + }, + + grep: function( elems, callback, invert ) { + var callbackInverse, + matches = [], + i = 0, + length = elems.length, + callbackExpect = !invert; + + // Go through the array, only saving the items + // that pass the validator function + for ( ; i < length; i++ ) { + callbackInverse = !callback( elems[ i ], i ); + if ( callbackInverse !== callbackExpect ) { + matches.push( elems[ i ] ); + } + } + + return matches; + }, + + // arg is for internal usage only + map: function( elems, callback, arg ) { + var length, value, + i = 0, + ret = []; + + // Go through the array, translating each of the items to their new values + if ( isArrayLike( elems ) ) { + length = elems.length; + for ( ; i < length; i++ ) { + value = callback( elems[ i ], i, arg ); + + if ( value != null ) { + ret.push( value ); + } + } + + // Go through every key on the object, + } else { + for ( i in elems ) { + value = callback( elems[ i ], i, arg ); + + if ( value != null ) { + ret.push( value ); + } + } + } + + // Flatten any nested arrays + return flat( ret ); + }, + + // A global GUID counter for objects + guid: 1, + + // jQuery.support is not used in Core but other projects attach their + // properties to it so it needs to exist. + support: support +} ); + +if ( typeof Symbol === "function" ) { + jQuery.fn[ Symbol.iterator ] = arr[ Symbol.iterator ]; +} + +// Populate the class2type map +jQuery.each( "Boolean Number String Function Array Date RegExp Object Error Symbol".split( " " ), + function( _i, name ) { + class2type[ "[object " + name + "]" ] = name.toLowerCase(); + } ); + +function isArrayLike( obj ) { + + // Support: real iOS 8.2 only (not reproducible in simulator) + // `in` check used to prevent JIT error (gh-2145) + // hasOwn isn't used here due to false negatives + // regarding Nodelist length in IE + var length = !!obj && "length" in obj && obj.length, + type = toType( obj ); + + if ( isFunction( obj ) || isWindow( obj ) ) { + return false; + } + + return type === "array" || length === 0 || + typeof length === "number" && length > 0 && ( length - 1 ) in obj; +} +var Sizzle = +/*! + * Sizzle CSS Selector Engine v2.3.6 + * https://sizzlejs.com/ + * + * Copyright JS Foundation and other contributors + * Released under the MIT license + * https://js.foundation/ + * + * Date: 2021-02-16 + */ +( function( window ) { +var i, + support, + Expr, + getText, + isXML, + tokenize, + compile, + select, + outermostContext, + sortInput, + hasDuplicate, + + // Local document vars + setDocument, + document, + docElem, + documentIsHTML, + rbuggyQSA, + rbuggyMatches, + matches, + contains, + + // Instance-specific data + expando = "sizzle" + 1 * new Date(), + preferredDoc = window.document, + dirruns = 0, + done = 0, + classCache = createCache(), + tokenCache = createCache(), + compilerCache = createCache(), + nonnativeSelectorCache = createCache(), + sortOrder = function( a, b ) { + if ( a === b ) { + hasDuplicate = true; + } + return 0; + }, + + // Instance methods + hasOwn = ( {} ).hasOwnProperty, + arr = [], + pop = arr.pop, + pushNative = arr.push, + push = arr.push, + slice = arr.slice, + + // Use a stripped-down indexOf as it's faster than native + // https://jsperf.com/thor-indexof-vs-for/5 + indexOf = function( list, elem ) { + var i = 0, + len = list.length; + for ( ; i < len; i++ ) { + if ( list[ i ] === elem ) { + return i; + } + } + return -1; + }, + + booleans = "checked|selected|async|autofocus|autoplay|controls|defer|disabled|hidden|" + + "ismap|loop|multiple|open|readonly|required|scoped", + + // Regular expressions + + // http://www.w3.org/TR/css3-selectors/#whitespace + whitespace = "[\\x20\\t\\r\\n\\f]", + + // https://www.w3.org/TR/css-syntax-3/#ident-token-diagram + identifier = "(?:\\\\[\\da-fA-F]{1,6}" + whitespace + + "?|\\\\[^\\r\\n\\f]|[\\w-]|[^\0-\\x7f])+", + + // Attribute selectors: http://www.w3.org/TR/selectors/#attribute-selectors + attributes = "\\[" + whitespace + "*(" + identifier + ")(?:" + whitespace + + + // Operator (capture 2) + "*([*^$|!~]?=)" + whitespace + + + // "Attribute values must be CSS identifiers [capture 5] + // or strings [capture 3 or capture 4]" + "*(?:'((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\"|(" + identifier + "))|)" + + whitespace + "*\\]", + + pseudos = ":(" + identifier + ")(?:\\((" + + + // To reduce the number of selectors needing tokenize in the preFilter, prefer arguments: + // 1. quoted (capture 3; capture 4 or capture 5) + "('((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\")|" + + + // 2. simple (capture 6) + "((?:\\\\.|[^\\\\()[\\]]|" + attributes + ")*)|" + + + // 3. anything else (capture 2) + ".*" + + ")\\)|)", + + // Leading and non-escaped trailing whitespace, capturing some non-whitespace characters preceding the latter + rwhitespace = new RegExp( whitespace + "+", "g" ), + rtrim = new RegExp( "^" + whitespace + "+|((?:^|[^\\\\])(?:\\\\.)*)" + + whitespace + "+$", "g" ), + + rcomma = new RegExp( "^" + whitespace + "*," + whitespace + "*" ), + rcombinators = new RegExp( "^" + whitespace + "*([>+~]|" + whitespace + ")" + whitespace + + "*" ), + rdescend = new RegExp( whitespace + "|>" ), + + rpseudo = new RegExp( pseudos ), + ridentifier = new RegExp( "^" + identifier + "$" ), + + matchExpr = { + "ID": new RegExp( "^#(" + identifier + ")" ), + "CLASS": new RegExp( "^\\.(" + identifier + ")" ), + "TAG": new RegExp( "^(" + identifier + "|[*])" ), + "ATTR": new RegExp( "^" + attributes ), + "PSEUDO": new RegExp( "^" + pseudos ), + "CHILD": new RegExp( "^:(only|first|last|nth|nth-last)-(child|of-type)(?:\\(" + + whitespace + "*(even|odd|(([+-]|)(\\d*)n|)" + whitespace + "*(?:([+-]|)" + + whitespace + "*(\\d+)|))" + whitespace + "*\\)|)", "i" ), + "bool": new RegExp( "^(?:" + booleans + ")$", "i" ), + + // For use in libraries implementing .is() + // We use this for POS matching in `select` + "needsContext": new RegExp( "^" + whitespace + + "*[>+~]|:(even|odd|eq|gt|lt|nth|first|last)(?:\\(" + whitespace + + "*((?:-\\d)?\\d*)" + whitespace + "*\\)|)(?=[^-]|$)", "i" ) + }, + + rhtml = /HTML$/i, + rinputs = /^(?:input|select|textarea|button)$/i, + rheader = /^h\d$/i, + + rnative = /^[^{]+\{\s*\[native \w/, + + // Easily-parseable/retrievable ID or TAG or CLASS selectors + rquickExpr = /^(?:#([\w-]+)|(\w+)|\.([\w-]+))$/, + + rsibling = /[+~]/, + + // CSS escapes + // http://www.w3.org/TR/CSS21/syndata.html#escaped-characters + runescape = new RegExp( "\\\\[\\da-fA-F]{1,6}" + whitespace + "?|\\\\([^\\r\\n\\f])", "g" ), + funescape = function( escape, nonHex ) { + var high = "0x" + escape.slice( 1 ) - 0x10000; + + return nonHex ? + + // Strip the backslash prefix from a non-hex escape sequence + nonHex : + + // Replace a hexadecimal escape sequence with the encoded Unicode code point + // Support: IE <=11+ + // For values outside the Basic Multilingual Plane (BMP), manually construct a + // surrogate pair + high < 0 ? + String.fromCharCode( high + 0x10000 ) : + String.fromCharCode( high >> 10 | 0xD800, high & 0x3FF | 0xDC00 ); + }, + + // CSS string/identifier serialization + // https://drafts.csswg.org/cssom/#common-serializing-idioms + rcssescape = /([\0-\x1f\x7f]|^-?\d)|^-$|[^\0-\x1f\x7f-\uFFFF\w-]/g, + fcssescape = function( ch, asCodePoint ) { + if ( asCodePoint ) { + + // U+0000 NULL becomes U+FFFD REPLACEMENT CHARACTER + if ( ch === "\0" ) { + return "\uFFFD"; + } + + // Control characters and (dependent upon position) numbers get escaped as code points + return ch.slice( 0, -1 ) + "\\" + + ch.charCodeAt( ch.length - 1 ).toString( 16 ) + " "; + } + + // Other potentially-special ASCII characters get backslash-escaped + return "\\" + ch; + }, + + // Used for iframes + // See setDocument() + // Removing the function wrapper causes a "Permission Denied" + // error in IE + unloadHandler = function() { + setDocument(); + }, + + inDisabledFieldset = addCombinator( + function( elem ) { + return elem.disabled === true && elem.nodeName.toLowerCase() === "fieldset"; + }, + { dir: "parentNode", next: "legend" } + ); + +// Optimize for push.apply( _, NodeList ) +try { + push.apply( + ( arr = slice.call( preferredDoc.childNodes ) ), + preferredDoc.childNodes + ); + + // Support: Android<4.0 + // Detect silently failing push.apply + // eslint-disable-next-line no-unused-expressions + arr[ preferredDoc.childNodes.length ].nodeType; +} catch ( e ) { + push = { apply: arr.length ? + + // Leverage slice if possible + function( target, els ) { + pushNative.apply( target, slice.call( els ) ); + } : + + // Support: IE<9 + // Otherwise append directly + function( target, els ) { + var j = target.length, + i = 0; + + // Can't trust NodeList.length + while ( ( target[ j++ ] = els[ i++ ] ) ) {} + target.length = j - 1; + } + }; +} + +function Sizzle( selector, context, results, seed ) { + var m, i, elem, nid, match, groups, newSelector, + newContext = context && context.ownerDocument, + + // nodeType defaults to 9, since context defaults to document + nodeType = context ? context.nodeType : 9; + + results = results || []; + + // Return early from calls with invalid selector or context + if ( typeof selector !== "string" || !selector || + nodeType !== 1 && nodeType !== 9 && nodeType !== 11 ) { + + return results; + } + + // Try to shortcut find operations (as opposed to filters) in HTML documents + if ( !seed ) { + setDocument( context ); + context = context || document; + + if ( documentIsHTML ) { + + // If the selector is sufficiently simple, try using a "get*By*" DOM method + // (excepting DocumentFragment context, where the methods don't exist) + if ( nodeType !== 11 && ( match = rquickExpr.exec( selector ) ) ) { + + // ID selector + if ( ( m = match[ 1 ] ) ) { + + // Document context + if ( nodeType === 9 ) { + if ( ( elem = context.getElementById( m ) ) ) { + + // Support: IE, Opera, Webkit + // TODO: identify versions + // getElementById can match elements by name instead of ID + if ( elem.id === m ) { + results.push( elem ); + return results; + } + } else { + return results; + } + + // Element context + } else { + + // Support: IE, Opera, Webkit + // TODO: identify versions + // getElementById can match elements by name instead of ID + if ( newContext && ( elem = newContext.getElementById( m ) ) && + contains( context, elem ) && + elem.id === m ) { + + results.push( elem ); + return results; + } + } + + // Type selector + } else if ( match[ 2 ] ) { + push.apply( results, context.getElementsByTagName( selector ) ); + return results; + + // Class selector + } else if ( ( m = match[ 3 ] ) && support.getElementsByClassName && + context.getElementsByClassName ) { + + push.apply( results, context.getElementsByClassName( m ) ); + return results; + } + } + + // Take advantage of querySelectorAll + if ( support.qsa && + !nonnativeSelectorCache[ selector + " " ] && + ( !rbuggyQSA || !rbuggyQSA.test( selector ) ) && + + // Support: IE 8 only + // Exclude object elements + ( nodeType !== 1 || context.nodeName.toLowerCase() !== "object" ) ) { + + newSelector = selector; + newContext = context; + + // qSA considers elements outside a scoping root when evaluating child or + // descendant combinators, which is not what we want. + // In such cases, we work around the behavior by prefixing every selector in the + // list with an ID selector referencing the scope context. + // The technique has to be used as well when a leading combinator is used + // as such selectors are not recognized by querySelectorAll. + // Thanks to Andrew Dupont for this technique. + if ( nodeType === 1 && + ( rdescend.test( selector ) || rcombinators.test( selector ) ) ) { + + // Expand context for sibling selectors + newContext = rsibling.test( selector ) && testContext( context.parentNode ) || + context; + + // We can use :scope instead of the ID hack if the browser + // supports it & if we're not changing the context. + if ( newContext !== context || !support.scope ) { + + // Capture the context ID, setting it first if necessary + if ( ( nid = context.getAttribute( "id" ) ) ) { + nid = nid.replace( rcssescape, fcssescape ); + } else { + context.setAttribute( "id", ( nid = expando ) ); + } + } + + // Prefix every selector in the list + groups = tokenize( selector ); + i = groups.length; + while ( i-- ) { + groups[ i ] = ( nid ? "#" + nid : ":scope" ) + " " + + toSelector( groups[ i ] ); + } + newSelector = groups.join( "," ); + } + + try { + push.apply( results, + newContext.querySelectorAll( newSelector ) + ); + return results; + } catch ( qsaError ) { + nonnativeSelectorCache( selector, true ); + } finally { + if ( nid === expando ) { + context.removeAttribute( "id" ); + } + } + } + } + } + + // All others + return select( selector.replace( rtrim, "$1" ), context, results, seed ); +} + +/** + * Create key-value caches of limited size + * @returns {function(string, object)} Returns the Object data after storing it on itself with + * property name the (space-suffixed) string and (if the cache is larger than Expr.cacheLength) + * deleting the oldest entry + */ +function createCache() { + var keys = []; + + function cache( key, value ) { + + // Use (key + " ") to avoid collision with native prototype properties (see Issue #157) + if ( keys.push( key + " " ) > Expr.cacheLength ) { + + // Only keep the most recent entries + delete cache[ keys.shift() ]; + } + return ( cache[ key + " " ] = value ); + } + return cache; +} + +/** + * Mark a function for special use by Sizzle + * @param {Function} fn The function to mark + */ +function markFunction( fn ) { + fn[ expando ] = true; + return fn; +} + +/** + * Support testing using an element + * @param {Function} fn Passed the created element and returns a boolean result + */ +function assert( fn ) { + var el = document.createElement( "fieldset" ); + + try { + return !!fn( el ); + } catch ( e ) { + return false; + } finally { + + // Remove from its parent by default + if ( el.parentNode ) { + el.parentNode.removeChild( el ); + } + + // release memory in IE + el = null; + } +} + +/** + * Adds the same handler for all of the specified attrs + * @param {String} attrs Pipe-separated list of attributes + * @param {Function} handler The method that will be applied + */ +function addHandle( attrs, handler ) { + var arr = attrs.split( "|" ), + i = arr.length; + + while ( i-- ) { + Expr.attrHandle[ arr[ i ] ] = handler; + } +} + +/** + * Checks document order of two siblings + * @param {Element} a + * @param {Element} b + * @returns {Number} Returns less than 0 if a precedes b, greater than 0 if a follows b + */ +function siblingCheck( a, b ) { + var cur = b && a, + diff = cur && a.nodeType === 1 && b.nodeType === 1 && + a.sourceIndex - b.sourceIndex; + + // Use IE sourceIndex if available on both nodes + if ( diff ) { + return diff; + } + + // Check if b follows a + if ( cur ) { + while ( ( cur = cur.nextSibling ) ) { + if ( cur === b ) { + return -1; + } + } + } + + return a ? 1 : -1; +} + +/** + * Returns a function to use in pseudos for input types + * @param {String} type + */ +function createInputPseudo( type ) { + return function( elem ) { + var name = elem.nodeName.toLowerCase(); + return name === "input" && elem.type === type; + }; +} + +/** + * Returns a function to use in pseudos for buttons + * @param {String} type + */ +function createButtonPseudo( type ) { + return function( elem ) { + var name = elem.nodeName.toLowerCase(); + return ( name === "input" || name === "button" ) && elem.type === type; + }; +} + +/** + * Returns a function to use in pseudos for :enabled/:disabled + * @param {Boolean} disabled true for :disabled; false for :enabled + */ +function createDisabledPseudo( disabled ) { + + // Known :disabled false positives: fieldset[disabled] > legend:nth-of-type(n+2) :can-disable + return function( elem ) { + + // Only certain elements can match :enabled or :disabled + // https://html.spec.whatwg.org/multipage/scripting.html#selector-enabled + // https://html.spec.whatwg.org/multipage/scripting.html#selector-disabled + if ( "form" in elem ) { + + // Check for inherited disabledness on relevant non-disabled elements: + // * listed form-associated elements in a disabled fieldset + // https://html.spec.whatwg.org/multipage/forms.html#category-listed + // https://html.spec.whatwg.org/multipage/forms.html#concept-fe-disabled + // * option elements in a disabled optgroup + // https://html.spec.whatwg.org/multipage/forms.html#concept-option-disabled + // All such elements have a "form" property. + if ( elem.parentNode && elem.disabled === false ) { + + // Option elements defer to a parent optgroup if present + if ( "label" in elem ) { + if ( "label" in elem.parentNode ) { + return elem.parentNode.disabled === disabled; + } else { + return elem.disabled === disabled; + } + } + + // Support: IE 6 - 11 + // Use the isDisabled shortcut property to check for disabled fieldset ancestors + return elem.isDisabled === disabled || + + // Where there is no isDisabled, check manually + /* jshint -W018 */ + elem.isDisabled !== !disabled && + inDisabledFieldset( elem ) === disabled; + } + + return elem.disabled === disabled; + + // Try to winnow out elements that can't be disabled before trusting the disabled property. + // Some victims get caught in our net (label, legend, menu, track), but it shouldn't + // even exist on them, let alone have a boolean value. + } else if ( "label" in elem ) { + return elem.disabled === disabled; + } + + // Remaining elements are neither :enabled nor :disabled + return false; + }; +} + +/** + * Returns a function to use in pseudos for positionals + * @param {Function} fn + */ +function createPositionalPseudo( fn ) { + return markFunction( function( argument ) { + argument = +argument; + return markFunction( function( seed, matches ) { + var j, + matchIndexes = fn( [], seed.length, argument ), + i = matchIndexes.length; + + // Match elements found at the specified indexes + while ( i-- ) { + if ( seed[ ( j = matchIndexes[ i ] ) ] ) { + seed[ j ] = !( matches[ j ] = seed[ j ] ); + } + } + } ); + } ); +} + +/** + * Checks a node for validity as a Sizzle context + * @param {Element|Object=} context + * @returns {Element|Object|Boolean} The input node if acceptable, otherwise a falsy value + */ +function testContext( context ) { + return context && typeof context.getElementsByTagName !== "undefined" && context; +} + +// Expose support vars for convenience +support = Sizzle.support = {}; + +/** + * Detects XML nodes + * @param {Element|Object} elem An element or a document + * @returns {Boolean} True iff elem is a non-HTML XML node + */ +isXML = Sizzle.isXML = function( elem ) { + var namespace = elem && elem.namespaceURI, + docElem = elem && ( elem.ownerDocument || elem ).documentElement; + + // Support: IE <=8 + // Assume HTML when documentElement doesn't yet exist, such as inside loading iframes + // https://bugs.jquery.com/ticket/4833 + return !rhtml.test( namespace || docElem && docElem.nodeName || "HTML" ); +}; + +/** + * Sets document-related variables once based on the current document + * @param {Element|Object} [doc] An element or document object to use to set the document + * @returns {Object} Returns the current document + */ +setDocument = Sizzle.setDocument = function( node ) { + var hasCompare, subWindow, + doc = node ? node.ownerDocument || node : preferredDoc; + + // Return early if doc is invalid or already selected + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( doc == document || doc.nodeType !== 9 || !doc.documentElement ) { + return document; + } + + // Update global variables + document = doc; + docElem = document.documentElement; + documentIsHTML = !isXML( document ); + + // Support: IE 9 - 11+, Edge 12 - 18+ + // Accessing iframe documents after unload throws "permission denied" errors (jQuery #13936) + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( preferredDoc != document && + ( subWindow = document.defaultView ) && subWindow.top !== subWindow ) { + + // Support: IE 11, Edge + if ( subWindow.addEventListener ) { + subWindow.addEventListener( "unload", unloadHandler, false ); + + // Support: IE 9 - 10 only + } else if ( subWindow.attachEvent ) { + subWindow.attachEvent( "onunload", unloadHandler ); + } + } + + // Support: IE 8 - 11+, Edge 12 - 18+, Chrome <=16 - 25 only, Firefox <=3.6 - 31 only, + // Safari 4 - 5 only, Opera <=11.6 - 12.x only + // IE/Edge & older browsers don't support the :scope pseudo-class. + // Support: Safari 6.0 only + // Safari 6.0 supports :scope but it's an alias of :root there. + support.scope = assert( function( el ) { + docElem.appendChild( el ).appendChild( document.createElement( "div" ) ); + return typeof el.querySelectorAll !== "undefined" && + !el.querySelectorAll( ":scope fieldset div" ).length; + } ); + + /* Attributes + ---------------------------------------------------------------------- */ + + // Support: IE<8 + // Verify that getAttribute really returns attributes and not properties + // (excepting IE8 booleans) + support.attributes = assert( function( el ) { + el.className = "i"; + return !el.getAttribute( "className" ); + } ); + + /* getElement(s)By* + ---------------------------------------------------------------------- */ + + // Check if getElementsByTagName("*") returns only elements + support.getElementsByTagName = assert( function( el ) { + el.appendChild( document.createComment( "" ) ); + return !el.getElementsByTagName( "*" ).length; + } ); + + // Support: IE<9 + support.getElementsByClassName = rnative.test( document.getElementsByClassName ); + + // Support: IE<10 + // Check if getElementById returns elements by name + // The broken getElementById methods don't pick up programmatically-set names, + // so use a roundabout getElementsByName test + support.getById = assert( function( el ) { + docElem.appendChild( el ).id = expando; + return !document.getElementsByName || !document.getElementsByName( expando ).length; + } ); + + // ID filter and find + if ( support.getById ) { + Expr.filter[ "ID" ] = function( id ) { + var attrId = id.replace( runescape, funescape ); + return function( elem ) { + return elem.getAttribute( "id" ) === attrId; + }; + }; + Expr.find[ "ID" ] = function( id, context ) { + if ( typeof context.getElementById !== "undefined" && documentIsHTML ) { + var elem = context.getElementById( id ); + return elem ? [ elem ] : []; + } + }; + } else { + Expr.filter[ "ID" ] = function( id ) { + var attrId = id.replace( runescape, funescape ); + return function( elem ) { + var node = typeof elem.getAttributeNode !== "undefined" && + elem.getAttributeNode( "id" ); + return node && node.value === attrId; + }; + }; + + // Support: IE 6 - 7 only + // getElementById is not reliable as a find shortcut + Expr.find[ "ID" ] = function( id, context ) { + if ( typeof context.getElementById !== "undefined" && documentIsHTML ) { + var node, i, elems, + elem = context.getElementById( id ); + + if ( elem ) { + + // Verify the id attribute + node = elem.getAttributeNode( "id" ); + if ( node && node.value === id ) { + return [ elem ]; + } + + // Fall back on getElementsByName + elems = context.getElementsByName( id ); + i = 0; + while ( ( elem = elems[ i++ ] ) ) { + node = elem.getAttributeNode( "id" ); + if ( node && node.value === id ) { + return [ elem ]; + } + } + } + + return []; + } + }; + } + + // Tag + Expr.find[ "TAG" ] = support.getElementsByTagName ? + function( tag, context ) { + if ( typeof context.getElementsByTagName !== "undefined" ) { + return context.getElementsByTagName( tag ); + + // DocumentFragment nodes don't have gEBTN + } else if ( support.qsa ) { + return context.querySelectorAll( tag ); + } + } : + + function( tag, context ) { + var elem, + tmp = [], + i = 0, + + // By happy coincidence, a (broken) gEBTN appears on DocumentFragment nodes too + results = context.getElementsByTagName( tag ); + + // Filter out possible comments + if ( tag === "*" ) { + while ( ( elem = results[ i++ ] ) ) { + if ( elem.nodeType === 1 ) { + tmp.push( elem ); + } + } + + return tmp; + } + return results; + }; + + // Class + Expr.find[ "CLASS" ] = support.getElementsByClassName && function( className, context ) { + if ( typeof context.getElementsByClassName !== "undefined" && documentIsHTML ) { + return context.getElementsByClassName( className ); + } + }; + + /* QSA/matchesSelector + ---------------------------------------------------------------------- */ + + // QSA and matchesSelector support + + // matchesSelector(:active) reports false when true (IE9/Opera 11.5) + rbuggyMatches = []; + + // qSa(:focus) reports false when true (Chrome 21) + // We allow this because of a bug in IE8/9 that throws an error + // whenever `document.activeElement` is accessed on an iframe + // So, we allow :focus to pass through QSA all the time to avoid the IE error + // See https://bugs.jquery.com/ticket/13378 + rbuggyQSA = []; + + if ( ( support.qsa = rnative.test( document.querySelectorAll ) ) ) { + + // Build QSA regex + // Regex strategy adopted from Diego Perini + assert( function( el ) { + + var input; + + // Select is set to empty string on purpose + // This is to test IE's treatment of not explicitly + // setting a boolean content attribute, + // since its presence should be enough + // https://bugs.jquery.com/ticket/12359 + docElem.appendChild( el ).innerHTML = "<a id='" + expando + "'></a>" + + "<select id='" + expando + "-\r\\' msallowcapture=''>" + + "<option selected=''></option></select>"; + + // Support: IE8, Opera 11-12.16 + // Nothing should be selected when empty strings follow ^= or $= or *= + // The test attribute must be unknown in Opera but "safe" for WinRT + // https://msdn.microsoft.com/en-us/library/ie/hh465388.aspx#attribute_section + if ( el.querySelectorAll( "[msallowcapture^='']" ).length ) { + rbuggyQSA.push( "[*^$]=" + whitespace + "*(?:''|\"\")" ); + } + + // Support: IE8 + // Boolean attributes and "value" are not treated correctly + if ( !el.querySelectorAll( "[selected]" ).length ) { + rbuggyQSA.push( "\\[" + whitespace + "*(?:value|" + booleans + ")" ); + } + + // Support: Chrome<29, Android<4.4, Safari<7.0+, iOS<7.0+, PhantomJS<1.9.8+ + if ( !el.querySelectorAll( "[id~=" + expando + "-]" ).length ) { + rbuggyQSA.push( "~=" ); + } + + // Support: IE 11+, Edge 15 - 18+ + // IE 11/Edge don't find elements on a `[name='']` query in some cases. + // Adding a temporary attribute to the document before the selection works + // around the issue. + // Interestingly, IE 10 & older don't seem to have the issue. + input = document.createElement( "input" ); + input.setAttribute( "name", "" ); + el.appendChild( input ); + if ( !el.querySelectorAll( "[name='']" ).length ) { + rbuggyQSA.push( "\\[" + whitespace + "*name" + whitespace + "*=" + + whitespace + "*(?:''|\"\")" ); + } + + // Webkit/Opera - :checked should return selected option elements + // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked + // IE8 throws error here and will not see later tests + if ( !el.querySelectorAll( ":checked" ).length ) { + rbuggyQSA.push( ":checked" ); + } + + // Support: Safari 8+, iOS 8+ + // https://bugs.webkit.org/show_bug.cgi?id=136851 + // In-page `selector#id sibling-combinator selector` fails + if ( !el.querySelectorAll( "a#" + expando + "+*" ).length ) { + rbuggyQSA.push( ".#.+[+~]" ); + } + + // Support: Firefox <=3.6 - 5 only + // Old Firefox doesn't throw on a badly-escaped identifier. + el.querySelectorAll( "\\\f" ); + rbuggyQSA.push( "[\\r\\n\\f]" ); + } ); + + assert( function( el ) { + el.innerHTML = "<a href='' disabled='disabled'></a>" + + "<select disabled='disabled'><option/></select>"; + + // Support: Windows 8 Native Apps + // The type and name attributes are restricted during .innerHTML assignment + var input = document.createElement( "input" ); + input.setAttribute( "type", "hidden" ); + el.appendChild( input ).setAttribute( "name", "D" ); + + // Support: IE8 + // Enforce case-sensitivity of name attribute + if ( el.querySelectorAll( "[name=d]" ).length ) { + rbuggyQSA.push( "name" + whitespace + "*[*^$|!~]?=" ); + } + + // FF 3.5 - :enabled/:disabled and hidden elements (hidden elements are still enabled) + // IE8 throws error here and will not see later tests + if ( el.querySelectorAll( ":enabled" ).length !== 2 ) { + rbuggyQSA.push( ":enabled", ":disabled" ); + } + + // Support: IE9-11+ + // IE's :disabled selector does not pick up the children of disabled fieldsets + docElem.appendChild( el ).disabled = true; + if ( el.querySelectorAll( ":disabled" ).length !== 2 ) { + rbuggyQSA.push( ":enabled", ":disabled" ); + } + + // Support: Opera 10 - 11 only + // Opera 10-11 does not throw on post-comma invalid pseudos + el.querySelectorAll( "*,:x" ); + rbuggyQSA.push( ",.*:" ); + } ); + } + + if ( ( support.matchesSelector = rnative.test( ( matches = docElem.matches || + docElem.webkitMatchesSelector || + docElem.mozMatchesSelector || + docElem.oMatchesSelector || + docElem.msMatchesSelector ) ) ) ) { + + assert( function( el ) { + + // Check to see if it's possible to do matchesSelector + // on a disconnected node (IE 9) + support.disconnectedMatch = matches.call( el, "*" ); + + // This should fail with an exception + // Gecko does not error, returns false instead + matches.call( el, "[s!='']:x" ); + rbuggyMatches.push( "!=", pseudos ); + } ); + } + + rbuggyQSA = rbuggyQSA.length && new RegExp( rbuggyQSA.join( "|" ) ); + rbuggyMatches = rbuggyMatches.length && new RegExp( rbuggyMatches.join( "|" ) ); + + /* Contains + ---------------------------------------------------------------------- */ + hasCompare = rnative.test( docElem.compareDocumentPosition ); + + // Element contains another + // Purposefully self-exclusive + // As in, an element does not contain itself + contains = hasCompare || rnative.test( docElem.contains ) ? + function( a, b ) { + var adown = a.nodeType === 9 ? a.documentElement : a, + bup = b && b.parentNode; + return a === bup || !!( bup && bup.nodeType === 1 && ( + adown.contains ? + adown.contains( bup ) : + a.compareDocumentPosition && a.compareDocumentPosition( bup ) & 16 + ) ); + } : + function( a, b ) { + if ( b ) { + while ( ( b = b.parentNode ) ) { + if ( b === a ) { + return true; + } + } + } + return false; + }; + + /* Sorting + ---------------------------------------------------------------------- */ + + // Document order sorting + sortOrder = hasCompare ? + function( a, b ) { + + // Flag for duplicate removal + if ( a === b ) { + hasDuplicate = true; + return 0; + } + + // Sort on method existence if only one input has compareDocumentPosition + var compare = !a.compareDocumentPosition - !b.compareDocumentPosition; + if ( compare ) { + return compare; + } + + // Calculate position if both inputs belong to the same document + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + compare = ( a.ownerDocument || a ) == ( b.ownerDocument || b ) ? + a.compareDocumentPosition( b ) : + + // Otherwise we know they are disconnected + 1; + + // Disconnected nodes + if ( compare & 1 || + ( !support.sortDetached && b.compareDocumentPosition( a ) === compare ) ) { + + // Choose the first element that is related to our preferred document + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( a == document || a.ownerDocument == preferredDoc && + contains( preferredDoc, a ) ) { + return -1; + } + + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( b == document || b.ownerDocument == preferredDoc && + contains( preferredDoc, b ) ) { + return 1; + } + + // Maintain original order + return sortInput ? + ( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) : + 0; + } + + return compare & 4 ? -1 : 1; + } : + function( a, b ) { + + // Exit early if the nodes are identical + if ( a === b ) { + hasDuplicate = true; + return 0; + } + + var cur, + i = 0, + aup = a.parentNode, + bup = b.parentNode, + ap = [ a ], + bp = [ b ]; + + // Parentless nodes are either documents or disconnected + if ( !aup || !bup ) { + + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + /* eslint-disable eqeqeq */ + return a == document ? -1 : + b == document ? 1 : + /* eslint-enable eqeqeq */ + aup ? -1 : + bup ? 1 : + sortInput ? + ( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) : + 0; + + // If the nodes are siblings, we can do a quick check + } else if ( aup === bup ) { + return siblingCheck( a, b ); + } + + // Otherwise we need full lists of their ancestors for comparison + cur = a; + while ( ( cur = cur.parentNode ) ) { + ap.unshift( cur ); + } + cur = b; + while ( ( cur = cur.parentNode ) ) { + bp.unshift( cur ); + } + + // Walk down the tree looking for a discrepancy + while ( ap[ i ] === bp[ i ] ) { + i++; + } + + return i ? + + // Do a sibling check if the nodes have a common ancestor + siblingCheck( ap[ i ], bp[ i ] ) : + + // Otherwise nodes in our document sort first + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + /* eslint-disable eqeqeq */ + ap[ i ] == preferredDoc ? -1 : + bp[ i ] == preferredDoc ? 1 : + /* eslint-enable eqeqeq */ + 0; + }; + + return document; +}; + +Sizzle.matches = function( expr, elements ) { + return Sizzle( expr, null, null, elements ); +}; + +Sizzle.matchesSelector = function( elem, expr ) { + setDocument( elem ); + + if ( support.matchesSelector && documentIsHTML && + !nonnativeSelectorCache[ expr + " " ] && + ( !rbuggyMatches || !rbuggyMatches.test( expr ) ) && + ( !rbuggyQSA || !rbuggyQSA.test( expr ) ) ) { + + try { + var ret = matches.call( elem, expr ); + + // IE 9's matchesSelector returns false on disconnected nodes + if ( ret || support.disconnectedMatch || + + // As well, disconnected nodes are said to be in a document + // fragment in IE 9 + elem.document && elem.document.nodeType !== 11 ) { + return ret; + } + } catch ( e ) { + nonnativeSelectorCache( expr, true ); + } + } + + return Sizzle( expr, document, null, [ elem ] ).length > 0; +}; + +Sizzle.contains = function( context, elem ) { + + // Set document vars if needed + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( ( context.ownerDocument || context ) != document ) { + setDocument( context ); + } + return contains( context, elem ); +}; + +Sizzle.attr = function( elem, name ) { + + // Set document vars if needed + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( ( elem.ownerDocument || elem ) != document ) { + setDocument( elem ); + } + + var fn = Expr.attrHandle[ name.toLowerCase() ], + + // Don't get fooled by Object.prototype properties (jQuery #13807) + val = fn && hasOwn.call( Expr.attrHandle, name.toLowerCase() ) ? + fn( elem, name, !documentIsHTML ) : + undefined; + + return val !== undefined ? + val : + support.attributes || !documentIsHTML ? + elem.getAttribute( name ) : + ( val = elem.getAttributeNode( name ) ) && val.specified ? + val.value : + null; +}; + +Sizzle.escape = function( sel ) { + return ( sel + "" ).replace( rcssescape, fcssescape ); +}; + +Sizzle.error = function( msg ) { + throw new Error( "Syntax error, unrecognized expression: " + msg ); +}; + +/** + * Document sorting and removing duplicates + * @param {ArrayLike} results + */ +Sizzle.uniqueSort = function( results ) { + var elem, + duplicates = [], + j = 0, + i = 0; + + // Unless we *know* we can detect duplicates, assume their presence + hasDuplicate = !support.detectDuplicates; + sortInput = !support.sortStable && results.slice( 0 ); + results.sort( sortOrder ); + + if ( hasDuplicate ) { + while ( ( elem = results[ i++ ] ) ) { + if ( elem === results[ i ] ) { + j = duplicates.push( i ); + } + } + while ( j-- ) { + results.splice( duplicates[ j ], 1 ); + } + } + + // Clear input after sorting to release objects + // See https://github.com/jquery/sizzle/pull/225 + sortInput = null; + + return results; +}; + +/** + * Utility function for retrieving the text value of an array of DOM nodes + * @param {Array|Element} elem + */ +getText = Sizzle.getText = function( elem ) { + var node, + ret = "", + i = 0, + nodeType = elem.nodeType; + + if ( !nodeType ) { + + // If no nodeType, this is expected to be an array + while ( ( node = elem[ i++ ] ) ) { + + // Do not traverse comment nodes + ret += getText( node ); + } + } else if ( nodeType === 1 || nodeType === 9 || nodeType === 11 ) { + + // Use textContent for elements + // innerText usage removed for consistency of new lines (jQuery #11153) + if ( typeof elem.textContent === "string" ) { + return elem.textContent; + } else { + + // Traverse its children + for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) { + ret += getText( elem ); + } + } + } else if ( nodeType === 3 || nodeType === 4 ) { + return elem.nodeValue; + } + + // Do not include comment or processing instruction nodes + + return ret; +}; + +Expr = Sizzle.selectors = { + + // Can be adjusted by the user + cacheLength: 50, + + createPseudo: markFunction, + + match: matchExpr, + + attrHandle: {}, + + find: {}, + + relative: { + ">": { dir: "parentNode", first: true }, + " ": { dir: "parentNode" }, + "+": { dir: "previousSibling", first: true }, + "~": { dir: "previousSibling" } + }, + + preFilter: { + "ATTR": function( match ) { + match[ 1 ] = match[ 1 ].replace( runescape, funescape ); + + // Move the given value to match[3] whether quoted or unquoted + match[ 3 ] = ( match[ 3 ] || match[ 4 ] || + match[ 5 ] || "" ).replace( runescape, funescape ); + + if ( match[ 2 ] === "~=" ) { + match[ 3 ] = " " + match[ 3 ] + " "; + } + + return match.slice( 0, 4 ); + }, + + "CHILD": function( match ) { + + /* matches from matchExpr["CHILD"] + 1 type (only|nth|...) + 2 what (child|of-type) + 3 argument (even|odd|\d*|\d*n([+-]\d+)?|...) + 4 xn-component of xn+y argument ([+-]?\d*n|) + 5 sign of xn-component + 6 x of xn-component + 7 sign of y-component + 8 y of y-component + */ + match[ 1 ] = match[ 1 ].toLowerCase(); + + if ( match[ 1 ].slice( 0, 3 ) === "nth" ) { + + // nth-* requires argument + if ( !match[ 3 ] ) { + Sizzle.error( match[ 0 ] ); + } + + // numeric x and y parameters for Expr.filter.CHILD + // remember that false/true cast respectively to 0/1 + match[ 4 ] = +( match[ 4 ] ? + match[ 5 ] + ( match[ 6 ] || 1 ) : + 2 * ( match[ 3 ] === "even" || match[ 3 ] === "odd" ) ); + match[ 5 ] = +( ( match[ 7 ] + match[ 8 ] ) || match[ 3 ] === "odd" ); + + // other types prohibit arguments + } else if ( match[ 3 ] ) { + Sizzle.error( match[ 0 ] ); + } + + return match; + }, + + "PSEUDO": function( match ) { + var excess, + unquoted = !match[ 6 ] && match[ 2 ]; + + if ( matchExpr[ "CHILD" ].test( match[ 0 ] ) ) { + return null; + } + + // Accept quoted arguments as-is + if ( match[ 3 ] ) { + match[ 2 ] = match[ 4 ] || match[ 5 ] || ""; + + // Strip excess characters from unquoted arguments + } else if ( unquoted && rpseudo.test( unquoted ) && + + // Get excess from tokenize (recursively) + ( excess = tokenize( unquoted, true ) ) && + + // advance to the next closing parenthesis + ( excess = unquoted.indexOf( ")", unquoted.length - excess ) - unquoted.length ) ) { + + // excess is a negative index + match[ 0 ] = match[ 0 ].slice( 0, excess ); + match[ 2 ] = unquoted.slice( 0, excess ); + } + + // Return only captures needed by the pseudo filter method (type and argument) + return match.slice( 0, 3 ); + } + }, + + filter: { + + "TAG": function( nodeNameSelector ) { + var nodeName = nodeNameSelector.replace( runescape, funescape ).toLowerCase(); + return nodeNameSelector === "*" ? + function() { + return true; + } : + function( elem ) { + return elem.nodeName && elem.nodeName.toLowerCase() === nodeName; + }; + }, + + "CLASS": function( className ) { + var pattern = classCache[ className + " " ]; + + return pattern || + ( pattern = new RegExp( "(^|" + whitespace + + ")" + className + "(" + whitespace + "|$)" ) ) && classCache( + className, function( elem ) { + return pattern.test( + typeof elem.className === "string" && elem.className || + typeof elem.getAttribute !== "undefined" && + elem.getAttribute( "class" ) || + "" + ); + } ); + }, + + "ATTR": function( name, operator, check ) { + return function( elem ) { + var result = Sizzle.attr( elem, name ); + + if ( result == null ) { + return operator === "!="; + } + if ( !operator ) { + return true; + } + + result += ""; + + /* eslint-disable max-len */ + + return operator === "=" ? result === check : + operator === "!=" ? result !== check : + operator === "^=" ? check && result.indexOf( check ) === 0 : + operator === "*=" ? check && result.indexOf( check ) > -1 : + operator === "$=" ? check && result.slice( -check.length ) === check : + operator === "~=" ? ( " " + result.replace( rwhitespace, " " ) + " " ).indexOf( check ) > -1 : + operator === "|=" ? result === check || result.slice( 0, check.length + 1 ) === check + "-" : + false; + /* eslint-enable max-len */ + + }; + }, + + "CHILD": function( type, what, _argument, first, last ) { + var simple = type.slice( 0, 3 ) !== "nth", + forward = type.slice( -4 ) !== "last", + ofType = what === "of-type"; + + return first === 1 && last === 0 ? + + // Shortcut for :nth-*(n) + function( elem ) { + return !!elem.parentNode; + } : + + function( elem, _context, xml ) { + var cache, uniqueCache, outerCache, node, nodeIndex, start, + dir = simple !== forward ? "nextSibling" : "previousSibling", + parent = elem.parentNode, + name = ofType && elem.nodeName.toLowerCase(), + useCache = !xml && !ofType, + diff = false; + + if ( parent ) { + + // :(first|last|only)-(child|of-type) + if ( simple ) { + while ( dir ) { + node = elem; + while ( ( node = node[ dir ] ) ) { + if ( ofType ? + node.nodeName.toLowerCase() === name : + node.nodeType === 1 ) { + + return false; + } + } + + // Reverse direction for :only-* (if we haven't yet done so) + start = dir = type === "only" && !start && "nextSibling"; + } + return true; + } + + start = [ forward ? parent.firstChild : parent.lastChild ]; + + // non-xml :nth-child(...) stores cache data on `parent` + if ( forward && useCache ) { + + // Seek `elem` from a previously-cached index + + // ...in a gzip-friendly way + node = parent; + outerCache = node[ expando ] || ( node[ expando ] = {} ); + + // Support: IE <9 only + // Defend against cloned attroperties (jQuery gh-1709) + uniqueCache = outerCache[ node.uniqueID ] || + ( outerCache[ node.uniqueID ] = {} ); + + cache = uniqueCache[ type ] || []; + nodeIndex = cache[ 0 ] === dirruns && cache[ 1 ]; + diff = nodeIndex && cache[ 2 ]; + node = nodeIndex && parent.childNodes[ nodeIndex ]; + + while ( ( node = ++nodeIndex && node && node[ dir ] || + + // Fallback to seeking `elem` from the start + ( diff = nodeIndex = 0 ) || start.pop() ) ) { + + // When found, cache indexes on `parent` and break + if ( node.nodeType === 1 && ++diff && node === elem ) { + uniqueCache[ type ] = [ dirruns, nodeIndex, diff ]; + break; + } + } + + } else { + + // Use previously-cached element index if available + if ( useCache ) { + + // ...in a gzip-friendly way + node = elem; + outerCache = node[ expando ] || ( node[ expando ] = {} ); + + // Support: IE <9 only + // Defend against cloned attroperties (jQuery gh-1709) + uniqueCache = outerCache[ node.uniqueID ] || + ( outerCache[ node.uniqueID ] = {} ); + + cache = uniqueCache[ type ] || []; + nodeIndex = cache[ 0 ] === dirruns && cache[ 1 ]; + diff = nodeIndex; + } + + // xml :nth-child(...) + // or :nth-last-child(...) or :nth(-last)?-of-type(...) + if ( diff === false ) { + + // Use the same loop as above to seek `elem` from the start + while ( ( node = ++nodeIndex && node && node[ dir ] || + ( diff = nodeIndex = 0 ) || start.pop() ) ) { + + if ( ( ofType ? + node.nodeName.toLowerCase() === name : + node.nodeType === 1 ) && + ++diff ) { + + // Cache the index of each encountered element + if ( useCache ) { + outerCache = node[ expando ] || + ( node[ expando ] = {} ); + + // Support: IE <9 only + // Defend against cloned attroperties (jQuery gh-1709) + uniqueCache = outerCache[ node.uniqueID ] || + ( outerCache[ node.uniqueID ] = {} ); + + uniqueCache[ type ] = [ dirruns, diff ]; + } + + if ( node === elem ) { + break; + } + } + } + } + } + + // Incorporate the offset, then check against cycle size + diff -= last; + return diff === first || ( diff % first === 0 && diff / first >= 0 ); + } + }; + }, + + "PSEUDO": function( pseudo, argument ) { + + // pseudo-class names are case-insensitive + // http://www.w3.org/TR/selectors/#pseudo-classes + // Prioritize by case sensitivity in case custom pseudos are added with uppercase letters + // Remember that setFilters inherits from pseudos + var args, + fn = Expr.pseudos[ pseudo ] || Expr.setFilters[ pseudo.toLowerCase() ] || + Sizzle.error( "unsupported pseudo: " + pseudo ); + + // The user may use createPseudo to indicate that + // arguments are needed to create the filter function + // just as Sizzle does + if ( fn[ expando ] ) { + return fn( argument ); + } + + // But maintain support for old signatures + if ( fn.length > 1 ) { + args = [ pseudo, pseudo, "", argument ]; + return Expr.setFilters.hasOwnProperty( pseudo.toLowerCase() ) ? + markFunction( function( seed, matches ) { + var idx, + matched = fn( seed, argument ), + i = matched.length; + while ( i-- ) { + idx = indexOf( seed, matched[ i ] ); + seed[ idx ] = !( matches[ idx ] = matched[ i ] ); + } + } ) : + function( elem ) { + return fn( elem, 0, args ); + }; + } + + return fn; + } + }, + + pseudos: { + + // Potentially complex pseudos + "not": markFunction( function( selector ) { + + // Trim the selector passed to compile + // to avoid treating leading and trailing + // spaces as combinators + var input = [], + results = [], + matcher = compile( selector.replace( rtrim, "$1" ) ); + + return matcher[ expando ] ? + markFunction( function( seed, matches, _context, xml ) { + var elem, + unmatched = matcher( seed, null, xml, [] ), + i = seed.length; + + // Match elements unmatched by `matcher` + while ( i-- ) { + if ( ( elem = unmatched[ i ] ) ) { + seed[ i ] = !( matches[ i ] = elem ); + } + } + } ) : + function( elem, _context, xml ) { + input[ 0 ] = elem; + matcher( input, null, xml, results ); + + // Don't keep the element (issue #299) + input[ 0 ] = null; + return !results.pop(); + }; + } ), + + "has": markFunction( function( selector ) { + return function( elem ) { + return Sizzle( selector, elem ).length > 0; + }; + } ), + + "contains": markFunction( function( text ) { + text = text.replace( runescape, funescape ); + return function( elem ) { + return ( elem.textContent || getText( elem ) ).indexOf( text ) > -1; + }; + } ), + + // "Whether an element is represented by a :lang() selector + // is based solely on the element's language value + // being equal to the identifier C, + // or beginning with the identifier C immediately followed by "-". + // The matching of C against the element's language value is performed case-insensitively. + // The identifier C does not have to be a valid language name." + // http://www.w3.org/TR/selectors/#lang-pseudo + "lang": markFunction( function( lang ) { + + // lang value must be a valid identifier + if ( !ridentifier.test( lang || "" ) ) { + Sizzle.error( "unsupported lang: " + lang ); + } + lang = lang.replace( runescape, funescape ).toLowerCase(); + return function( elem ) { + var elemLang; + do { + if ( ( elemLang = documentIsHTML ? + elem.lang : + elem.getAttribute( "xml:lang" ) || elem.getAttribute( "lang" ) ) ) { + + elemLang = elemLang.toLowerCase(); + return elemLang === lang || elemLang.indexOf( lang + "-" ) === 0; + } + } while ( ( elem = elem.parentNode ) && elem.nodeType === 1 ); + return false; + }; + } ), + + // Miscellaneous + "target": function( elem ) { + var hash = window.location && window.location.hash; + return hash && hash.slice( 1 ) === elem.id; + }, + + "root": function( elem ) { + return elem === docElem; + }, + + "focus": function( elem ) { + return elem === document.activeElement && + ( !document.hasFocus || document.hasFocus() ) && + !!( elem.type || elem.href || ~elem.tabIndex ); + }, + + // Boolean properties + "enabled": createDisabledPseudo( false ), + "disabled": createDisabledPseudo( true ), + + "checked": function( elem ) { + + // In CSS3, :checked should return both checked and selected elements + // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked + var nodeName = elem.nodeName.toLowerCase(); + return ( nodeName === "input" && !!elem.checked ) || + ( nodeName === "option" && !!elem.selected ); + }, + + "selected": function( elem ) { + + // Accessing this property makes selected-by-default + // options in Safari work properly + if ( elem.parentNode ) { + // eslint-disable-next-line no-unused-expressions + elem.parentNode.selectedIndex; + } + + return elem.selected === true; + }, + + // Contents + "empty": function( elem ) { + + // http://www.w3.org/TR/selectors/#empty-pseudo + // :empty is negated by element (1) or content nodes (text: 3; cdata: 4; entity ref: 5), + // but not by others (comment: 8; processing instruction: 7; etc.) + // nodeType < 6 works because attributes (2) do not appear as children + for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) { + if ( elem.nodeType < 6 ) { + return false; + } + } + return true; + }, + + "parent": function( elem ) { + return !Expr.pseudos[ "empty" ]( elem ); + }, + + // Element/input types + "header": function( elem ) { + return rheader.test( elem.nodeName ); + }, + + "input": function( elem ) { + return rinputs.test( elem.nodeName ); + }, + + "button": function( elem ) { + var name = elem.nodeName.toLowerCase(); + return name === "input" && elem.type === "button" || name === "button"; + }, + + "text": function( elem ) { + var attr; + return elem.nodeName.toLowerCase() === "input" && + elem.type === "text" && + + // Support: IE<8 + // New HTML5 attribute values (e.g., "search") appear with elem.type === "text" + ( ( attr = elem.getAttribute( "type" ) ) == null || + attr.toLowerCase() === "text" ); + }, + + // Position-in-collection + "first": createPositionalPseudo( function() { + return [ 0 ]; + } ), + + "last": createPositionalPseudo( function( _matchIndexes, length ) { + return [ length - 1 ]; + } ), + + "eq": createPositionalPseudo( function( _matchIndexes, length, argument ) { + return [ argument < 0 ? argument + length : argument ]; + } ), + + "even": createPositionalPseudo( function( matchIndexes, length ) { + var i = 0; + for ( ; i < length; i += 2 ) { + matchIndexes.push( i ); + } + return matchIndexes; + } ), + + "odd": createPositionalPseudo( function( matchIndexes, length ) { + var i = 1; + for ( ; i < length; i += 2 ) { + matchIndexes.push( i ); + } + return matchIndexes; + } ), + + "lt": createPositionalPseudo( function( matchIndexes, length, argument ) { + var i = argument < 0 ? + argument + length : + argument > length ? + length : + argument; + for ( ; --i >= 0; ) { + matchIndexes.push( i ); + } + return matchIndexes; + } ), + + "gt": createPositionalPseudo( function( matchIndexes, length, argument ) { + var i = argument < 0 ? argument + length : argument; + for ( ; ++i < length; ) { + matchIndexes.push( i ); + } + return matchIndexes; + } ) + } +}; + +Expr.pseudos[ "nth" ] = Expr.pseudos[ "eq" ]; + +// Add button/input type pseudos +for ( i in { radio: true, checkbox: true, file: true, password: true, image: true } ) { + Expr.pseudos[ i ] = createInputPseudo( i ); +} +for ( i in { submit: true, reset: true } ) { + Expr.pseudos[ i ] = createButtonPseudo( i ); +} + +// Easy API for creating new setFilters +function setFilters() {} +setFilters.prototype = Expr.filters = Expr.pseudos; +Expr.setFilters = new setFilters(); + +tokenize = Sizzle.tokenize = function( selector, parseOnly ) { + var matched, match, tokens, type, + soFar, groups, preFilters, + cached = tokenCache[ selector + " " ]; + + if ( cached ) { + return parseOnly ? 0 : cached.slice( 0 ); + } + + soFar = selector; + groups = []; + preFilters = Expr.preFilter; + + while ( soFar ) { + + // Comma and first run + if ( !matched || ( match = rcomma.exec( soFar ) ) ) { + if ( match ) { + + // Don't consume trailing commas as valid + soFar = soFar.slice( match[ 0 ].length ) || soFar; + } + groups.push( ( tokens = [] ) ); + } + + matched = false; + + // Combinators + if ( ( match = rcombinators.exec( soFar ) ) ) { + matched = match.shift(); + tokens.push( { + value: matched, + + // Cast descendant combinators to space + type: match[ 0 ].replace( rtrim, " " ) + } ); + soFar = soFar.slice( matched.length ); + } + + // Filters + for ( type in Expr.filter ) { + if ( ( match = matchExpr[ type ].exec( soFar ) ) && ( !preFilters[ type ] || + ( match = preFilters[ type ]( match ) ) ) ) { + matched = match.shift(); + tokens.push( { + value: matched, + type: type, + matches: match + } ); + soFar = soFar.slice( matched.length ); + } + } + + if ( !matched ) { + break; + } + } + + // Return the length of the invalid excess + // if we're just parsing + // Otherwise, throw an error or return tokens + return parseOnly ? + soFar.length : + soFar ? + Sizzle.error( selector ) : + + // Cache the tokens + tokenCache( selector, groups ).slice( 0 ); +}; + +function toSelector( tokens ) { + var i = 0, + len = tokens.length, + selector = ""; + for ( ; i < len; i++ ) { + selector += tokens[ i ].value; + } + return selector; +} + +function addCombinator( matcher, combinator, base ) { + var dir = combinator.dir, + skip = combinator.next, + key = skip || dir, + checkNonElements = base && key === "parentNode", + doneName = done++; + + return combinator.first ? + + // Check against closest ancestor/preceding element + function( elem, context, xml ) { + while ( ( elem = elem[ dir ] ) ) { + if ( elem.nodeType === 1 || checkNonElements ) { + return matcher( elem, context, xml ); + } + } + return false; + } : + + // Check against all ancestor/preceding elements + function( elem, context, xml ) { + var oldCache, uniqueCache, outerCache, + newCache = [ dirruns, doneName ]; + + // We can't set arbitrary data on XML nodes, so they don't benefit from combinator caching + if ( xml ) { + while ( ( elem = elem[ dir ] ) ) { + if ( elem.nodeType === 1 || checkNonElements ) { + if ( matcher( elem, context, xml ) ) { + return true; + } + } + } + } else { + while ( ( elem = elem[ dir ] ) ) { + if ( elem.nodeType === 1 || checkNonElements ) { + outerCache = elem[ expando ] || ( elem[ expando ] = {} ); + + // Support: IE <9 only + // Defend against cloned attroperties (jQuery gh-1709) + uniqueCache = outerCache[ elem.uniqueID ] || + ( outerCache[ elem.uniqueID ] = {} ); + + if ( skip && skip === elem.nodeName.toLowerCase() ) { + elem = elem[ dir ] || elem; + } else if ( ( oldCache = uniqueCache[ key ] ) && + oldCache[ 0 ] === dirruns && oldCache[ 1 ] === doneName ) { + + // Assign to newCache so results back-propagate to previous elements + return ( newCache[ 2 ] = oldCache[ 2 ] ); + } else { + + // Reuse newcache so results back-propagate to previous elements + uniqueCache[ key ] = newCache; + + // A match means we're done; a fail means we have to keep checking + if ( ( newCache[ 2 ] = matcher( elem, context, xml ) ) ) { + return true; + } + } + } + } + } + return false; + }; +} + +function elementMatcher( matchers ) { + return matchers.length > 1 ? + function( elem, context, xml ) { + var i = matchers.length; + while ( i-- ) { + if ( !matchers[ i ]( elem, context, xml ) ) { + return false; + } + } + return true; + } : + matchers[ 0 ]; +} + +function multipleContexts( selector, contexts, results ) { + var i = 0, + len = contexts.length; + for ( ; i < len; i++ ) { + Sizzle( selector, contexts[ i ], results ); + } + return results; +} + +function condense( unmatched, map, filter, context, xml ) { + var elem, + newUnmatched = [], + i = 0, + len = unmatched.length, + mapped = map != null; + + for ( ; i < len; i++ ) { + if ( ( elem = unmatched[ i ] ) ) { + if ( !filter || filter( elem, context, xml ) ) { + newUnmatched.push( elem ); + if ( mapped ) { + map.push( i ); + } + } + } + } + + return newUnmatched; +} + +function setMatcher( preFilter, selector, matcher, postFilter, postFinder, postSelector ) { + if ( postFilter && !postFilter[ expando ] ) { + postFilter = setMatcher( postFilter ); + } + if ( postFinder && !postFinder[ expando ] ) { + postFinder = setMatcher( postFinder, postSelector ); + } + return markFunction( function( seed, results, context, xml ) { + var temp, i, elem, + preMap = [], + postMap = [], + preexisting = results.length, + + // Get initial elements from seed or context + elems = seed || multipleContexts( + selector || "*", + context.nodeType ? [ context ] : context, + [] + ), + + // Prefilter to get matcher input, preserving a map for seed-results synchronization + matcherIn = preFilter && ( seed || !selector ) ? + condense( elems, preMap, preFilter, context, xml ) : + elems, + + matcherOut = matcher ? + + // If we have a postFinder, or filtered seed, or non-seed postFilter or preexisting results, + postFinder || ( seed ? preFilter : preexisting || postFilter ) ? + + // ...intermediate processing is necessary + [] : + + // ...otherwise use results directly + results : + matcherIn; + + // Find primary matches + if ( matcher ) { + matcher( matcherIn, matcherOut, context, xml ); + } + + // Apply postFilter + if ( postFilter ) { + temp = condense( matcherOut, postMap ); + postFilter( temp, [], context, xml ); + + // Un-match failing elements by moving them back to matcherIn + i = temp.length; + while ( i-- ) { + if ( ( elem = temp[ i ] ) ) { + matcherOut[ postMap[ i ] ] = !( matcherIn[ postMap[ i ] ] = elem ); + } + } + } + + if ( seed ) { + if ( postFinder || preFilter ) { + if ( postFinder ) { + + // Get the final matcherOut by condensing this intermediate into postFinder contexts + temp = []; + i = matcherOut.length; + while ( i-- ) { + if ( ( elem = matcherOut[ i ] ) ) { + + // Restore matcherIn since elem is not yet a final match + temp.push( ( matcherIn[ i ] = elem ) ); + } + } + postFinder( null, ( matcherOut = [] ), temp, xml ); + } + + // Move matched elements from seed to results to keep them synchronized + i = matcherOut.length; + while ( i-- ) { + if ( ( elem = matcherOut[ i ] ) && + ( temp = postFinder ? indexOf( seed, elem ) : preMap[ i ] ) > -1 ) { + + seed[ temp ] = !( results[ temp ] = elem ); + } + } + } + + // Add elements to results, through postFinder if defined + } else { + matcherOut = condense( + matcherOut === results ? + matcherOut.splice( preexisting, matcherOut.length ) : + matcherOut + ); + if ( postFinder ) { + postFinder( null, results, matcherOut, xml ); + } else { + push.apply( results, matcherOut ); + } + } + } ); +} + +function matcherFromTokens( tokens ) { + var checkContext, matcher, j, + len = tokens.length, + leadingRelative = Expr.relative[ tokens[ 0 ].type ], + implicitRelative = leadingRelative || Expr.relative[ " " ], + i = leadingRelative ? 1 : 0, + + // The foundational matcher ensures that elements are reachable from top-level context(s) + matchContext = addCombinator( function( elem ) { + return elem === checkContext; + }, implicitRelative, true ), + matchAnyContext = addCombinator( function( elem ) { + return indexOf( checkContext, elem ) > -1; + }, implicitRelative, true ), + matchers = [ function( elem, context, xml ) { + var ret = ( !leadingRelative && ( xml || context !== outermostContext ) ) || ( + ( checkContext = context ).nodeType ? + matchContext( elem, context, xml ) : + matchAnyContext( elem, context, xml ) ); + + // Avoid hanging onto element (issue #299) + checkContext = null; + return ret; + } ]; + + for ( ; i < len; i++ ) { + if ( ( matcher = Expr.relative[ tokens[ i ].type ] ) ) { + matchers = [ addCombinator( elementMatcher( matchers ), matcher ) ]; + } else { + matcher = Expr.filter[ tokens[ i ].type ].apply( null, tokens[ i ].matches ); + + // Return special upon seeing a positional matcher + if ( matcher[ expando ] ) { + + // Find the next relative operator (if any) for proper handling + j = ++i; + for ( ; j < len; j++ ) { + if ( Expr.relative[ tokens[ j ].type ] ) { + break; + } + } + return setMatcher( + i > 1 && elementMatcher( matchers ), + i > 1 && toSelector( + + // If the preceding token was a descendant combinator, insert an implicit any-element `*` + tokens + .slice( 0, i - 1 ) + .concat( { value: tokens[ i - 2 ].type === " " ? "*" : "" } ) + ).replace( rtrim, "$1" ), + matcher, + i < j && matcherFromTokens( tokens.slice( i, j ) ), + j < len && matcherFromTokens( ( tokens = tokens.slice( j ) ) ), + j < len && toSelector( tokens ) + ); + } + matchers.push( matcher ); + } + } + + return elementMatcher( matchers ); +} + +function matcherFromGroupMatchers( elementMatchers, setMatchers ) { + var bySet = setMatchers.length > 0, + byElement = elementMatchers.length > 0, + superMatcher = function( seed, context, xml, results, outermost ) { + var elem, j, matcher, + matchedCount = 0, + i = "0", + unmatched = seed && [], + setMatched = [], + contextBackup = outermostContext, + + // We must always have either seed elements or outermost context + elems = seed || byElement && Expr.find[ "TAG" ]( "*", outermost ), + + // Use integer dirruns iff this is the outermost matcher + dirrunsUnique = ( dirruns += contextBackup == null ? 1 : Math.random() || 0.1 ), + len = elems.length; + + if ( outermost ) { + + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + outermostContext = context == document || context || outermost; + } + + // Add elements passing elementMatchers directly to results + // Support: IE<9, Safari + // Tolerate NodeList properties (IE: "length"; Safari: <number>) matching elements by id + for ( ; i !== len && ( elem = elems[ i ] ) != null; i++ ) { + if ( byElement && elem ) { + j = 0; + + // Support: IE 11+, Edge 17 - 18+ + // IE/Edge sometimes throw a "Permission denied" error when strict-comparing + // two documents; shallow comparisons work. + // eslint-disable-next-line eqeqeq + if ( !context && elem.ownerDocument != document ) { + setDocument( elem ); + xml = !documentIsHTML; + } + while ( ( matcher = elementMatchers[ j++ ] ) ) { + if ( matcher( elem, context || document, xml ) ) { + results.push( elem ); + break; + } + } + if ( outermost ) { + dirruns = dirrunsUnique; + } + } + + // Track unmatched elements for set filters + if ( bySet ) { + + // They will have gone through all possible matchers + if ( ( elem = !matcher && elem ) ) { + matchedCount--; + } + + // Lengthen the array for every element, matched or not + if ( seed ) { + unmatched.push( elem ); + } + } + } + + // `i` is now the count of elements visited above, and adding it to `matchedCount` + // makes the latter nonnegative. + matchedCount += i; + + // Apply set filters to unmatched elements + // NOTE: This can be skipped if there are no unmatched elements (i.e., `matchedCount` + // equals `i`), unless we didn't visit _any_ elements in the above loop because we have + // no element matchers and no seed. + // Incrementing an initially-string "0" `i` allows `i` to remain a string only in that + // case, which will result in a "00" `matchedCount` that differs from `i` but is also + // numerically zero. + if ( bySet && i !== matchedCount ) { + j = 0; + while ( ( matcher = setMatchers[ j++ ] ) ) { + matcher( unmatched, setMatched, context, xml ); + } + + if ( seed ) { + + // Reintegrate element matches to eliminate the need for sorting + if ( matchedCount > 0 ) { + while ( i-- ) { + if ( !( unmatched[ i ] || setMatched[ i ] ) ) { + setMatched[ i ] = pop.call( results ); + } + } + } + + // Discard index placeholder values to get only actual matches + setMatched = condense( setMatched ); + } + + // Add matches to results + push.apply( results, setMatched ); + + // Seedless set matches succeeding multiple successful matchers stipulate sorting + if ( outermost && !seed && setMatched.length > 0 && + ( matchedCount + setMatchers.length ) > 1 ) { + + Sizzle.uniqueSort( results ); + } + } + + // Override manipulation of globals by nested matchers + if ( outermost ) { + dirruns = dirrunsUnique; + outermostContext = contextBackup; + } + + return unmatched; + }; + + return bySet ? + markFunction( superMatcher ) : + superMatcher; +} + +compile = Sizzle.compile = function( selector, match /* Internal Use Only */ ) { + var i, + setMatchers = [], + elementMatchers = [], + cached = compilerCache[ selector + " " ]; + + if ( !cached ) { + + // Generate a function of recursive functions that can be used to check each element + if ( !match ) { + match = tokenize( selector ); + } + i = match.length; + while ( i-- ) { + cached = matcherFromTokens( match[ i ] ); + if ( cached[ expando ] ) { + setMatchers.push( cached ); + } else { + elementMatchers.push( cached ); + } + } + + // Cache the compiled function + cached = compilerCache( + selector, + matcherFromGroupMatchers( elementMatchers, setMatchers ) + ); + + // Save selector and tokenization + cached.selector = selector; + } + return cached; +}; + +/** + * A low-level selection function that works with Sizzle's compiled + * selector functions + * @param {String|Function} selector A selector or a pre-compiled + * selector function built with Sizzle.compile + * @param {Element} context + * @param {Array} [results] + * @param {Array} [seed] A set of elements to match against + */ +select = Sizzle.select = function( selector, context, results, seed ) { + var i, tokens, token, type, find, + compiled = typeof selector === "function" && selector, + match = !seed && tokenize( ( selector = compiled.selector || selector ) ); + + results = results || []; + + // Try to minimize operations if there is only one selector in the list and no seed + // (the latter of which guarantees us context) + if ( match.length === 1 ) { + + // Reduce context if the leading compound selector is an ID + tokens = match[ 0 ] = match[ 0 ].slice( 0 ); + if ( tokens.length > 2 && ( token = tokens[ 0 ] ).type === "ID" && + context.nodeType === 9 && documentIsHTML && Expr.relative[ tokens[ 1 ].type ] ) { + + context = ( Expr.find[ "ID" ]( token.matches[ 0 ] + .replace( runescape, funescape ), context ) || [] )[ 0 ]; + if ( !context ) { + return results; + + // Precompiled matchers will still verify ancestry, so step up a level + } else if ( compiled ) { + context = context.parentNode; + } + + selector = selector.slice( tokens.shift().value.length ); + } + + // Fetch a seed set for right-to-left matching + i = matchExpr[ "needsContext" ].test( selector ) ? 0 : tokens.length; + while ( i-- ) { + token = tokens[ i ]; + + // Abort if we hit a combinator + if ( Expr.relative[ ( type = token.type ) ] ) { + break; + } + if ( ( find = Expr.find[ type ] ) ) { + + // Search, expanding context for leading sibling combinators + if ( ( seed = find( + token.matches[ 0 ].replace( runescape, funescape ), + rsibling.test( tokens[ 0 ].type ) && testContext( context.parentNode ) || + context + ) ) ) { + + // If seed is empty or no tokens remain, we can return early + tokens.splice( i, 1 ); + selector = seed.length && toSelector( tokens ); + if ( !selector ) { + push.apply( results, seed ); + return results; + } + + break; + } + } + } + } + + // Compile and execute a filtering function if one is not provided + // Provide `match` to avoid retokenization if we modified the selector above + ( compiled || compile( selector, match ) )( + seed, + context, + !documentIsHTML, + results, + !context || rsibling.test( selector ) && testContext( context.parentNode ) || context + ); + return results; +}; + +// One-time assignments + +// Sort stability +support.sortStable = expando.split( "" ).sort( sortOrder ).join( "" ) === expando; + +// Support: Chrome 14-35+ +// Always assume duplicates if they aren't passed to the comparison function +support.detectDuplicates = !!hasDuplicate; + +// Initialize against the default document +setDocument(); + +// Support: Webkit<537.32 - Safari 6.0.3/Chrome 25 (fixed in Chrome 27) +// Detached nodes confoundingly follow *each other* +support.sortDetached = assert( function( el ) { + + // Should return 1, but returns 4 (following) + return el.compareDocumentPosition( document.createElement( "fieldset" ) ) & 1; +} ); + +// Support: IE<8 +// Prevent attribute/property "interpolation" +// https://msdn.microsoft.com/en-us/library/ms536429%28VS.85%29.aspx +if ( !assert( function( el ) { + el.innerHTML = "<a href='#'></a>"; + return el.firstChild.getAttribute( "href" ) === "#"; +} ) ) { + addHandle( "type|href|height|width", function( elem, name, isXML ) { + if ( !isXML ) { + return elem.getAttribute( name, name.toLowerCase() === "type" ? 1 : 2 ); + } + } ); +} + +// Support: IE<9 +// Use defaultValue in place of getAttribute("value") +if ( !support.attributes || !assert( function( el ) { + el.innerHTML = "<input/>"; + el.firstChild.setAttribute( "value", "" ); + return el.firstChild.getAttribute( "value" ) === ""; +} ) ) { + addHandle( "value", function( elem, _name, isXML ) { + if ( !isXML && elem.nodeName.toLowerCase() === "input" ) { + return elem.defaultValue; + } + } ); +} + +// Support: IE<9 +// Use getAttributeNode to fetch booleans when getAttribute lies +if ( !assert( function( el ) { + return el.getAttribute( "disabled" ) == null; +} ) ) { + addHandle( booleans, function( elem, name, isXML ) { + var val; + if ( !isXML ) { + return elem[ name ] === true ? name.toLowerCase() : + ( val = elem.getAttributeNode( name ) ) && val.specified ? + val.value : + null; + } + } ); +} + +return Sizzle; + +} )( window ); + + + +jQuery.find = Sizzle; +jQuery.expr = Sizzle.selectors; + +// Deprecated +jQuery.expr[ ":" ] = jQuery.expr.pseudos; +jQuery.uniqueSort = jQuery.unique = Sizzle.uniqueSort; +jQuery.text = Sizzle.getText; +jQuery.isXMLDoc = Sizzle.isXML; +jQuery.contains = Sizzle.contains; +jQuery.escapeSelector = Sizzle.escape; + + + + +var dir = function( elem, dir, until ) { + var matched = [], + truncate = until !== undefined; + + while ( ( elem = elem[ dir ] ) && elem.nodeType !== 9 ) { + if ( elem.nodeType === 1 ) { + if ( truncate && jQuery( elem ).is( until ) ) { + break; + } + matched.push( elem ); + } + } + return matched; +}; + + +var siblings = function( n, elem ) { + var matched = []; + + for ( ; n; n = n.nextSibling ) { + if ( n.nodeType === 1 && n !== elem ) { + matched.push( n ); + } + } + + return matched; +}; + + +var rneedsContext = jQuery.expr.match.needsContext; + + + +function nodeName( elem, name ) { + + return elem.nodeName && elem.nodeName.toLowerCase() === name.toLowerCase(); + +} +var rsingleTag = ( /^<([a-z][^\/\0>:\x20\t\r\n\f]*)[\x20\t\r\n\f]*\/?>(?:<\/\1>|)$/i ); + + + +// Implement the identical functionality for filter and not +function winnow( elements, qualifier, not ) { + if ( isFunction( qualifier ) ) { + return jQuery.grep( elements, function( elem, i ) { + return !!qualifier.call( elem, i, elem ) !== not; + } ); + } + + // Single element + if ( qualifier.nodeType ) { + return jQuery.grep( elements, function( elem ) { + return ( elem === qualifier ) !== not; + } ); + } + + // Arraylike of elements (jQuery, arguments, Array) + if ( typeof qualifier !== "string" ) { + return jQuery.grep( elements, function( elem ) { + return ( indexOf.call( qualifier, elem ) > -1 ) !== not; + } ); + } + + // Filtered directly for both simple and complex selectors + return jQuery.filter( qualifier, elements, not ); +} + +jQuery.filter = function( expr, elems, not ) { + var elem = elems[ 0 ]; + + if ( not ) { + expr = ":not(" + expr + ")"; + } + + if ( elems.length === 1 && elem.nodeType === 1 ) { + return jQuery.find.matchesSelector( elem, expr ) ? [ elem ] : []; + } + + return jQuery.find.matches( expr, jQuery.grep( elems, function( elem ) { + return elem.nodeType === 1; + } ) ); +}; + +jQuery.fn.extend( { + find: function( selector ) { + var i, ret, + len = this.length, + self = this; + + if ( typeof selector !== "string" ) { + return this.pushStack( jQuery( selector ).filter( function() { + for ( i = 0; i < len; i++ ) { + if ( jQuery.contains( self[ i ], this ) ) { + return true; + } + } + } ) ); + } + + ret = this.pushStack( [] ); + + for ( i = 0; i < len; i++ ) { + jQuery.find( selector, self[ i ], ret ); + } + + return len > 1 ? jQuery.uniqueSort( ret ) : ret; + }, + filter: function( selector ) { + return this.pushStack( winnow( this, selector || [], false ) ); + }, + not: function( selector ) { + return this.pushStack( winnow( this, selector || [], true ) ); + }, + is: function( selector ) { + return !!winnow( + this, + + // If this is a positional/relative selector, check membership in the returned set + // so $("p:first").is("p:last") won't return true for a doc with two "p". + typeof selector === "string" && rneedsContext.test( selector ) ? + jQuery( selector ) : + selector || [], + false + ).length; + } +} ); + + +// Initialize a jQuery object + + +// A central reference to the root jQuery(document) +var rootjQuery, + + // A simple way to check for HTML strings + // Prioritize #id over <tag> to avoid XSS via location.hash (#9521) + // Strict HTML recognition (#11290: must start with <) + // Shortcut simple #id case for speed + rquickExpr = /^(?:\s*(<[\w\W]+>)[^>]*|#([\w-]+))$/, + + init = jQuery.fn.init = function( selector, context, root ) { + var match, elem; + + // HANDLE: $(""), $(null), $(undefined), $(false) + if ( !selector ) { + return this; + } + + // Method init() accepts an alternate rootjQuery + // so migrate can support jQuery.sub (gh-2101) + root = root || rootjQuery; + + // Handle HTML strings + if ( typeof selector === "string" ) { + if ( selector[ 0 ] === "<" && + selector[ selector.length - 1 ] === ">" && + selector.length >= 3 ) { + + // Assume that strings that start and end with <> are HTML and skip the regex check + match = [ null, selector, null ]; + + } else { + match = rquickExpr.exec( selector ); + } + + // Match html or make sure no context is specified for #id + if ( match && ( match[ 1 ] || !context ) ) { + + // HANDLE: $(html) -> $(array) + if ( match[ 1 ] ) { + context = context instanceof jQuery ? context[ 0 ] : context; + + // Option to run scripts is true for back-compat + // Intentionally let the error be thrown if parseHTML is not present + jQuery.merge( this, jQuery.parseHTML( + match[ 1 ], + context && context.nodeType ? context.ownerDocument || context : document, + true + ) ); + + // HANDLE: $(html, props) + if ( rsingleTag.test( match[ 1 ] ) && jQuery.isPlainObject( context ) ) { + for ( match in context ) { + + // Properties of context are called as methods if possible + if ( isFunction( this[ match ] ) ) { + this[ match ]( context[ match ] ); + + // ...and otherwise set as attributes + } else { + this.attr( match, context[ match ] ); + } + } + } + + return this; + + // HANDLE: $(#id) + } else { + elem = document.getElementById( match[ 2 ] ); + + if ( elem ) { + + // Inject the element directly into the jQuery object + this[ 0 ] = elem; + this.length = 1; + } + return this; + } + + // HANDLE: $(expr, $(...)) + } else if ( !context || context.jquery ) { + return ( context || root ).find( selector ); + + // HANDLE: $(expr, context) + // (which is just equivalent to: $(context).find(expr) + } else { + return this.constructor( context ).find( selector ); + } + + // HANDLE: $(DOMElement) + } else if ( selector.nodeType ) { + this[ 0 ] = selector; + this.length = 1; + return this; + + // HANDLE: $(function) + // Shortcut for document ready + } else if ( isFunction( selector ) ) { + return root.ready !== undefined ? + root.ready( selector ) : + + // Execute immediately if ready is not present + selector( jQuery ); + } + + return jQuery.makeArray( selector, this ); + }; + +// Give the init function the jQuery prototype for later instantiation +init.prototype = jQuery.fn; + +// Initialize central reference +rootjQuery = jQuery( document ); + + +var rparentsprev = /^(?:parents|prev(?:Until|All))/, + + // Methods guaranteed to produce a unique set when starting from a unique set + guaranteedUnique = { + children: true, + contents: true, + next: true, + prev: true + }; + +jQuery.fn.extend( { + has: function( target ) { + var targets = jQuery( target, this ), + l = targets.length; + + return this.filter( function() { + var i = 0; + for ( ; i < l; i++ ) { + if ( jQuery.contains( this, targets[ i ] ) ) { + return true; + } + } + } ); + }, + + closest: function( selectors, context ) { + var cur, + i = 0, + l = this.length, + matched = [], + targets = typeof selectors !== "string" && jQuery( selectors ); + + // Positional selectors never match, since there's no _selection_ context + if ( !rneedsContext.test( selectors ) ) { + for ( ; i < l; i++ ) { + for ( cur = this[ i ]; cur && cur !== context; cur = cur.parentNode ) { + + // Always skip document fragments + if ( cur.nodeType < 11 && ( targets ? + targets.index( cur ) > -1 : + + // Don't pass non-elements to Sizzle + cur.nodeType === 1 && + jQuery.find.matchesSelector( cur, selectors ) ) ) { + + matched.push( cur ); + break; + } + } + } + } + + return this.pushStack( matched.length > 1 ? jQuery.uniqueSort( matched ) : matched ); + }, + + // Determine the position of an element within the set + index: function( elem ) { + + // No argument, return index in parent + if ( !elem ) { + return ( this[ 0 ] && this[ 0 ].parentNode ) ? this.first().prevAll().length : -1; + } + + // Index in selector + if ( typeof elem === "string" ) { + return indexOf.call( jQuery( elem ), this[ 0 ] ); + } + + // Locate the position of the desired element + return indexOf.call( this, + + // If it receives a jQuery object, the first element is used + elem.jquery ? elem[ 0 ] : elem + ); + }, + + add: function( selector, context ) { + return this.pushStack( + jQuery.uniqueSort( + jQuery.merge( this.get(), jQuery( selector, context ) ) + ) + ); + }, + + addBack: function( selector ) { + return this.add( selector == null ? + this.prevObject : this.prevObject.filter( selector ) + ); + } +} ); + +function sibling( cur, dir ) { + while ( ( cur = cur[ dir ] ) && cur.nodeType !== 1 ) {} + return cur; +} + +jQuery.each( { + parent: function( elem ) { + var parent = elem.parentNode; + return parent && parent.nodeType !== 11 ? parent : null; + }, + parents: function( elem ) { + return dir( elem, "parentNode" ); + }, + parentsUntil: function( elem, _i, until ) { + return dir( elem, "parentNode", until ); + }, + next: function( elem ) { + return sibling( elem, "nextSibling" ); + }, + prev: function( elem ) { + return sibling( elem, "previousSibling" ); + }, + nextAll: function( elem ) { + return dir( elem, "nextSibling" ); + }, + prevAll: function( elem ) { + return dir( elem, "previousSibling" ); + }, + nextUntil: function( elem, _i, until ) { + return dir( elem, "nextSibling", until ); + }, + prevUntil: function( elem, _i, until ) { + return dir( elem, "previousSibling", until ); + }, + siblings: function( elem ) { + return siblings( ( elem.parentNode || {} ).firstChild, elem ); + }, + children: function( elem ) { + return siblings( elem.firstChild ); + }, + contents: function( elem ) { + if ( elem.contentDocument != null && + + // Support: IE 11+ + // <object> elements with no `data` attribute has an object + // `contentDocument` with a `null` prototype. + getProto( elem.contentDocument ) ) { + + return elem.contentDocument; + } + + // Support: IE 9 - 11 only, iOS 7 only, Android Browser <=4.3 only + // Treat the template element as a regular one in browsers that + // don't support it. + if ( nodeName( elem, "template" ) ) { + elem = elem.content || elem; + } + + return jQuery.merge( [], elem.childNodes ); + } +}, function( name, fn ) { + jQuery.fn[ name ] = function( until, selector ) { + var matched = jQuery.map( this, fn, until ); + + if ( name.slice( -5 ) !== "Until" ) { + selector = until; + } + + if ( selector && typeof selector === "string" ) { + matched = jQuery.filter( selector, matched ); + } + + if ( this.length > 1 ) { + + // Remove duplicates + if ( !guaranteedUnique[ name ] ) { + jQuery.uniqueSort( matched ); + } + + // Reverse order for parents* and prev-derivatives + if ( rparentsprev.test( name ) ) { + matched.reverse(); + } + } + + return this.pushStack( matched ); + }; +} ); +var rnothtmlwhite = ( /[^\x20\t\r\n\f]+/g ); + + + +// Convert String-formatted options into Object-formatted ones +function createOptions( options ) { + var object = {}; + jQuery.each( options.match( rnothtmlwhite ) || [], function( _, flag ) { + object[ flag ] = true; + } ); + return object; +} + +/* + * Create a callback list using the following parameters: + * + * options: an optional list of space-separated options that will change how + * the callback list behaves or a more traditional option object + * + * By default a callback list will act like an event callback list and can be + * "fired" multiple times. + * + * Possible options: + * + * once: will ensure the callback list can only be fired once (like a Deferred) + * + * memory: will keep track of previous values and will call any callback added + * after the list has been fired right away with the latest "memorized" + * values (like a Deferred) + * + * unique: will ensure a callback can only be added once (no duplicate in the list) + * + * stopOnFalse: interrupt callings when a callback returns false + * + */ +jQuery.Callbacks = function( options ) { + + // Convert options from String-formatted to Object-formatted if needed + // (we check in cache first) + options = typeof options === "string" ? + createOptions( options ) : + jQuery.extend( {}, options ); + + var // Flag to know if list is currently firing + firing, + + // Last fire value for non-forgettable lists + memory, + + // Flag to know if list was already fired + fired, + + // Flag to prevent firing + locked, + + // Actual callback list + list = [], + + // Queue of execution data for repeatable lists + queue = [], + + // Index of currently firing callback (modified by add/remove as needed) + firingIndex = -1, + + // Fire callbacks + fire = function() { + + // Enforce single-firing + locked = locked || options.once; + + // Execute callbacks for all pending executions, + // respecting firingIndex overrides and runtime changes + fired = firing = true; + for ( ; queue.length; firingIndex = -1 ) { + memory = queue.shift(); + while ( ++firingIndex < list.length ) { + + // Run callback and check for early termination + if ( list[ firingIndex ].apply( memory[ 0 ], memory[ 1 ] ) === false && + options.stopOnFalse ) { + + // Jump to end and forget the data so .add doesn't re-fire + firingIndex = list.length; + memory = false; + } + } + } + + // Forget the data if we're done with it + if ( !options.memory ) { + memory = false; + } + + firing = false; + + // Clean up if we're done firing for good + if ( locked ) { + + // Keep an empty list if we have data for future add calls + if ( memory ) { + list = []; + + // Otherwise, this object is spent + } else { + list = ""; + } + } + }, + + // Actual Callbacks object + self = { + + // Add a callback or a collection of callbacks to the list + add: function() { + if ( list ) { + + // If we have memory from a past run, we should fire after adding + if ( memory && !firing ) { + firingIndex = list.length - 1; + queue.push( memory ); + } + + ( function add( args ) { + jQuery.each( args, function( _, arg ) { + if ( isFunction( arg ) ) { + if ( !options.unique || !self.has( arg ) ) { + list.push( arg ); + } + } else if ( arg && arg.length && toType( arg ) !== "string" ) { + + // Inspect recursively + add( arg ); + } + } ); + } )( arguments ); + + if ( memory && !firing ) { + fire(); + } + } + return this; + }, + + // Remove a callback from the list + remove: function() { + jQuery.each( arguments, function( _, arg ) { + var index; + while ( ( index = jQuery.inArray( arg, list, index ) ) > -1 ) { + list.splice( index, 1 ); + + // Handle firing indexes + if ( index <= firingIndex ) { + firingIndex--; + } + } + } ); + return this; + }, + + // Check if a given callback is in the list. + // If no argument is given, return whether or not list has callbacks attached. + has: function( fn ) { + return fn ? + jQuery.inArray( fn, list ) > -1 : + list.length > 0; + }, + + // Remove all callbacks from the list + empty: function() { + if ( list ) { + list = []; + } + return this; + }, + + // Disable .fire and .add + // Abort any current/pending executions + // Clear all callbacks and values + disable: function() { + locked = queue = []; + list = memory = ""; + return this; + }, + disabled: function() { + return !list; + }, + + // Disable .fire + // Also disable .add unless we have memory (since it would have no effect) + // Abort any pending executions + lock: function() { + locked = queue = []; + if ( !memory && !firing ) { + list = memory = ""; + } + return this; + }, + locked: function() { + return !!locked; + }, + + // Call all callbacks with the given context and arguments + fireWith: function( context, args ) { + if ( !locked ) { + args = args || []; + args = [ context, args.slice ? args.slice() : args ]; + queue.push( args ); + if ( !firing ) { + fire(); + } + } + return this; + }, + + // Call all the callbacks with the given arguments + fire: function() { + self.fireWith( this, arguments ); + return this; + }, + + // To know if the callbacks have already been called at least once + fired: function() { + return !!fired; + } + }; + + return self; +}; + + +function Identity( v ) { + return v; +} +function Thrower( ex ) { + throw ex; +} + +function adoptValue( value, resolve, reject, noValue ) { + var method; + + try { + + // Check for promise aspect first to privilege synchronous behavior + if ( value && isFunction( ( method = value.promise ) ) ) { + method.call( value ).done( resolve ).fail( reject ); + + // Other thenables + } else if ( value && isFunction( ( method = value.then ) ) ) { + method.call( value, resolve, reject ); + + // Other non-thenables + } else { + + // Control `resolve` arguments by letting Array#slice cast boolean `noValue` to integer: + // * false: [ value ].slice( 0 ) => resolve( value ) + // * true: [ value ].slice( 1 ) => resolve() + resolve.apply( undefined, [ value ].slice( noValue ) ); + } + + // For Promises/A+, convert exceptions into rejections + // Since jQuery.when doesn't unwrap thenables, we can skip the extra checks appearing in + // Deferred#then to conditionally suppress rejection. + } catch ( value ) { + + // Support: Android 4.0 only + // Strict mode functions invoked without .call/.apply get global-object context + reject.apply( undefined, [ value ] ); + } +} + +jQuery.extend( { + + Deferred: function( func ) { + var tuples = [ + + // action, add listener, callbacks, + // ... .then handlers, argument index, [final state] + [ "notify", "progress", jQuery.Callbacks( "memory" ), + jQuery.Callbacks( "memory" ), 2 ], + [ "resolve", "done", jQuery.Callbacks( "once memory" ), + jQuery.Callbacks( "once memory" ), 0, "resolved" ], + [ "reject", "fail", jQuery.Callbacks( "once memory" ), + jQuery.Callbacks( "once memory" ), 1, "rejected" ] + ], + state = "pending", + promise = { + state: function() { + return state; + }, + always: function() { + deferred.done( arguments ).fail( arguments ); + return this; + }, + "catch": function( fn ) { + return promise.then( null, fn ); + }, + + // Keep pipe for back-compat + pipe: function( /* fnDone, fnFail, fnProgress */ ) { + var fns = arguments; + + return jQuery.Deferred( function( newDefer ) { + jQuery.each( tuples, function( _i, tuple ) { + + // Map tuples (progress, done, fail) to arguments (done, fail, progress) + var fn = isFunction( fns[ tuple[ 4 ] ] ) && fns[ tuple[ 4 ] ]; + + // deferred.progress(function() { bind to newDefer or newDefer.notify }) + // deferred.done(function() { bind to newDefer or newDefer.resolve }) + // deferred.fail(function() { bind to newDefer or newDefer.reject }) + deferred[ tuple[ 1 ] ]( function() { + var returned = fn && fn.apply( this, arguments ); + if ( returned && isFunction( returned.promise ) ) { + returned.promise() + .progress( newDefer.notify ) + .done( newDefer.resolve ) + .fail( newDefer.reject ); + } else { + newDefer[ tuple[ 0 ] + "With" ]( + this, + fn ? [ returned ] : arguments + ); + } + } ); + } ); + fns = null; + } ).promise(); + }, + then: function( onFulfilled, onRejected, onProgress ) { + var maxDepth = 0; + function resolve( depth, deferred, handler, special ) { + return function() { + var that = this, + args = arguments, + mightThrow = function() { + var returned, then; + + // Support: Promises/A+ section 2.3.3.3.3 + // https://promisesaplus.com/#point-59 + // Ignore double-resolution attempts + if ( depth < maxDepth ) { + return; + } + + returned = handler.apply( that, args ); + + // Support: Promises/A+ section 2.3.1 + // https://promisesaplus.com/#point-48 + if ( returned === deferred.promise() ) { + throw new TypeError( "Thenable self-resolution" ); + } + + // Support: Promises/A+ sections 2.3.3.1, 3.5 + // https://promisesaplus.com/#point-54 + // https://promisesaplus.com/#point-75 + // Retrieve `then` only once + then = returned && + + // Support: Promises/A+ section 2.3.4 + // https://promisesaplus.com/#point-64 + // Only check objects and functions for thenability + ( typeof returned === "object" || + typeof returned === "function" ) && + returned.then; + + // Handle a returned thenable + if ( isFunction( then ) ) { + + // Special processors (notify) just wait for resolution + if ( special ) { + then.call( + returned, + resolve( maxDepth, deferred, Identity, special ), + resolve( maxDepth, deferred, Thrower, special ) + ); + + // Normal processors (resolve) also hook into progress + } else { + + // ...and disregard older resolution values + maxDepth++; + + then.call( + returned, + resolve( maxDepth, deferred, Identity, special ), + resolve( maxDepth, deferred, Thrower, special ), + resolve( maxDepth, deferred, Identity, + deferred.notifyWith ) + ); + } + + // Handle all other returned values + } else { + + // Only substitute handlers pass on context + // and multiple values (non-spec behavior) + if ( handler !== Identity ) { + that = undefined; + args = [ returned ]; + } + + // Process the value(s) + // Default process is resolve + ( special || deferred.resolveWith )( that, args ); + } + }, + + // Only normal processors (resolve) catch and reject exceptions + process = special ? + mightThrow : + function() { + try { + mightThrow(); + } catch ( e ) { + + if ( jQuery.Deferred.exceptionHook ) { + jQuery.Deferred.exceptionHook( e, + process.stackTrace ); + } + + // Support: Promises/A+ section 2.3.3.3.4.1 + // https://promisesaplus.com/#point-61 + // Ignore post-resolution exceptions + if ( depth + 1 >= maxDepth ) { + + // Only substitute handlers pass on context + // and multiple values (non-spec behavior) + if ( handler !== Thrower ) { + that = undefined; + args = [ e ]; + } + + deferred.rejectWith( that, args ); + } + } + }; + + // Support: Promises/A+ section 2.3.3.3.1 + // https://promisesaplus.com/#point-57 + // Re-resolve promises immediately to dodge false rejection from + // subsequent errors + if ( depth ) { + process(); + } else { + + // Call an optional hook to record the stack, in case of exception + // since it's otherwise lost when execution goes async + if ( jQuery.Deferred.getStackHook ) { + process.stackTrace = jQuery.Deferred.getStackHook(); + } + window.setTimeout( process ); + } + }; + } + + return jQuery.Deferred( function( newDefer ) { + + // progress_handlers.add( ... ) + tuples[ 0 ][ 3 ].add( + resolve( + 0, + newDefer, + isFunction( onProgress ) ? + onProgress : + Identity, + newDefer.notifyWith + ) + ); + + // fulfilled_handlers.add( ... ) + tuples[ 1 ][ 3 ].add( + resolve( + 0, + newDefer, + isFunction( onFulfilled ) ? + onFulfilled : + Identity + ) + ); + + // rejected_handlers.add( ... ) + tuples[ 2 ][ 3 ].add( + resolve( + 0, + newDefer, + isFunction( onRejected ) ? + onRejected : + Thrower + ) + ); + } ).promise(); + }, + + // Get a promise for this deferred + // If obj is provided, the promise aspect is added to the object + promise: function( obj ) { + return obj != null ? jQuery.extend( obj, promise ) : promise; + } + }, + deferred = {}; + + // Add list-specific methods + jQuery.each( tuples, function( i, tuple ) { + var list = tuple[ 2 ], + stateString = tuple[ 5 ]; + + // promise.progress = list.add + // promise.done = list.add + // promise.fail = list.add + promise[ tuple[ 1 ] ] = list.add; + + // Handle state + if ( stateString ) { + list.add( + function() { + + // state = "resolved" (i.e., fulfilled) + // state = "rejected" + state = stateString; + }, + + // rejected_callbacks.disable + // fulfilled_callbacks.disable + tuples[ 3 - i ][ 2 ].disable, + + // rejected_handlers.disable + // fulfilled_handlers.disable + tuples[ 3 - i ][ 3 ].disable, + + // progress_callbacks.lock + tuples[ 0 ][ 2 ].lock, + + // progress_handlers.lock + tuples[ 0 ][ 3 ].lock + ); + } + + // progress_handlers.fire + // fulfilled_handlers.fire + // rejected_handlers.fire + list.add( tuple[ 3 ].fire ); + + // deferred.notify = function() { deferred.notifyWith(...) } + // deferred.resolve = function() { deferred.resolveWith(...) } + // deferred.reject = function() { deferred.rejectWith(...) } + deferred[ tuple[ 0 ] ] = function() { + deferred[ tuple[ 0 ] + "With" ]( this === deferred ? undefined : this, arguments ); + return this; + }; + + // deferred.notifyWith = list.fireWith + // deferred.resolveWith = list.fireWith + // deferred.rejectWith = list.fireWith + deferred[ tuple[ 0 ] + "With" ] = list.fireWith; + } ); + + // Make the deferred a promise + promise.promise( deferred ); + + // Call given func if any + if ( func ) { + func.call( deferred, deferred ); + } + + // All done! + return deferred; + }, + + // Deferred helper + when: function( singleValue ) { + var + + // count of uncompleted subordinates + remaining = arguments.length, + + // count of unprocessed arguments + i = remaining, + + // subordinate fulfillment data + resolveContexts = Array( i ), + resolveValues = slice.call( arguments ), + + // the primary Deferred + primary = jQuery.Deferred(), + + // subordinate callback factory + updateFunc = function( i ) { + return function( value ) { + resolveContexts[ i ] = this; + resolveValues[ i ] = arguments.length > 1 ? slice.call( arguments ) : value; + if ( !( --remaining ) ) { + primary.resolveWith( resolveContexts, resolveValues ); + } + }; + }; + + // Single- and empty arguments are adopted like Promise.resolve + if ( remaining <= 1 ) { + adoptValue( singleValue, primary.done( updateFunc( i ) ).resolve, primary.reject, + !remaining ); + + // Use .then() to unwrap secondary thenables (cf. gh-3000) + if ( primary.state() === "pending" || + isFunction( resolveValues[ i ] && resolveValues[ i ].then ) ) { + + return primary.then(); + } + } + + // Multiple arguments are aggregated like Promise.all array elements + while ( i-- ) { + adoptValue( resolveValues[ i ], updateFunc( i ), primary.reject ); + } + + return primary.promise(); + } +} ); + + +// These usually indicate a programmer mistake during development, +// warn about them ASAP rather than swallowing them by default. +var rerrorNames = /^(Eval|Internal|Range|Reference|Syntax|Type|URI)Error$/; + +jQuery.Deferred.exceptionHook = function( error, stack ) { + + // Support: IE 8 - 9 only + // Console exists when dev tools are open, which can happen at any time + if ( window.console && window.console.warn && error && rerrorNames.test( error.name ) ) { + window.console.warn( "jQuery.Deferred exception: " + error.message, error.stack, stack ); + } +}; + + + + +jQuery.readyException = function( error ) { + window.setTimeout( function() { + throw error; + } ); +}; + + + + +// The deferred used on DOM ready +var readyList = jQuery.Deferred(); + +jQuery.fn.ready = function( fn ) { + + readyList + .then( fn ) + + // Wrap jQuery.readyException in a function so that the lookup + // happens at the time of error handling instead of callback + // registration. + .catch( function( error ) { + jQuery.readyException( error ); + } ); + + return this; +}; + +jQuery.extend( { + + // Is the DOM ready to be used? Set to true once it occurs. + isReady: false, + + // A counter to track how many items to wait for before + // the ready event fires. See #6781 + readyWait: 1, + + // Handle when the DOM is ready + ready: function( wait ) { + + // Abort if there are pending holds or we're already ready + if ( wait === true ? --jQuery.readyWait : jQuery.isReady ) { + return; + } + + // Remember that the DOM is ready + jQuery.isReady = true; + + // If a normal DOM Ready event fired, decrement, and wait if need be + if ( wait !== true && --jQuery.readyWait > 0 ) { + return; + } + + // If there are functions bound, to execute + readyList.resolveWith( document, [ jQuery ] ); + } +} ); + +jQuery.ready.then = readyList.then; + +// The ready event handler and self cleanup method +function completed() { + document.removeEventListener( "DOMContentLoaded", completed ); + window.removeEventListener( "load", completed ); + jQuery.ready(); +} + +// Catch cases where $(document).ready() is called +// after the browser event has already occurred. +// Support: IE <=9 - 10 only +// Older IE sometimes signals "interactive" too soon +if ( document.readyState === "complete" || + ( document.readyState !== "loading" && !document.documentElement.doScroll ) ) { + + // Handle it asynchronously to allow scripts the opportunity to delay ready + window.setTimeout( jQuery.ready ); + +} else { + + // Use the handy event callback + document.addEventListener( "DOMContentLoaded", completed ); + + // A fallback to window.onload, that will always work + window.addEventListener( "load", completed ); +} + + + + +// Multifunctional method to get and set values of a collection +// The value/s can optionally be executed if it's a function +var access = function( elems, fn, key, value, chainable, emptyGet, raw ) { + var i = 0, + len = elems.length, + bulk = key == null; + + // Sets many values + if ( toType( key ) === "object" ) { + chainable = true; + for ( i in key ) { + access( elems, fn, i, key[ i ], true, emptyGet, raw ); + } + + // Sets one value + } else if ( value !== undefined ) { + chainable = true; + + if ( !isFunction( value ) ) { + raw = true; + } + + if ( bulk ) { + + // Bulk operations run against the entire set + if ( raw ) { + fn.call( elems, value ); + fn = null; + + // ...except when executing function values + } else { + bulk = fn; + fn = function( elem, _key, value ) { + return bulk.call( jQuery( elem ), value ); + }; + } + } + + if ( fn ) { + for ( ; i < len; i++ ) { + fn( + elems[ i ], key, raw ? + value : + value.call( elems[ i ], i, fn( elems[ i ], key ) ) + ); + } + } + } + + if ( chainable ) { + return elems; + } + + // Gets + if ( bulk ) { + return fn.call( elems ); + } + + return len ? fn( elems[ 0 ], key ) : emptyGet; +}; + + +// Matches dashed string for camelizing +var rmsPrefix = /^-ms-/, + rdashAlpha = /-([a-z])/g; + +// Used by camelCase as callback to replace() +function fcamelCase( _all, letter ) { + return letter.toUpperCase(); +} + +// Convert dashed to camelCase; used by the css and data modules +// Support: IE <=9 - 11, Edge 12 - 15 +// Microsoft forgot to hump their vendor prefix (#9572) +function camelCase( string ) { + return string.replace( rmsPrefix, "ms-" ).replace( rdashAlpha, fcamelCase ); +} +var acceptData = function( owner ) { + + // Accepts only: + // - Node + // - Node.ELEMENT_NODE + // - Node.DOCUMENT_NODE + // - Object + // - Any + return owner.nodeType === 1 || owner.nodeType === 9 || !( +owner.nodeType ); +}; + + + + +function Data() { + this.expando = jQuery.expando + Data.uid++; +} + +Data.uid = 1; + +Data.prototype = { + + cache: function( owner ) { + + // Check if the owner object already has a cache + var value = owner[ this.expando ]; + + // If not, create one + if ( !value ) { + value = {}; + + // We can accept data for non-element nodes in modern browsers, + // but we should not, see #8335. + // Always return an empty object. + if ( acceptData( owner ) ) { + + // If it is a node unlikely to be stringify-ed or looped over + // use plain assignment + if ( owner.nodeType ) { + owner[ this.expando ] = value; + + // Otherwise secure it in a non-enumerable property + // configurable must be true to allow the property to be + // deleted when data is removed + } else { + Object.defineProperty( owner, this.expando, { + value: value, + configurable: true + } ); + } + } + } + + return value; + }, + set: function( owner, data, value ) { + var prop, + cache = this.cache( owner ); + + // Handle: [ owner, key, value ] args + // Always use camelCase key (gh-2257) + if ( typeof data === "string" ) { + cache[ camelCase( data ) ] = value; + + // Handle: [ owner, { properties } ] args + } else { + + // Copy the properties one-by-one to the cache object + for ( prop in data ) { + cache[ camelCase( prop ) ] = data[ prop ]; + } + } + return cache; + }, + get: function( owner, key ) { + return key === undefined ? + this.cache( owner ) : + + // Always use camelCase key (gh-2257) + owner[ this.expando ] && owner[ this.expando ][ camelCase( key ) ]; + }, + access: function( owner, key, value ) { + + // In cases where either: + // + // 1. No key was specified + // 2. A string key was specified, but no value provided + // + // Take the "read" path and allow the get method to determine + // which value to return, respectively either: + // + // 1. The entire cache object + // 2. The data stored at the key + // + if ( key === undefined || + ( ( key && typeof key === "string" ) && value === undefined ) ) { + + return this.get( owner, key ); + } + + // When the key is not a string, or both a key and value + // are specified, set or extend (existing objects) with either: + // + // 1. An object of properties + // 2. A key and value + // + this.set( owner, key, value ); + + // Since the "set" path can have two possible entry points + // return the expected data based on which path was taken[*] + return value !== undefined ? value : key; + }, + remove: function( owner, key ) { + var i, + cache = owner[ this.expando ]; + + if ( cache === undefined ) { + return; + } + + if ( key !== undefined ) { + + // Support array or space separated string of keys + if ( Array.isArray( key ) ) { + + // If key is an array of keys... + // We always set camelCase keys, so remove that. + key = key.map( camelCase ); + } else { + key = camelCase( key ); + + // If a key with the spaces exists, use it. + // Otherwise, create an array by matching non-whitespace + key = key in cache ? + [ key ] : + ( key.match( rnothtmlwhite ) || [] ); + } + + i = key.length; + + while ( i-- ) { + delete cache[ key[ i ] ]; + } + } + + // Remove the expando if there's no more data + if ( key === undefined || jQuery.isEmptyObject( cache ) ) { + + // Support: Chrome <=35 - 45 + // Webkit & Blink performance suffers when deleting properties + // from DOM nodes, so set to undefined instead + // https://bugs.chromium.org/p/chromium/issues/detail?id=378607 (bug restricted) + if ( owner.nodeType ) { + owner[ this.expando ] = undefined; + } else { + delete owner[ this.expando ]; + } + } + }, + hasData: function( owner ) { + var cache = owner[ this.expando ]; + return cache !== undefined && !jQuery.isEmptyObject( cache ); + } +}; +var dataPriv = new Data(); + +var dataUser = new Data(); + + + +// Implementation Summary +// +// 1. Enforce API surface and semantic compatibility with 1.9.x branch +// 2. Improve the module's maintainability by reducing the storage +// paths to a single mechanism. +// 3. Use the same single mechanism to support "private" and "user" data. +// 4. _Never_ expose "private" data to user code (TODO: Drop _data, _removeData) +// 5. Avoid exposing implementation details on user objects (eg. expando properties) +// 6. Provide a clear path for implementation upgrade to WeakMap in 2014 + +var rbrace = /^(?:\{[\w\W]*\}|\[[\w\W]*\])$/, + rmultiDash = /[A-Z]/g; + +function getData( data ) { + if ( data === "true" ) { + return true; + } + + if ( data === "false" ) { + return false; + } + + if ( data === "null" ) { + return null; + } + + // Only convert to a number if it doesn't change the string + if ( data === +data + "" ) { + return +data; + } + + if ( rbrace.test( data ) ) { + return JSON.parse( data ); + } + + return data; +} + +function dataAttr( elem, key, data ) { + var name; + + // If nothing was found internally, try to fetch any + // data from the HTML5 data-* attribute + if ( data === undefined && elem.nodeType === 1 ) { + name = "data-" + key.replace( rmultiDash, "-$&" ).toLowerCase(); + data = elem.getAttribute( name ); + + if ( typeof data === "string" ) { + try { + data = getData( data ); + } catch ( e ) {} + + // Make sure we set the data so it isn't changed later + dataUser.set( elem, key, data ); + } else { + data = undefined; + } + } + return data; +} + +jQuery.extend( { + hasData: function( elem ) { + return dataUser.hasData( elem ) || dataPriv.hasData( elem ); + }, + + data: function( elem, name, data ) { + return dataUser.access( elem, name, data ); + }, + + removeData: function( elem, name ) { + dataUser.remove( elem, name ); + }, + + // TODO: Now that all calls to _data and _removeData have been replaced + // with direct calls to dataPriv methods, these can be deprecated. + _data: function( elem, name, data ) { + return dataPriv.access( elem, name, data ); + }, + + _removeData: function( elem, name ) { + dataPriv.remove( elem, name ); + } +} ); + +jQuery.fn.extend( { + data: function( key, value ) { + var i, name, data, + elem = this[ 0 ], + attrs = elem && elem.attributes; + + // Gets all values + if ( key === undefined ) { + if ( this.length ) { + data = dataUser.get( elem ); + + if ( elem.nodeType === 1 && !dataPriv.get( elem, "hasDataAttrs" ) ) { + i = attrs.length; + while ( i-- ) { + + // Support: IE 11 only + // The attrs elements can be null (#14894) + if ( attrs[ i ] ) { + name = attrs[ i ].name; + if ( name.indexOf( "data-" ) === 0 ) { + name = camelCase( name.slice( 5 ) ); + dataAttr( elem, name, data[ name ] ); + } + } + } + dataPriv.set( elem, "hasDataAttrs", true ); + } + } + + return data; + } + + // Sets multiple values + if ( typeof key === "object" ) { + return this.each( function() { + dataUser.set( this, key ); + } ); + } + + return access( this, function( value ) { + var data; + + // The calling jQuery object (element matches) is not empty + // (and therefore has an element appears at this[ 0 ]) and the + // `value` parameter was not undefined. An empty jQuery object + // will result in `undefined` for elem = this[ 0 ] which will + // throw an exception if an attempt to read a data cache is made. + if ( elem && value === undefined ) { + + // Attempt to get data from the cache + // The key will always be camelCased in Data + data = dataUser.get( elem, key ); + if ( data !== undefined ) { + return data; + } + + // Attempt to "discover" the data in + // HTML5 custom data-* attrs + data = dataAttr( elem, key ); + if ( data !== undefined ) { + return data; + } + + // We tried really hard, but the data doesn't exist. + return; + } + + // Set the data... + this.each( function() { + + // We always store the camelCased key + dataUser.set( this, key, value ); + } ); + }, null, value, arguments.length > 1, null, true ); + }, + + removeData: function( key ) { + return this.each( function() { + dataUser.remove( this, key ); + } ); + } +} ); + + +jQuery.extend( { + queue: function( elem, type, data ) { + var queue; + + if ( elem ) { + type = ( type || "fx" ) + "queue"; + queue = dataPriv.get( elem, type ); + + // Speed up dequeue by getting out quickly if this is just a lookup + if ( data ) { + if ( !queue || Array.isArray( data ) ) { + queue = dataPriv.access( elem, type, jQuery.makeArray( data ) ); + } else { + queue.push( data ); + } + } + return queue || []; + } + }, + + dequeue: function( elem, type ) { + type = type || "fx"; + + var queue = jQuery.queue( elem, type ), + startLength = queue.length, + fn = queue.shift(), + hooks = jQuery._queueHooks( elem, type ), + next = function() { + jQuery.dequeue( elem, type ); + }; + + // If the fx queue is dequeued, always remove the progress sentinel + if ( fn === "inprogress" ) { + fn = queue.shift(); + startLength--; + } + + if ( fn ) { + + // Add a progress sentinel to prevent the fx queue from being + // automatically dequeued + if ( type === "fx" ) { + queue.unshift( "inprogress" ); + } + + // Clear up the last queue stop function + delete hooks.stop; + fn.call( elem, next, hooks ); + } + + if ( !startLength && hooks ) { + hooks.empty.fire(); + } + }, + + // Not public - generate a queueHooks object, or return the current one + _queueHooks: function( elem, type ) { + var key = type + "queueHooks"; + return dataPriv.get( elem, key ) || dataPriv.access( elem, key, { + empty: jQuery.Callbacks( "once memory" ).add( function() { + dataPriv.remove( elem, [ type + "queue", key ] ); + } ) + } ); + } +} ); + +jQuery.fn.extend( { + queue: function( type, data ) { + var setter = 2; + + if ( typeof type !== "string" ) { + data = type; + type = "fx"; + setter--; + } + + if ( arguments.length < setter ) { + return jQuery.queue( this[ 0 ], type ); + } + + return data === undefined ? + this : + this.each( function() { + var queue = jQuery.queue( this, type, data ); + + // Ensure a hooks for this queue + jQuery._queueHooks( this, type ); + + if ( type === "fx" && queue[ 0 ] !== "inprogress" ) { + jQuery.dequeue( this, type ); + } + } ); + }, + dequeue: function( type ) { + return this.each( function() { + jQuery.dequeue( this, type ); + } ); + }, + clearQueue: function( type ) { + return this.queue( type || "fx", [] ); + }, + + // Get a promise resolved when queues of a certain type + // are emptied (fx is the type by default) + promise: function( type, obj ) { + var tmp, + count = 1, + defer = jQuery.Deferred(), + elements = this, + i = this.length, + resolve = function() { + if ( !( --count ) ) { + defer.resolveWith( elements, [ elements ] ); + } + }; + + if ( typeof type !== "string" ) { + obj = type; + type = undefined; + } + type = type || "fx"; + + while ( i-- ) { + tmp = dataPriv.get( elements[ i ], type + "queueHooks" ); + if ( tmp && tmp.empty ) { + count++; + tmp.empty.add( resolve ); + } + } + resolve(); + return defer.promise( obj ); + } +} ); +var pnum = ( /[+-]?(?:\d*\.|)\d+(?:[eE][+-]?\d+|)/ ).source; + +var rcssNum = new RegExp( "^(?:([+-])=|)(" + pnum + ")([a-z%]*)$", "i" ); + + +var cssExpand = [ "Top", "Right", "Bottom", "Left" ]; + +var documentElement = document.documentElement; + + + + var isAttached = function( elem ) { + return jQuery.contains( elem.ownerDocument, elem ); + }, + composed = { composed: true }; + + // Support: IE 9 - 11+, Edge 12 - 18+, iOS 10.0 - 10.2 only + // Check attachment across shadow DOM boundaries when possible (gh-3504) + // Support: iOS 10.0-10.2 only + // Early iOS 10 versions support `attachShadow` but not `getRootNode`, + // leading to errors. We need to check for `getRootNode`. + if ( documentElement.getRootNode ) { + isAttached = function( elem ) { + return jQuery.contains( elem.ownerDocument, elem ) || + elem.getRootNode( composed ) === elem.ownerDocument; + }; + } +var isHiddenWithinTree = function( elem, el ) { + + // isHiddenWithinTree might be called from jQuery#filter function; + // in that case, element will be second argument + elem = el || elem; + + // Inline style trumps all + return elem.style.display === "none" || + elem.style.display === "" && + + // Otherwise, check computed style + // Support: Firefox <=43 - 45 + // Disconnected elements can have computed display: none, so first confirm that elem is + // in the document. + isAttached( elem ) && + + jQuery.css( elem, "display" ) === "none"; + }; + + + +function adjustCSS( elem, prop, valueParts, tween ) { + var adjusted, scale, + maxIterations = 20, + currentValue = tween ? + function() { + return tween.cur(); + } : + function() { + return jQuery.css( elem, prop, "" ); + }, + initial = currentValue(), + unit = valueParts && valueParts[ 3 ] || ( jQuery.cssNumber[ prop ] ? "" : "px" ), + + // Starting value computation is required for potential unit mismatches + initialInUnit = elem.nodeType && + ( jQuery.cssNumber[ prop ] || unit !== "px" && +initial ) && + rcssNum.exec( jQuery.css( elem, prop ) ); + + if ( initialInUnit && initialInUnit[ 3 ] !== unit ) { + + // Support: Firefox <=54 + // Halve the iteration target value to prevent interference from CSS upper bounds (gh-2144) + initial = initial / 2; + + // Trust units reported by jQuery.css + unit = unit || initialInUnit[ 3 ]; + + // Iteratively approximate from a nonzero starting point + initialInUnit = +initial || 1; + + while ( maxIterations-- ) { + + // Evaluate and update our best guess (doubling guesses that zero out). + // Finish if the scale equals or crosses 1 (making the old*new product non-positive). + jQuery.style( elem, prop, initialInUnit + unit ); + if ( ( 1 - scale ) * ( 1 - ( scale = currentValue() / initial || 0.5 ) ) <= 0 ) { + maxIterations = 0; + } + initialInUnit = initialInUnit / scale; + + } + + initialInUnit = initialInUnit * 2; + jQuery.style( elem, prop, initialInUnit + unit ); + + // Make sure we update the tween properties later on + valueParts = valueParts || []; + } + + if ( valueParts ) { + initialInUnit = +initialInUnit || +initial || 0; + + // Apply relative offset (+=/-=) if specified + adjusted = valueParts[ 1 ] ? + initialInUnit + ( valueParts[ 1 ] + 1 ) * valueParts[ 2 ] : + +valueParts[ 2 ]; + if ( tween ) { + tween.unit = unit; + tween.start = initialInUnit; + tween.end = adjusted; + } + } + return adjusted; +} + + +var defaultDisplayMap = {}; + +function getDefaultDisplay( elem ) { + var temp, + doc = elem.ownerDocument, + nodeName = elem.nodeName, + display = defaultDisplayMap[ nodeName ]; + + if ( display ) { + return display; + } + + temp = doc.body.appendChild( doc.createElement( nodeName ) ); + display = jQuery.css( temp, "display" ); + + temp.parentNode.removeChild( temp ); + + if ( display === "none" ) { + display = "block"; + } + defaultDisplayMap[ nodeName ] = display; + + return display; +} + +function showHide( elements, show ) { + var display, elem, + values = [], + index = 0, + length = elements.length; + + // Determine new display value for elements that need to change + for ( ; index < length; index++ ) { + elem = elements[ index ]; + if ( !elem.style ) { + continue; + } + + display = elem.style.display; + if ( show ) { + + // Since we force visibility upon cascade-hidden elements, an immediate (and slow) + // check is required in this first loop unless we have a nonempty display value (either + // inline or about-to-be-restored) + if ( display === "none" ) { + values[ index ] = dataPriv.get( elem, "display" ) || null; + if ( !values[ index ] ) { + elem.style.display = ""; + } + } + if ( elem.style.display === "" && isHiddenWithinTree( elem ) ) { + values[ index ] = getDefaultDisplay( elem ); + } + } else { + if ( display !== "none" ) { + values[ index ] = "none"; + + // Remember what we're overwriting + dataPriv.set( elem, "display", display ); + } + } + } + + // Set the display of the elements in a second loop to avoid constant reflow + for ( index = 0; index < length; index++ ) { + if ( values[ index ] != null ) { + elements[ index ].style.display = values[ index ]; + } + } + + return elements; +} + +jQuery.fn.extend( { + show: function() { + return showHide( this, true ); + }, + hide: function() { + return showHide( this ); + }, + toggle: function( state ) { + if ( typeof state === "boolean" ) { + return state ? this.show() : this.hide(); + } + + return this.each( function() { + if ( isHiddenWithinTree( this ) ) { + jQuery( this ).show(); + } else { + jQuery( this ).hide(); + } + } ); + } +} ); +var rcheckableType = ( /^(?:checkbox|radio)$/i ); + +var rtagName = ( /<([a-z][^\/\0>\x20\t\r\n\f]*)/i ); + +var rscriptType = ( /^$|^module$|\/(?:java|ecma)script/i ); + + + +( function() { + var fragment = document.createDocumentFragment(), + div = fragment.appendChild( document.createElement( "div" ) ), + input = document.createElement( "input" ); + + // Support: Android 4.0 - 4.3 only + // Check state lost if the name is set (#11217) + // Support: Windows Web Apps (WWA) + // `name` and `type` must use .setAttribute for WWA (#14901) + input.setAttribute( "type", "radio" ); + input.setAttribute( "checked", "checked" ); + input.setAttribute( "name", "t" ); + + div.appendChild( input ); + + // Support: Android <=4.1 only + // Older WebKit doesn't clone checked state correctly in fragments + support.checkClone = div.cloneNode( true ).cloneNode( true ).lastChild.checked; + + // Support: IE <=11 only + // Make sure textarea (and checkbox) defaultValue is properly cloned + div.innerHTML = "<textarea>x</textarea>"; + support.noCloneChecked = !!div.cloneNode( true ).lastChild.defaultValue; + + // Support: IE <=9 only + // IE <=9 replaces <option> tags with their contents when inserted outside of + // the select element. + div.innerHTML = "<option></option>"; + support.option = !!div.lastChild; +} )(); + + +// We have to close these tags to support XHTML (#13200) +var wrapMap = { + + // XHTML parsers do not magically insert elements in the + // same way that tag soup parsers do. So we cannot shorten + // this by omitting <tbody> or other required elements. + thead: [ 1, "<table>", "</table>" ], + col: [ 2, "<table><colgroup>", "</colgroup></table>" ], + tr: [ 2, "<table><tbody>", "</tbody></table>" ], + td: [ 3, "<table><tbody><tr>", "</tr></tbody></table>" ], + + _default: [ 0, "", "" ] +}; + +wrapMap.tbody = wrapMap.tfoot = wrapMap.colgroup = wrapMap.caption = wrapMap.thead; +wrapMap.th = wrapMap.td; + +// Support: IE <=9 only +if ( !support.option ) { + wrapMap.optgroup = wrapMap.option = [ 1, "<select multiple='multiple'>", "</select>" ]; +} + + +function getAll( context, tag ) { + + // Support: IE <=9 - 11 only + // Use typeof to avoid zero-argument method invocation on host objects (#15151) + var ret; + + if ( typeof context.getElementsByTagName !== "undefined" ) { + ret = context.getElementsByTagName( tag || "*" ); + + } else if ( typeof context.querySelectorAll !== "undefined" ) { + ret = context.querySelectorAll( tag || "*" ); + + } else { + ret = []; + } + + if ( tag === undefined || tag && nodeName( context, tag ) ) { + return jQuery.merge( [ context ], ret ); + } + + return ret; +} + + +// Mark scripts as having already been evaluated +function setGlobalEval( elems, refElements ) { + var i = 0, + l = elems.length; + + for ( ; i < l; i++ ) { + dataPriv.set( + elems[ i ], + "globalEval", + !refElements || dataPriv.get( refElements[ i ], "globalEval" ) + ); + } +} + + +var rhtml = /<|&#?\w+;/; + +function buildFragment( elems, context, scripts, selection, ignored ) { + var elem, tmp, tag, wrap, attached, j, + fragment = context.createDocumentFragment(), + nodes = [], + i = 0, + l = elems.length; + + for ( ; i < l; i++ ) { + elem = elems[ i ]; + + if ( elem || elem === 0 ) { + + // Add nodes directly + if ( toType( elem ) === "object" ) { + + // Support: Android <=4.0 only, PhantomJS 1 only + // push.apply(_, arraylike) throws on ancient WebKit + jQuery.merge( nodes, elem.nodeType ? [ elem ] : elem ); + + // Convert non-html into a text node + } else if ( !rhtml.test( elem ) ) { + nodes.push( context.createTextNode( elem ) ); + + // Convert html into DOM nodes + } else { + tmp = tmp || fragment.appendChild( context.createElement( "div" ) ); + + // Deserialize a standard representation + tag = ( rtagName.exec( elem ) || [ "", "" ] )[ 1 ].toLowerCase(); + wrap = wrapMap[ tag ] || wrapMap._default; + tmp.innerHTML = wrap[ 1 ] + jQuery.htmlPrefilter( elem ) + wrap[ 2 ]; + + // Descend through wrappers to the right content + j = wrap[ 0 ]; + while ( j-- ) { + tmp = tmp.lastChild; + } + + // Support: Android <=4.0 only, PhantomJS 1 only + // push.apply(_, arraylike) throws on ancient WebKit + jQuery.merge( nodes, tmp.childNodes ); + + // Remember the top-level container + tmp = fragment.firstChild; + + // Ensure the created nodes are orphaned (#12392) + tmp.textContent = ""; + } + } + } + + // Remove wrapper from fragment + fragment.textContent = ""; + + i = 0; + while ( ( elem = nodes[ i++ ] ) ) { + + // Skip elements already in the context collection (trac-4087) + if ( selection && jQuery.inArray( elem, selection ) > -1 ) { + if ( ignored ) { + ignored.push( elem ); + } + continue; + } + + attached = isAttached( elem ); + + // Append to fragment + tmp = getAll( fragment.appendChild( elem ), "script" ); + + // Preserve script evaluation history + if ( attached ) { + setGlobalEval( tmp ); + } + + // Capture executables + if ( scripts ) { + j = 0; + while ( ( elem = tmp[ j++ ] ) ) { + if ( rscriptType.test( elem.type || "" ) ) { + scripts.push( elem ); + } + } + } + } + + return fragment; +} + + +var rtypenamespace = /^([^.]*)(?:\.(.+)|)/; + +function returnTrue() { + return true; +} + +function returnFalse() { + return false; +} + +// Support: IE <=9 - 11+ +// focus() and blur() are asynchronous, except when they are no-op. +// So expect focus to be synchronous when the element is already active, +// and blur to be synchronous when the element is not already active. +// (focus and blur are always synchronous in other supported browsers, +// this just defines when we can count on it). +function expectSync( elem, type ) { + return ( elem === safeActiveElement() ) === ( type === "focus" ); +} + +// Support: IE <=9 only +// Accessing document.activeElement can throw unexpectedly +// https://bugs.jquery.com/ticket/13393 +function safeActiveElement() { + try { + return document.activeElement; + } catch ( err ) { } +} + +function on( elem, types, selector, data, fn, one ) { + var origFn, type; + + // Types can be a map of types/handlers + if ( typeof types === "object" ) { + + // ( types-Object, selector, data ) + if ( typeof selector !== "string" ) { + + // ( types-Object, data ) + data = data || selector; + selector = undefined; + } + for ( type in types ) { + on( elem, type, selector, data, types[ type ], one ); + } + return elem; + } + + if ( data == null && fn == null ) { + + // ( types, fn ) + fn = selector; + data = selector = undefined; + } else if ( fn == null ) { + if ( typeof selector === "string" ) { + + // ( types, selector, fn ) + fn = data; + data = undefined; + } else { + + // ( types, data, fn ) + fn = data; + data = selector; + selector = undefined; + } + } + if ( fn === false ) { + fn = returnFalse; + } else if ( !fn ) { + return elem; + } + + if ( one === 1 ) { + origFn = fn; + fn = function( event ) { + + // Can use an empty set, since event contains the info + jQuery().off( event ); + return origFn.apply( this, arguments ); + }; + + // Use same guid so caller can remove using origFn + fn.guid = origFn.guid || ( origFn.guid = jQuery.guid++ ); + } + return elem.each( function() { + jQuery.event.add( this, types, fn, data, selector ); + } ); +} + +/* + * Helper functions for managing events -- not part of the public interface. + * Props to Dean Edwards' addEvent library for many of the ideas. + */ +jQuery.event = { + + global: {}, + + add: function( elem, types, handler, data, selector ) { + + var handleObjIn, eventHandle, tmp, + events, t, handleObj, + special, handlers, type, namespaces, origType, + elemData = dataPriv.get( elem ); + + // Only attach events to objects that accept data + if ( !acceptData( elem ) ) { + return; + } + + // Caller can pass in an object of custom data in lieu of the handler + if ( handler.handler ) { + handleObjIn = handler; + handler = handleObjIn.handler; + selector = handleObjIn.selector; + } + + // Ensure that invalid selectors throw exceptions at attach time + // Evaluate against documentElement in case elem is a non-element node (e.g., document) + if ( selector ) { + jQuery.find.matchesSelector( documentElement, selector ); + } + + // Make sure that the handler has a unique ID, used to find/remove it later + if ( !handler.guid ) { + handler.guid = jQuery.guid++; + } + + // Init the element's event structure and main handler, if this is the first + if ( !( events = elemData.events ) ) { + events = elemData.events = Object.create( null ); + } + if ( !( eventHandle = elemData.handle ) ) { + eventHandle = elemData.handle = function( e ) { + + // Discard the second event of a jQuery.event.trigger() and + // when an event is called after a page has unloaded + return typeof jQuery !== "undefined" && jQuery.event.triggered !== e.type ? + jQuery.event.dispatch.apply( elem, arguments ) : undefined; + }; + } + + // Handle multiple events separated by a space + types = ( types || "" ).match( rnothtmlwhite ) || [ "" ]; + t = types.length; + while ( t-- ) { + tmp = rtypenamespace.exec( types[ t ] ) || []; + type = origType = tmp[ 1 ]; + namespaces = ( tmp[ 2 ] || "" ).split( "." ).sort(); + + // There *must* be a type, no attaching namespace-only handlers + if ( !type ) { + continue; + } + + // If event changes its type, use the special event handlers for the changed type + special = jQuery.event.special[ type ] || {}; + + // If selector defined, determine special event api type, otherwise given type + type = ( selector ? special.delegateType : special.bindType ) || type; + + // Update special based on newly reset type + special = jQuery.event.special[ type ] || {}; + + // handleObj is passed to all event handlers + handleObj = jQuery.extend( { + type: type, + origType: origType, + data: data, + handler: handler, + guid: handler.guid, + selector: selector, + needsContext: selector && jQuery.expr.match.needsContext.test( selector ), + namespace: namespaces.join( "." ) + }, handleObjIn ); + + // Init the event handler queue if we're the first + if ( !( handlers = events[ type ] ) ) { + handlers = events[ type ] = []; + handlers.delegateCount = 0; + + // Only use addEventListener if the special events handler returns false + if ( !special.setup || + special.setup.call( elem, data, namespaces, eventHandle ) === false ) { + + if ( elem.addEventListener ) { + elem.addEventListener( type, eventHandle ); + } + } + } + + if ( special.add ) { + special.add.call( elem, handleObj ); + + if ( !handleObj.handler.guid ) { + handleObj.handler.guid = handler.guid; + } + } + + // Add to the element's handler list, delegates in front + if ( selector ) { + handlers.splice( handlers.delegateCount++, 0, handleObj ); + } else { + handlers.push( handleObj ); + } + + // Keep track of which events have ever been used, for event optimization + jQuery.event.global[ type ] = true; + } + + }, + + // Detach an event or set of events from an element + remove: function( elem, types, handler, selector, mappedTypes ) { + + var j, origCount, tmp, + events, t, handleObj, + special, handlers, type, namespaces, origType, + elemData = dataPriv.hasData( elem ) && dataPriv.get( elem ); + + if ( !elemData || !( events = elemData.events ) ) { + return; + } + + // Once for each type.namespace in types; type may be omitted + types = ( types || "" ).match( rnothtmlwhite ) || [ "" ]; + t = types.length; + while ( t-- ) { + tmp = rtypenamespace.exec( types[ t ] ) || []; + type = origType = tmp[ 1 ]; + namespaces = ( tmp[ 2 ] || "" ).split( "." ).sort(); + + // Unbind all events (on this namespace, if provided) for the element + if ( !type ) { + for ( type in events ) { + jQuery.event.remove( elem, type + types[ t ], handler, selector, true ); + } + continue; + } + + special = jQuery.event.special[ type ] || {}; + type = ( selector ? special.delegateType : special.bindType ) || type; + handlers = events[ type ] || []; + tmp = tmp[ 2 ] && + new RegExp( "(^|\\.)" + namespaces.join( "\\.(?:.*\\.|)" ) + "(\\.|$)" ); + + // Remove matching events + origCount = j = handlers.length; + while ( j-- ) { + handleObj = handlers[ j ]; + + if ( ( mappedTypes || origType === handleObj.origType ) && + ( !handler || handler.guid === handleObj.guid ) && + ( !tmp || tmp.test( handleObj.namespace ) ) && + ( !selector || selector === handleObj.selector || + selector === "**" && handleObj.selector ) ) { + handlers.splice( j, 1 ); + + if ( handleObj.selector ) { + handlers.delegateCount--; + } + if ( special.remove ) { + special.remove.call( elem, handleObj ); + } + } + } + + // Remove generic event handler if we removed something and no more handlers exist + // (avoids potential for endless recursion during removal of special event handlers) + if ( origCount && !handlers.length ) { + if ( !special.teardown || + special.teardown.call( elem, namespaces, elemData.handle ) === false ) { + + jQuery.removeEvent( elem, type, elemData.handle ); + } + + delete events[ type ]; + } + } + + // Remove data and the expando if it's no longer used + if ( jQuery.isEmptyObject( events ) ) { + dataPriv.remove( elem, "handle events" ); + } + }, + + dispatch: function( nativeEvent ) { + + var i, j, ret, matched, handleObj, handlerQueue, + args = new Array( arguments.length ), + + // Make a writable jQuery.Event from the native event object + event = jQuery.event.fix( nativeEvent ), + + handlers = ( + dataPriv.get( this, "events" ) || Object.create( null ) + )[ event.type ] || [], + special = jQuery.event.special[ event.type ] || {}; + + // Use the fix-ed jQuery.Event rather than the (read-only) native event + args[ 0 ] = event; + + for ( i = 1; i < arguments.length; i++ ) { + args[ i ] = arguments[ i ]; + } + + event.delegateTarget = this; + + // Call the preDispatch hook for the mapped type, and let it bail if desired + if ( special.preDispatch && special.preDispatch.call( this, event ) === false ) { + return; + } + + // Determine handlers + handlerQueue = jQuery.event.handlers.call( this, event, handlers ); + + // Run delegates first; they may want to stop propagation beneath us + i = 0; + while ( ( matched = handlerQueue[ i++ ] ) && !event.isPropagationStopped() ) { + event.currentTarget = matched.elem; + + j = 0; + while ( ( handleObj = matched.handlers[ j++ ] ) && + !event.isImmediatePropagationStopped() ) { + + // If the event is namespaced, then each handler is only invoked if it is + // specially universal or its namespaces are a superset of the event's. + if ( !event.rnamespace || handleObj.namespace === false || + event.rnamespace.test( handleObj.namespace ) ) { + + event.handleObj = handleObj; + event.data = handleObj.data; + + ret = ( ( jQuery.event.special[ handleObj.origType ] || {} ).handle || + handleObj.handler ).apply( matched.elem, args ); + + if ( ret !== undefined ) { + if ( ( event.result = ret ) === false ) { + event.preventDefault(); + event.stopPropagation(); + } + } + } + } + } + + // Call the postDispatch hook for the mapped type + if ( special.postDispatch ) { + special.postDispatch.call( this, event ); + } + + return event.result; + }, + + handlers: function( event, handlers ) { + var i, handleObj, sel, matchedHandlers, matchedSelectors, + handlerQueue = [], + delegateCount = handlers.delegateCount, + cur = event.target; + + // Find delegate handlers + if ( delegateCount && + + // Support: IE <=9 + // Black-hole SVG <use> instance trees (trac-13180) + cur.nodeType && + + // Support: Firefox <=42 + // Suppress spec-violating clicks indicating a non-primary pointer button (trac-3861) + // https://www.w3.org/TR/DOM-Level-3-Events/#event-type-click + // Support: IE 11 only + // ...but not arrow key "clicks" of radio inputs, which can have `button` -1 (gh-2343) + !( event.type === "click" && event.button >= 1 ) ) { + + for ( ; cur !== this; cur = cur.parentNode || this ) { + + // Don't check non-elements (#13208) + // Don't process clicks on disabled elements (#6911, #8165, #11382, #11764) + if ( cur.nodeType === 1 && !( event.type === "click" && cur.disabled === true ) ) { + matchedHandlers = []; + matchedSelectors = {}; + for ( i = 0; i < delegateCount; i++ ) { + handleObj = handlers[ i ]; + + // Don't conflict with Object.prototype properties (#13203) + sel = handleObj.selector + " "; + + if ( matchedSelectors[ sel ] === undefined ) { + matchedSelectors[ sel ] = handleObj.needsContext ? + jQuery( sel, this ).index( cur ) > -1 : + jQuery.find( sel, this, null, [ cur ] ).length; + } + if ( matchedSelectors[ sel ] ) { + matchedHandlers.push( handleObj ); + } + } + if ( matchedHandlers.length ) { + handlerQueue.push( { elem: cur, handlers: matchedHandlers } ); + } + } + } + } + + // Add the remaining (directly-bound) handlers + cur = this; + if ( delegateCount < handlers.length ) { + handlerQueue.push( { elem: cur, handlers: handlers.slice( delegateCount ) } ); + } + + return handlerQueue; + }, + + addProp: function( name, hook ) { + Object.defineProperty( jQuery.Event.prototype, name, { + enumerable: true, + configurable: true, + + get: isFunction( hook ) ? + function() { + if ( this.originalEvent ) { + return hook( this.originalEvent ); + } + } : + function() { + if ( this.originalEvent ) { + return this.originalEvent[ name ]; + } + }, + + set: function( value ) { + Object.defineProperty( this, name, { + enumerable: true, + configurable: true, + writable: true, + value: value + } ); + } + } ); + }, + + fix: function( originalEvent ) { + return originalEvent[ jQuery.expando ] ? + originalEvent : + new jQuery.Event( originalEvent ); + }, + + special: { + load: { + + // Prevent triggered image.load events from bubbling to window.load + noBubble: true + }, + click: { + + // Utilize native event to ensure correct state for checkable inputs + setup: function( data ) { + + // For mutual compressibility with _default, replace `this` access with a local var. + // `|| data` is dead code meant only to preserve the variable through minification. + var el = this || data; + + // Claim the first handler + if ( rcheckableType.test( el.type ) && + el.click && nodeName( el, "input" ) ) { + + // dataPriv.set( el, "click", ... ) + leverageNative( el, "click", returnTrue ); + } + + // Return false to allow normal processing in the caller + return false; + }, + trigger: function( data ) { + + // For mutual compressibility with _default, replace `this` access with a local var. + // `|| data` is dead code meant only to preserve the variable through minification. + var el = this || data; + + // Force setup before triggering a click + if ( rcheckableType.test( el.type ) && + el.click && nodeName( el, "input" ) ) { + + leverageNative( el, "click" ); + } + + // Return non-false to allow normal event-path propagation + return true; + }, + + // For cross-browser consistency, suppress native .click() on links + // Also prevent it if we're currently inside a leveraged native-event stack + _default: function( event ) { + var target = event.target; + return rcheckableType.test( target.type ) && + target.click && nodeName( target, "input" ) && + dataPriv.get( target, "click" ) || + nodeName( target, "a" ); + } + }, + + beforeunload: { + postDispatch: function( event ) { + + // Support: Firefox 20+ + // Firefox doesn't alert if the returnValue field is not set. + if ( event.result !== undefined && event.originalEvent ) { + event.originalEvent.returnValue = event.result; + } + } + } + } +}; + +// Ensure the presence of an event listener that handles manually-triggered +// synthetic events by interrupting progress until reinvoked in response to +// *native* events that it fires directly, ensuring that state changes have +// already occurred before other listeners are invoked. +function leverageNative( el, type, expectSync ) { + + // Missing expectSync indicates a trigger call, which must force setup through jQuery.event.add + if ( !expectSync ) { + if ( dataPriv.get( el, type ) === undefined ) { + jQuery.event.add( el, type, returnTrue ); + } + return; + } + + // Register the controller as a special universal handler for all event namespaces + dataPriv.set( el, type, false ); + jQuery.event.add( el, type, { + namespace: false, + handler: function( event ) { + var notAsync, result, + saved = dataPriv.get( this, type ); + + if ( ( event.isTrigger & 1 ) && this[ type ] ) { + + // Interrupt processing of the outer synthetic .trigger()ed event + // Saved data should be false in such cases, but might be a leftover capture object + // from an async native handler (gh-4350) + if ( !saved.length ) { + + // Store arguments for use when handling the inner native event + // There will always be at least one argument (an event object), so this array + // will not be confused with a leftover capture object. + saved = slice.call( arguments ); + dataPriv.set( this, type, saved ); + + // Trigger the native event and capture its result + // Support: IE <=9 - 11+ + // focus() and blur() are asynchronous + notAsync = expectSync( this, type ); + this[ type ](); + result = dataPriv.get( this, type ); + if ( saved !== result || notAsync ) { + dataPriv.set( this, type, false ); + } else { + result = {}; + } + if ( saved !== result ) { + + // Cancel the outer synthetic event + event.stopImmediatePropagation(); + event.preventDefault(); + + // Support: Chrome 86+ + // In Chrome, if an element having a focusout handler is blurred by + // clicking outside of it, it invokes the handler synchronously. If + // that handler calls `.remove()` on the element, the data is cleared, + // leaving `result` undefined. We need to guard against this. + return result && result.value; + } + + // If this is an inner synthetic event for an event with a bubbling surrogate + // (focus or blur), assume that the surrogate already propagated from triggering the + // native event and prevent that from happening again here. + // This technically gets the ordering wrong w.r.t. to `.trigger()` (in which the + // bubbling surrogate propagates *after* the non-bubbling base), but that seems + // less bad than duplication. + } else if ( ( jQuery.event.special[ type ] || {} ).delegateType ) { + event.stopPropagation(); + } + + // If this is a native event triggered above, everything is now in order + // Fire an inner synthetic event with the original arguments + } else if ( saved.length ) { + + // ...and capture the result + dataPriv.set( this, type, { + value: jQuery.event.trigger( + + // Support: IE <=9 - 11+ + // Extend with the prototype to reset the above stopImmediatePropagation() + jQuery.extend( saved[ 0 ], jQuery.Event.prototype ), + saved.slice( 1 ), + this + ) + } ); + + // Abort handling of the native event + event.stopImmediatePropagation(); + } + } + } ); +} + +jQuery.removeEvent = function( elem, type, handle ) { + + // This "if" is needed for plain objects + if ( elem.removeEventListener ) { + elem.removeEventListener( type, handle ); + } +}; + +jQuery.Event = function( src, props ) { + + // Allow instantiation without the 'new' keyword + if ( !( this instanceof jQuery.Event ) ) { + return new jQuery.Event( src, props ); + } + + // Event object + if ( src && src.type ) { + this.originalEvent = src; + this.type = src.type; + + // Events bubbling up the document may have been marked as prevented + // by a handler lower down the tree; reflect the correct value. + this.isDefaultPrevented = src.defaultPrevented || + src.defaultPrevented === undefined && + + // Support: Android <=2.3 only + src.returnValue === false ? + returnTrue : + returnFalse; + + // Create target properties + // Support: Safari <=6 - 7 only + // Target should not be a text node (#504, #13143) + this.target = ( src.target && src.target.nodeType === 3 ) ? + src.target.parentNode : + src.target; + + this.currentTarget = src.currentTarget; + this.relatedTarget = src.relatedTarget; + + // Event type + } else { + this.type = src; + } + + // Put explicitly provided properties onto the event object + if ( props ) { + jQuery.extend( this, props ); + } + + // Create a timestamp if incoming event doesn't have one + this.timeStamp = src && src.timeStamp || Date.now(); + + // Mark it as fixed + this[ jQuery.expando ] = true; +}; + +// jQuery.Event is based on DOM3 Events as specified by the ECMAScript Language Binding +// https://www.w3.org/TR/2003/WD-DOM-Level-3-Events-20030331/ecma-script-binding.html +jQuery.Event.prototype = { + constructor: jQuery.Event, + isDefaultPrevented: returnFalse, + isPropagationStopped: returnFalse, + isImmediatePropagationStopped: returnFalse, + isSimulated: false, + + preventDefault: function() { + var e = this.originalEvent; + + this.isDefaultPrevented = returnTrue; + + if ( e && !this.isSimulated ) { + e.preventDefault(); + } + }, + stopPropagation: function() { + var e = this.originalEvent; + + this.isPropagationStopped = returnTrue; + + if ( e && !this.isSimulated ) { + e.stopPropagation(); + } + }, + stopImmediatePropagation: function() { + var e = this.originalEvent; + + this.isImmediatePropagationStopped = returnTrue; + + if ( e && !this.isSimulated ) { + e.stopImmediatePropagation(); + } + + this.stopPropagation(); + } +}; + +// Includes all common event props including KeyEvent and MouseEvent specific props +jQuery.each( { + altKey: true, + bubbles: true, + cancelable: true, + changedTouches: true, + ctrlKey: true, + detail: true, + eventPhase: true, + metaKey: true, + pageX: true, + pageY: true, + shiftKey: true, + view: true, + "char": true, + code: true, + charCode: true, + key: true, + keyCode: true, + button: true, + buttons: true, + clientX: true, + clientY: true, + offsetX: true, + offsetY: true, + pointerId: true, + pointerType: true, + screenX: true, + screenY: true, + targetTouches: true, + toElement: true, + touches: true, + which: true +}, jQuery.event.addProp ); + +jQuery.each( { focus: "focusin", blur: "focusout" }, function( type, delegateType ) { + jQuery.event.special[ type ] = { + + // Utilize native event if possible so blur/focus sequence is correct + setup: function() { + + // Claim the first handler + // dataPriv.set( this, "focus", ... ) + // dataPriv.set( this, "blur", ... ) + leverageNative( this, type, expectSync ); + + // Return false to allow normal processing in the caller + return false; + }, + trigger: function() { + + // Force setup before trigger + leverageNative( this, type ); + + // Return non-false to allow normal event-path propagation + return true; + }, + + // Suppress native focus or blur as it's already being fired + // in leverageNative. + _default: function() { + return true; + }, + + delegateType: delegateType + }; +} ); + +// Create mouseenter/leave events using mouseover/out and event-time checks +// so that event delegation works in jQuery. +// Do the same for pointerenter/pointerleave and pointerover/pointerout +// +// Support: Safari 7 only +// Safari sends mouseenter too often; see: +// https://bugs.chromium.org/p/chromium/issues/detail?id=470258 +// for the description of the bug (it existed in older Chrome versions as well). +jQuery.each( { + mouseenter: "mouseover", + mouseleave: "mouseout", + pointerenter: "pointerover", + pointerleave: "pointerout" +}, function( orig, fix ) { + jQuery.event.special[ orig ] = { + delegateType: fix, + bindType: fix, + + handle: function( event ) { + var ret, + target = this, + related = event.relatedTarget, + handleObj = event.handleObj; + + // For mouseenter/leave call the handler if related is outside the target. + // NB: No relatedTarget if the mouse left/entered the browser window + if ( !related || ( related !== target && !jQuery.contains( target, related ) ) ) { + event.type = handleObj.origType; + ret = handleObj.handler.apply( this, arguments ); + event.type = fix; + } + return ret; + } + }; +} ); + +jQuery.fn.extend( { + + on: function( types, selector, data, fn ) { + return on( this, types, selector, data, fn ); + }, + one: function( types, selector, data, fn ) { + return on( this, types, selector, data, fn, 1 ); + }, + off: function( types, selector, fn ) { + var handleObj, type; + if ( types && types.preventDefault && types.handleObj ) { + + // ( event ) dispatched jQuery.Event + handleObj = types.handleObj; + jQuery( types.delegateTarget ).off( + handleObj.namespace ? + handleObj.origType + "." + handleObj.namespace : + handleObj.origType, + handleObj.selector, + handleObj.handler + ); + return this; + } + if ( typeof types === "object" ) { + + // ( types-object [, selector] ) + for ( type in types ) { + this.off( type, selector, types[ type ] ); + } + return this; + } + if ( selector === false || typeof selector === "function" ) { + + // ( types [, fn] ) + fn = selector; + selector = undefined; + } + if ( fn === false ) { + fn = returnFalse; + } + return this.each( function() { + jQuery.event.remove( this, types, fn, selector ); + } ); + } +} ); + + +var + + // Support: IE <=10 - 11, Edge 12 - 13 only + // In IE/Edge using regex groups here causes severe slowdowns. + // See https://connect.microsoft.com/IE/feedback/details/1736512/ + rnoInnerhtml = /<script|<style|<link/i, + + // checked="checked" or checked + rchecked = /checked\s*(?:[^=]|=\s*.checked.)/i, + rcleanScript = /^\s*<!(?:\[CDATA\[|--)|(?:\]\]|--)>\s*$/g; + +// Prefer a tbody over its parent table for containing new rows +function manipulationTarget( elem, content ) { + if ( nodeName( elem, "table" ) && + nodeName( content.nodeType !== 11 ? content : content.firstChild, "tr" ) ) { + + return jQuery( elem ).children( "tbody" )[ 0 ] || elem; + } + + return elem; +} + +// Replace/restore the type attribute of script elements for safe DOM manipulation +function disableScript( elem ) { + elem.type = ( elem.getAttribute( "type" ) !== null ) + "/" + elem.type; + return elem; +} +function restoreScript( elem ) { + if ( ( elem.type || "" ).slice( 0, 5 ) === "true/" ) { + elem.type = elem.type.slice( 5 ); + } else { + elem.removeAttribute( "type" ); + } + + return elem; +} + +function cloneCopyEvent( src, dest ) { + var i, l, type, pdataOld, udataOld, udataCur, events; + + if ( dest.nodeType !== 1 ) { + return; + } + + // 1. Copy private data: events, handlers, etc. + if ( dataPriv.hasData( src ) ) { + pdataOld = dataPriv.get( src ); + events = pdataOld.events; + + if ( events ) { + dataPriv.remove( dest, "handle events" ); + + for ( type in events ) { + for ( i = 0, l = events[ type ].length; i < l; i++ ) { + jQuery.event.add( dest, type, events[ type ][ i ] ); + } + } + } + } + + // 2. Copy user data + if ( dataUser.hasData( src ) ) { + udataOld = dataUser.access( src ); + udataCur = jQuery.extend( {}, udataOld ); + + dataUser.set( dest, udataCur ); + } +} + +// Fix IE bugs, see support tests +function fixInput( src, dest ) { + var nodeName = dest.nodeName.toLowerCase(); + + // Fails to persist the checked state of a cloned checkbox or radio button. + if ( nodeName === "input" && rcheckableType.test( src.type ) ) { + dest.checked = src.checked; + + // Fails to return the selected option to the default selected state when cloning options + } else if ( nodeName === "input" || nodeName === "textarea" ) { + dest.defaultValue = src.defaultValue; + } +} + +function domManip( collection, args, callback, ignored ) { + + // Flatten any nested arrays + args = flat( args ); + + var fragment, first, scripts, hasScripts, node, doc, + i = 0, + l = collection.length, + iNoClone = l - 1, + value = args[ 0 ], + valueIsFunction = isFunction( value ); + + // We can't cloneNode fragments that contain checked, in WebKit + if ( valueIsFunction || + ( l > 1 && typeof value === "string" && + !support.checkClone && rchecked.test( value ) ) ) { + return collection.each( function( index ) { + var self = collection.eq( index ); + if ( valueIsFunction ) { + args[ 0 ] = value.call( this, index, self.html() ); + } + domManip( self, args, callback, ignored ); + } ); + } + + if ( l ) { + fragment = buildFragment( args, collection[ 0 ].ownerDocument, false, collection, ignored ); + first = fragment.firstChild; + + if ( fragment.childNodes.length === 1 ) { + fragment = first; + } + + // Require either new content or an interest in ignored elements to invoke the callback + if ( first || ignored ) { + scripts = jQuery.map( getAll( fragment, "script" ), disableScript ); + hasScripts = scripts.length; + + // Use the original fragment for the last item + // instead of the first because it can end up + // being emptied incorrectly in certain situations (#8070). + for ( ; i < l; i++ ) { + node = fragment; + + if ( i !== iNoClone ) { + node = jQuery.clone( node, true, true ); + + // Keep references to cloned scripts for later restoration + if ( hasScripts ) { + + // Support: Android <=4.0 only, PhantomJS 1 only + // push.apply(_, arraylike) throws on ancient WebKit + jQuery.merge( scripts, getAll( node, "script" ) ); + } + } + + callback.call( collection[ i ], node, i ); + } + + if ( hasScripts ) { + doc = scripts[ scripts.length - 1 ].ownerDocument; + + // Reenable scripts + jQuery.map( scripts, restoreScript ); + + // Evaluate executable scripts on first document insertion + for ( i = 0; i < hasScripts; i++ ) { + node = scripts[ i ]; + if ( rscriptType.test( node.type || "" ) && + !dataPriv.access( node, "globalEval" ) && + jQuery.contains( doc, node ) ) { + + if ( node.src && ( node.type || "" ).toLowerCase() !== "module" ) { + + // Optional AJAX dependency, but won't run scripts if not present + if ( jQuery._evalUrl && !node.noModule ) { + jQuery._evalUrl( node.src, { + nonce: node.nonce || node.getAttribute( "nonce" ) + }, doc ); + } + } else { + DOMEval( node.textContent.replace( rcleanScript, "" ), node, doc ); + } + } + } + } + } + } + + return collection; +} + +function remove( elem, selector, keepData ) { + var node, + nodes = selector ? jQuery.filter( selector, elem ) : elem, + i = 0; + + for ( ; ( node = nodes[ i ] ) != null; i++ ) { + if ( !keepData && node.nodeType === 1 ) { + jQuery.cleanData( getAll( node ) ); + } + + if ( node.parentNode ) { + if ( keepData && isAttached( node ) ) { + setGlobalEval( getAll( node, "script" ) ); + } + node.parentNode.removeChild( node ); + } + } + + return elem; +} + +jQuery.extend( { + htmlPrefilter: function( html ) { + return html; + }, + + clone: function( elem, dataAndEvents, deepDataAndEvents ) { + var i, l, srcElements, destElements, + clone = elem.cloneNode( true ), + inPage = isAttached( elem ); + + // Fix IE cloning issues + if ( !support.noCloneChecked && ( elem.nodeType === 1 || elem.nodeType === 11 ) && + !jQuery.isXMLDoc( elem ) ) { + + // We eschew Sizzle here for performance reasons: https://jsperf.com/getall-vs-sizzle/2 + destElements = getAll( clone ); + srcElements = getAll( elem ); + + for ( i = 0, l = srcElements.length; i < l; i++ ) { + fixInput( srcElements[ i ], destElements[ i ] ); + } + } + + // Copy the events from the original to the clone + if ( dataAndEvents ) { + if ( deepDataAndEvents ) { + srcElements = srcElements || getAll( elem ); + destElements = destElements || getAll( clone ); + + for ( i = 0, l = srcElements.length; i < l; i++ ) { + cloneCopyEvent( srcElements[ i ], destElements[ i ] ); + } + } else { + cloneCopyEvent( elem, clone ); + } + } + + // Preserve script evaluation history + destElements = getAll( clone, "script" ); + if ( destElements.length > 0 ) { + setGlobalEval( destElements, !inPage && getAll( elem, "script" ) ); + } + + // Return the cloned set + return clone; + }, + + cleanData: function( elems ) { + var data, elem, type, + special = jQuery.event.special, + i = 0; + + for ( ; ( elem = elems[ i ] ) !== undefined; i++ ) { + if ( acceptData( elem ) ) { + if ( ( data = elem[ dataPriv.expando ] ) ) { + if ( data.events ) { + for ( type in data.events ) { + if ( special[ type ] ) { + jQuery.event.remove( elem, type ); + + // This is a shortcut to avoid jQuery.event.remove's overhead + } else { + jQuery.removeEvent( elem, type, data.handle ); + } + } + } + + // Support: Chrome <=35 - 45+ + // Assign undefined instead of using delete, see Data#remove + elem[ dataPriv.expando ] = undefined; + } + if ( elem[ dataUser.expando ] ) { + + // Support: Chrome <=35 - 45+ + // Assign undefined instead of using delete, see Data#remove + elem[ dataUser.expando ] = undefined; + } + } + } + } +} ); + +jQuery.fn.extend( { + detach: function( selector ) { + return remove( this, selector, true ); + }, + + remove: function( selector ) { + return remove( this, selector ); + }, + + text: function( value ) { + return access( this, function( value ) { + return value === undefined ? + jQuery.text( this ) : + this.empty().each( function() { + if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) { + this.textContent = value; + } + } ); + }, null, value, arguments.length ); + }, + + append: function() { + return domManip( this, arguments, function( elem ) { + if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) { + var target = manipulationTarget( this, elem ); + target.appendChild( elem ); + } + } ); + }, + + prepend: function() { + return domManip( this, arguments, function( elem ) { + if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) { + var target = manipulationTarget( this, elem ); + target.insertBefore( elem, target.firstChild ); + } + } ); + }, + + before: function() { + return domManip( this, arguments, function( elem ) { + if ( this.parentNode ) { + this.parentNode.insertBefore( elem, this ); + } + } ); + }, + + after: function() { + return domManip( this, arguments, function( elem ) { + if ( this.parentNode ) { + this.parentNode.insertBefore( elem, this.nextSibling ); + } + } ); + }, + + empty: function() { + var elem, + i = 0; + + for ( ; ( elem = this[ i ] ) != null; i++ ) { + if ( elem.nodeType === 1 ) { + + // Prevent memory leaks + jQuery.cleanData( getAll( elem, false ) ); + + // Remove any remaining nodes + elem.textContent = ""; + } + } + + return this; + }, + + clone: function( dataAndEvents, deepDataAndEvents ) { + dataAndEvents = dataAndEvents == null ? false : dataAndEvents; + deepDataAndEvents = deepDataAndEvents == null ? dataAndEvents : deepDataAndEvents; + + return this.map( function() { + return jQuery.clone( this, dataAndEvents, deepDataAndEvents ); + } ); + }, + + html: function( value ) { + return access( this, function( value ) { + var elem = this[ 0 ] || {}, + i = 0, + l = this.length; + + if ( value === undefined && elem.nodeType === 1 ) { + return elem.innerHTML; + } + + // See if we can take a shortcut and just use innerHTML + if ( typeof value === "string" && !rnoInnerhtml.test( value ) && + !wrapMap[ ( rtagName.exec( value ) || [ "", "" ] )[ 1 ].toLowerCase() ] ) { + + value = jQuery.htmlPrefilter( value ); + + try { + for ( ; i < l; i++ ) { + elem = this[ i ] || {}; + + // Remove element nodes and prevent memory leaks + if ( elem.nodeType === 1 ) { + jQuery.cleanData( getAll( elem, false ) ); + elem.innerHTML = value; + } + } + + elem = 0; + + // If using innerHTML throws an exception, use the fallback method + } catch ( e ) {} + } + + if ( elem ) { + this.empty().append( value ); + } + }, null, value, arguments.length ); + }, + + replaceWith: function() { + var ignored = []; + + // Make the changes, replacing each non-ignored context element with the new content + return domManip( this, arguments, function( elem ) { + var parent = this.parentNode; + + if ( jQuery.inArray( this, ignored ) < 0 ) { + jQuery.cleanData( getAll( this ) ); + if ( parent ) { + parent.replaceChild( elem, this ); + } + } + + // Force callback invocation + }, ignored ); + } +} ); + +jQuery.each( { + appendTo: "append", + prependTo: "prepend", + insertBefore: "before", + insertAfter: "after", + replaceAll: "replaceWith" +}, function( name, original ) { + jQuery.fn[ name ] = function( selector ) { + var elems, + ret = [], + insert = jQuery( selector ), + last = insert.length - 1, + i = 0; + + for ( ; i <= last; i++ ) { + elems = i === last ? this : this.clone( true ); + jQuery( insert[ i ] )[ original ]( elems ); + + // Support: Android <=4.0 only, PhantomJS 1 only + // .get() because push.apply(_, arraylike) throws on ancient WebKit + push.apply( ret, elems.get() ); + } + + return this.pushStack( ret ); + }; +} ); +var rnumnonpx = new RegExp( "^(" + pnum + ")(?!px)[a-z%]+$", "i" ); + +var getStyles = function( elem ) { + + // Support: IE <=11 only, Firefox <=30 (#15098, #14150) + // IE throws on elements created in popups + // FF meanwhile throws on frame elements through "defaultView.getComputedStyle" + var view = elem.ownerDocument.defaultView; + + if ( !view || !view.opener ) { + view = window; + } + + return view.getComputedStyle( elem ); + }; + +var swap = function( elem, options, callback ) { + var ret, name, + old = {}; + + // Remember the old values, and insert the new ones + for ( name in options ) { + old[ name ] = elem.style[ name ]; + elem.style[ name ] = options[ name ]; + } + + ret = callback.call( elem ); + + // Revert the old values + for ( name in options ) { + elem.style[ name ] = old[ name ]; + } + + return ret; +}; + + +var rboxStyle = new RegExp( cssExpand.join( "|" ), "i" ); + + + +( function() { + + // Executing both pixelPosition & boxSizingReliable tests require only one layout + // so they're executed at the same time to save the second computation. + function computeStyleTests() { + + // This is a singleton, we need to execute it only once + if ( !div ) { + return; + } + + container.style.cssText = "position:absolute;left:-11111px;width:60px;" + + "margin-top:1px;padding:0;border:0"; + div.style.cssText = + "position:relative;display:block;box-sizing:border-box;overflow:scroll;" + + "margin:auto;border:1px;padding:1px;" + + "width:60%;top:1%"; + documentElement.appendChild( container ).appendChild( div ); + + var divStyle = window.getComputedStyle( div ); + pixelPositionVal = divStyle.top !== "1%"; + + // Support: Android 4.0 - 4.3 only, Firefox <=3 - 44 + reliableMarginLeftVal = roundPixelMeasures( divStyle.marginLeft ) === 12; + + // Support: Android 4.0 - 4.3 only, Safari <=9.1 - 10.1, iOS <=7.0 - 9.3 + // Some styles come back with percentage values, even though they shouldn't + div.style.right = "60%"; + pixelBoxStylesVal = roundPixelMeasures( divStyle.right ) === 36; + + // Support: IE 9 - 11 only + // Detect misreporting of content dimensions for box-sizing:border-box elements + boxSizingReliableVal = roundPixelMeasures( divStyle.width ) === 36; + + // Support: IE 9 only + // Detect overflow:scroll screwiness (gh-3699) + // Support: Chrome <=64 + // Don't get tricked when zoom affects offsetWidth (gh-4029) + div.style.position = "absolute"; + scrollboxSizeVal = roundPixelMeasures( div.offsetWidth / 3 ) === 12; + + documentElement.removeChild( container ); + + // Nullify the div so it wouldn't be stored in the memory and + // it will also be a sign that checks already performed + div = null; + } + + function roundPixelMeasures( measure ) { + return Math.round( parseFloat( measure ) ); + } + + var pixelPositionVal, boxSizingReliableVal, scrollboxSizeVal, pixelBoxStylesVal, + reliableTrDimensionsVal, reliableMarginLeftVal, + container = document.createElement( "div" ), + div = document.createElement( "div" ); + + // Finish early in limited (non-browser) environments + if ( !div.style ) { + return; + } + + // Support: IE <=9 - 11 only + // Style of cloned element affects source element cloned (#8908) + div.style.backgroundClip = "content-box"; + div.cloneNode( true ).style.backgroundClip = ""; + support.clearCloneStyle = div.style.backgroundClip === "content-box"; + + jQuery.extend( support, { + boxSizingReliable: function() { + computeStyleTests(); + return boxSizingReliableVal; + }, + pixelBoxStyles: function() { + computeStyleTests(); + return pixelBoxStylesVal; + }, + pixelPosition: function() { + computeStyleTests(); + return pixelPositionVal; + }, + reliableMarginLeft: function() { + computeStyleTests(); + return reliableMarginLeftVal; + }, + scrollboxSize: function() { + computeStyleTests(); + return scrollboxSizeVal; + }, + + // Support: IE 9 - 11+, Edge 15 - 18+ + // IE/Edge misreport `getComputedStyle` of table rows with width/height + // set in CSS while `offset*` properties report correct values. + // Behavior in IE 9 is more subtle than in newer versions & it passes + // some versions of this test; make sure not to make it pass there! + // + // Support: Firefox 70+ + // Only Firefox includes border widths + // in computed dimensions. (gh-4529) + reliableTrDimensions: function() { + var table, tr, trChild, trStyle; + if ( reliableTrDimensionsVal == null ) { + table = document.createElement( "table" ); + tr = document.createElement( "tr" ); + trChild = document.createElement( "div" ); + + table.style.cssText = "position:absolute;left:-11111px;border-collapse:separate"; + tr.style.cssText = "border:1px solid"; + + // Support: Chrome 86+ + // Height set through cssText does not get applied. + // Computed height then comes back as 0. + tr.style.height = "1px"; + trChild.style.height = "9px"; + + // Support: Android 8 Chrome 86+ + // In our bodyBackground.html iframe, + // display for all div elements is set to "inline", + // which causes a problem only in Android 8 Chrome 86. + // Ensuring the div is display: block + // gets around this issue. + trChild.style.display = "block"; + + documentElement + .appendChild( table ) + .appendChild( tr ) + .appendChild( trChild ); + + trStyle = window.getComputedStyle( tr ); + reliableTrDimensionsVal = ( parseInt( trStyle.height, 10 ) + + parseInt( trStyle.borderTopWidth, 10 ) + + parseInt( trStyle.borderBottomWidth, 10 ) ) === tr.offsetHeight; + + documentElement.removeChild( table ); + } + return reliableTrDimensionsVal; + } + } ); +} )(); + + +function curCSS( elem, name, computed ) { + var width, minWidth, maxWidth, ret, + + // Support: Firefox 51+ + // Retrieving style before computed somehow + // fixes an issue with getting wrong values + // on detached elements + style = elem.style; + + computed = computed || getStyles( elem ); + + // getPropertyValue is needed for: + // .css('filter') (IE 9 only, #12537) + // .css('--customProperty) (#3144) + if ( computed ) { + ret = computed.getPropertyValue( name ) || computed[ name ]; + + if ( ret === "" && !isAttached( elem ) ) { + ret = jQuery.style( elem, name ); + } + + // A tribute to the "awesome hack by Dean Edwards" + // Android Browser returns percentage for some values, + // but width seems to be reliably pixels. + // This is against the CSSOM draft spec: + // https://drafts.csswg.org/cssom/#resolved-values + if ( !support.pixelBoxStyles() && rnumnonpx.test( ret ) && rboxStyle.test( name ) ) { + + // Remember the original values + width = style.width; + minWidth = style.minWidth; + maxWidth = style.maxWidth; + + // Put in the new values to get a computed value out + style.minWidth = style.maxWidth = style.width = ret; + ret = computed.width; + + // Revert the changed values + style.width = width; + style.minWidth = minWidth; + style.maxWidth = maxWidth; + } + } + + return ret !== undefined ? + + // Support: IE <=9 - 11 only + // IE returns zIndex value as an integer. + ret + "" : + ret; +} + + +function addGetHookIf( conditionFn, hookFn ) { + + // Define the hook, we'll check on the first run if it's really needed. + return { + get: function() { + if ( conditionFn() ) { + + // Hook not needed (or it's not possible to use it due + // to missing dependency), remove it. + delete this.get; + return; + } + + // Hook needed; redefine it so that the support test is not executed again. + return ( this.get = hookFn ).apply( this, arguments ); + } + }; +} + + +var cssPrefixes = [ "Webkit", "Moz", "ms" ], + emptyStyle = document.createElement( "div" ).style, + vendorProps = {}; + +// Return a vendor-prefixed property or undefined +function vendorPropName( name ) { + + // Check for vendor prefixed names + var capName = name[ 0 ].toUpperCase() + name.slice( 1 ), + i = cssPrefixes.length; + + while ( i-- ) { + name = cssPrefixes[ i ] + capName; + if ( name in emptyStyle ) { + return name; + } + } +} + +// Return a potentially-mapped jQuery.cssProps or vendor prefixed property +function finalPropName( name ) { + var final = jQuery.cssProps[ name ] || vendorProps[ name ]; + + if ( final ) { + return final; + } + if ( name in emptyStyle ) { + return name; + } + return vendorProps[ name ] = vendorPropName( name ) || name; +} + + +var + + // Swappable if display is none or starts with table + // except "table", "table-cell", or "table-caption" + // See here for display values: https://developer.mozilla.org/en-US/docs/CSS/display + rdisplayswap = /^(none|table(?!-c[ea]).+)/, + rcustomProp = /^--/, + cssShow = { position: "absolute", visibility: "hidden", display: "block" }, + cssNormalTransform = { + letterSpacing: "0", + fontWeight: "400" + }; + +function setPositiveNumber( _elem, value, subtract ) { + + // Any relative (+/-) values have already been + // normalized at this point + var matches = rcssNum.exec( value ); + return matches ? + + // Guard against undefined "subtract", e.g., when used as in cssHooks + Math.max( 0, matches[ 2 ] - ( subtract || 0 ) ) + ( matches[ 3 ] || "px" ) : + value; +} + +function boxModelAdjustment( elem, dimension, box, isBorderBox, styles, computedVal ) { + var i = dimension === "width" ? 1 : 0, + extra = 0, + delta = 0; + + // Adjustment may not be necessary + if ( box === ( isBorderBox ? "border" : "content" ) ) { + return 0; + } + + for ( ; i < 4; i += 2 ) { + + // Both box models exclude margin + if ( box === "margin" ) { + delta += jQuery.css( elem, box + cssExpand[ i ], true, styles ); + } + + // If we get here with a content-box, we're seeking "padding" or "border" or "margin" + if ( !isBorderBox ) { + + // Add padding + delta += jQuery.css( elem, "padding" + cssExpand[ i ], true, styles ); + + // For "border" or "margin", add border + if ( box !== "padding" ) { + delta += jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles ); + + // But still keep track of it otherwise + } else { + extra += jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles ); + } + + // If we get here with a border-box (content + padding + border), we're seeking "content" or + // "padding" or "margin" + } else { + + // For "content", subtract padding + if ( box === "content" ) { + delta -= jQuery.css( elem, "padding" + cssExpand[ i ], true, styles ); + } + + // For "content" or "padding", subtract border + if ( box !== "margin" ) { + delta -= jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles ); + } + } + } + + // Account for positive content-box scroll gutter when requested by providing computedVal + if ( !isBorderBox && computedVal >= 0 ) { + + // offsetWidth/offsetHeight is a rounded sum of content, padding, scroll gutter, and border + // Assuming integer scroll gutter, subtract the rest and round down + delta += Math.max( 0, Math.ceil( + elem[ "offset" + dimension[ 0 ].toUpperCase() + dimension.slice( 1 ) ] - + computedVal - + delta - + extra - + 0.5 + + // If offsetWidth/offsetHeight is unknown, then we can't determine content-box scroll gutter + // Use an explicit zero to avoid NaN (gh-3964) + ) ) || 0; + } + + return delta; +} + +function getWidthOrHeight( elem, dimension, extra ) { + + // Start with computed style + var styles = getStyles( elem ), + + // To avoid forcing a reflow, only fetch boxSizing if we need it (gh-4322). + // Fake content-box until we know it's needed to know the true value. + boxSizingNeeded = !support.boxSizingReliable() || extra, + isBorderBox = boxSizingNeeded && + jQuery.css( elem, "boxSizing", false, styles ) === "border-box", + valueIsBorderBox = isBorderBox, + + val = curCSS( elem, dimension, styles ), + offsetProp = "offset" + dimension[ 0 ].toUpperCase() + dimension.slice( 1 ); + + // Support: Firefox <=54 + // Return a confounding non-pixel value or feign ignorance, as appropriate. + if ( rnumnonpx.test( val ) ) { + if ( !extra ) { + return val; + } + val = "auto"; + } + + + // Support: IE 9 - 11 only + // Use offsetWidth/offsetHeight for when box sizing is unreliable. + // In those cases, the computed value can be trusted to be border-box. + if ( ( !support.boxSizingReliable() && isBorderBox || + + // Support: IE 10 - 11+, Edge 15 - 18+ + // IE/Edge misreport `getComputedStyle` of table rows with width/height + // set in CSS while `offset*` properties report correct values. + // Interestingly, in some cases IE 9 doesn't suffer from this issue. + !support.reliableTrDimensions() && nodeName( elem, "tr" ) || + + // Fall back to offsetWidth/offsetHeight when value is "auto" + // This happens for inline elements with no explicit setting (gh-3571) + val === "auto" || + + // Support: Android <=4.1 - 4.3 only + // Also use offsetWidth/offsetHeight for misreported inline dimensions (gh-3602) + !parseFloat( val ) && jQuery.css( elem, "display", false, styles ) === "inline" ) && + + // Make sure the element is visible & connected + elem.getClientRects().length ) { + + isBorderBox = jQuery.css( elem, "boxSizing", false, styles ) === "border-box"; + + // Where available, offsetWidth/offsetHeight approximate border box dimensions. + // Where not available (e.g., SVG), assume unreliable box-sizing and interpret the + // retrieved value as a content box dimension. + valueIsBorderBox = offsetProp in elem; + if ( valueIsBorderBox ) { + val = elem[ offsetProp ]; + } + } + + // Normalize "" and auto + val = parseFloat( val ) || 0; + + // Adjust for the element's box model + return ( val + + boxModelAdjustment( + elem, + dimension, + extra || ( isBorderBox ? "border" : "content" ), + valueIsBorderBox, + styles, + + // Provide the current computed size to request scroll gutter calculation (gh-3589) + val + ) + ) + "px"; +} + +jQuery.extend( { + + // Add in style property hooks for overriding the default + // behavior of getting and setting a style property + cssHooks: { + opacity: { + get: function( elem, computed ) { + if ( computed ) { + + // We should always get a number back from opacity + var ret = curCSS( elem, "opacity" ); + return ret === "" ? "1" : ret; + } + } + } + }, + + // Don't automatically add "px" to these possibly-unitless properties + cssNumber: { + "animationIterationCount": true, + "columnCount": true, + "fillOpacity": true, + "flexGrow": true, + "flexShrink": true, + "fontWeight": true, + "gridArea": true, + "gridColumn": true, + "gridColumnEnd": true, + "gridColumnStart": true, + "gridRow": true, + "gridRowEnd": true, + "gridRowStart": true, + "lineHeight": true, + "opacity": true, + "order": true, + "orphans": true, + "widows": true, + "zIndex": true, + "zoom": true + }, + + // Add in properties whose names you wish to fix before + // setting or getting the value + cssProps: {}, + + // Get and set the style property on a DOM Node + style: function( elem, name, value, extra ) { + + // Don't set styles on text and comment nodes + if ( !elem || elem.nodeType === 3 || elem.nodeType === 8 || !elem.style ) { + return; + } + + // Make sure that we're working with the right name + var ret, type, hooks, + origName = camelCase( name ), + isCustomProp = rcustomProp.test( name ), + style = elem.style; + + // Make sure that we're working with the right name. We don't + // want to query the value if it is a CSS custom property + // since they are user-defined. + if ( !isCustomProp ) { + name = finalPropName( origName ); + } + + // Gets hook for the prefixed version, then unprefixed version + hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ]; + + // Check if we're setting a value + if ( value !== undefined ) { + type = typeof value; + + // Convert "+=" or "-=" to relative numbers (#7345) + if ( type === "string" && ( ret = rcssNum.exec( value ) ) && ret[ 1 ] ) { + value = adjustCSS( elem, name, ret ); + + // Fixes bug #9237 + type = "number"; + } + + // Make sure that null and NaN values aren't set (#7116) + if ( value == null || value !== value ) { + return; + } + + // If a number was passed in, add the unit (except for certain CSS properties) + // The isCustomProp check can be removed in jQuery 4.0 when we only auto-append + // "px" to a few hardcoded values. + if ( type === "number" && !isCustomProp ) { + value += ret && ret[ 3 ] || ( jQuery.cssNumber[ origName ] ? "" : "px" ); + } + + // background-* props affect original clone's values + if ( !support.clearCloneStyle && value === "" && name.indexOf( "background" ) === 0 ) { + style[ name ] = "inherit"; + } + + // If a hook was provided, use that value, otherwise just set the specified value + if ( !hooks || !( "set" in hooks ) || + ( value = hooks.set( elem, value, extra ) ) !== undefined ) { + + if ( isCustomProp ) { + style.setProperty( name, value ); + } else { + style[ name ] = value; + } + } + + } else { + + // If a hook was provided get the non-computed value from there + if ( hooks && "get" in hooks && + ( ret = hooks.get( elem, false, extra ) ) !== undefined ) { + + return ret; + } + + // Otherwise just get the value from the style object + return style[ name ]; + } + }, + + css: function( elem, name, extra, styles ) { + var val, num, hooks, + origName = camelCase( name ), + isCustomProp = rcustomProp.test( name ); + + // Make sure that we're working with the right name. We don't + // want to modify the value if it is a CSS custom property + // since they are user-defined. + if ( !isCustomProp ) { + name = finalPropName( origName ); + } + + // Try prefixed name followed by the unprefixed name + hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ]; + + // If a hook was provided get the computed value from there + if ( hooks && "get" in hooks ) { + val = hooks.get( elem, true, extra ); + } + + // Otherwise, if a way to get the computed value exists, use that + if ( val === undefined ) { + val = curCSS( elem, name, styles ); + } + + // Convert "normal" to computed value + if ( val === "normal" && name in cssNormalTransform ) { + val = cssNormalTransform[ name ]; + } + + // Make numeric if forced or a qualifier was provided and val looks numeric + if ( extra === "" || extra ) { + num = parseFloat( val ); + return extra === true || isFinite( num ) ? num || 0 : val; + } + + return val; + } +} ); + +jQuery.each( [ "height", "width" ], function( _i, dimension ) { + jQuery.cssHooks[ dimension ] = { + get: function( elem, computed, extra ) { + if ( computed ) { + + // Certain elements can have dimension info if we invisibly show them + // but it must have a current display style that would benefit + return rdisplayswap.test( jQuery.css( elem, "display" ) ) && + + // Support: Safari 8+ + // Table columns in Safari have non-zero offsetWidth & zero + // getBoundingClientRect().width unless display is changed. + // Support: IE <=11 only + // Running getBoundingClientRect on a disconnected node + // in IE throws an error. + ( !elem.getClientRects().length || !elem.getBoundingClientRect().width ) ? + swap( elem, cssShow, function() { + return getWidthOrHeight( elem, dimension, extra ); + } ) : + getWidthOrHeight( elem, dimension, extra ); + } + }, + + set: function( elem, value, extra ) { + var matches, + styles = getStyles( elem ), + + // Only read styles.position if the test has a chance to fail + // to avoid forcing a reflow. + scrollboxSizeBuggy = !support.scrollboxSize() && + styles.position === "absolute", + + // To avoid forcing a reflow, only fetch boxSizing if we need it (gh-3991) + boxSizingNeeded = scrollboxSizeBuggy || extra, + isBorderBox = boxSizingNeeded && + jQuery.css( elem, "boxSizing", false, styles ) === "border-box", + subtract = extra ? + boxModelAdjustment( + elem, + dimension, + extra, + isBorderBox, + styles + ) : + 0; + + // Account for unreliable border-box dimensions by comparing offset* to computed and + // faking a content-box to get border and padding (gh-3699) + if ( isBorderBox && scrollboxSizeBuggy ) { + subtract -= Math.ceil( + elem[ "offset" + dimension[ 0 ].toUpperCase() + dimension.slice( 1 ) ] - + parseFloat( styles[ dimension ] ) - + boxModelAdjustment( elem, dimension, "border", false, styles ) - + 0.5 + ); + } + + // Convert to pixels if value adjustment is needed + if ( subtract && ( matches = rcssNum.exec( value ) ) && + ( matches[ 3 ] || "px" ) !== "px" ) { + + elem.style[ dimension ] = value; + value = jQuery.css( elem, dimension ); + } + + return setPositiveNumber( elem, value, subtract ); + } + }; +} ); + +jQuery.cssHooks.marginLeft = addGetHookIf( support.reliableMarginLeft, + function( elem, computed ) { + if ( computed ) { + return ( parseFloat( curCSS( elem, "marginLeft" ) ) || + elem.getBoundingClientRect().left - + swap( elem, { marginLeft: 0 }, function() { + return elem.getBoundingClientRect().left; + } ) + ) + "px"; + } + } +); + +// These hooks are used by animate to expand properties +jQuery.each( { + margin: "", + padding: "", + border: "Width" +}, function( prefix, suffix ) { + jQuery.cssHooks[ prefix + suffix ] = { + expand: function( value ) { + var i = 0, + expanded = {}, + + // Assumes a single number if not a string + parts = typeof value === "string" ? value.split( " " ) : [ value ]; + + for ( ; i < 4; i++ ) { + expanded[ prefix + cssExpand[ i ] + suffix ] = + parts[ i ] || parts[ i - 2 ] || parts[ 0 ]; + } + + return expanded; + } + }; + + if ( prefix !== "margin" ) { + jQuery.cssHooks[ prefix + suffix ].set = setPositiveNumber; + } +} ); + +jQuery.fn.extend( { + css: function( name, value ) { + return access( this, function( elem, name, value ) { + var styles, len, + map = {}, + i = 0; + + if ( Array.isArray( name ) ) { + styles = getStyles( elem ); + len = name.length; + + for ( ; i < len; i++ ) { + map[ name[ i ] ] = jQuery.css( elem, name[ i ], false, styles ); + } + + return map; + } + + return value !== undefined ? + jQuery.style( elem, name, value ) : + jQuery.css( elem, name ); + }, name, value, arguments.length > 1 ); + } +} ); + + +function Tween( elem, options, prop, end, easing ) { + return new Tween.prototype.init( elem, options, prop, end, easing ); +} +jQuery.Tween = Tween; + +Tween.prototype = { + constructor: Tween, + init: function( elem, options, prop, end, easing, unit ) { + this.elem = elem; + this.prop = prop; + this.easing = easing || jQuery.easing._default; + this.options = options; + this.start = this.now = this.cur(); + this.end = end; + this.unit = unit || ( jQuery.cssNumber[ prop ] ? "" : "px" ); + }, + cur: function() { + var hooks = Tween.propHooks[ this.prop ]; + + return hooks && hooks.get ? + hooks.get( this ) : + Tween.propHooks._default.get( this ); + }, + run: function( percent ) { + var eased, + hooks = Tween.propHooks[ this.prop ]; + + if ( this.options.duration ) { + this.pos = eased = jQuery.easing[ this.easing ]( + percent, this.options.duration * percent, 0, 1, this.options.duration + ); + } else { + this.pos = eased = percent; + } + this.now = ( this.end - this.start ) * eased + this.start; + + if ( this.options.step ) { + this.options.step.call( this.elem, this.now, this ); + } + + if ( hooks && hooks.set ) { + hooks.set( this ); + } else { + Tween.propHooks._default.set( this ); + } + return this; + } +}; + +Tween.prototype.init.prototype = Tween.prototype; + +Tween.propHooks = { + _default: { + get: function( tween ) { + var result; + + // Use a property on the element directly when it is not a DOM element, + // or when there is no matching style property that exists. + if ( tween.elem.nodeType !== 1 || + tween.elem[ tween.prop ] != null && tween.elem.style[ tween.prop ] == null ) { + return tween.elem[ tween.prop ]; + } + + // Passing an empty string as a 3rd parameter to .css will automatically + // attempt a parseFloat and fallback to a string if the parse fails. + // Simple values such as "10px" are parsed to Float; + // complex values such as "rotate(1rad)" are returned as-is. + result = jQuery.css( tween.elem, tween.prop, "" ); + + // Empty strings, null, undefined and "auto" are converted to 0. + return !result || result === "auto" ? 0 : result; + }, + set: function( tween ) { + + // Use step hook for back compat. + // Use cssHook if its there. + // Use .style if available and use plain properties where available. + if ( jQuery.fx.step[ tween.prop ] ) { + jQuery.fx.step[ tween.prop ]( tween ); + } else if ( tween.elem.nodeType === 1 && ( + jQuery.cssHooks[ tween.prop ] || + tween.elem.style[ finalPropName( tween.prop ) ] != null ) ) { + jQuery.style( tween.elem, tween.prop, tween.now + tween.unit ); + } else { + tween.elem[ tween.prop ] = tween.now; + } + } + } +}; + +// Support: IE <=9 only +// Panic based approach to setting things on disconnected nodes +Tween.propHooks.scrollTop = Tween.propHooks.scrollLeft = { + set: function( tween ) { + if ( tween.elem.nodeType && tween.elem.parentNode ) { + tween.elem[ tween.prop ] = tween.now; + } + } +}; + +jQuery.easing = { + linear: function( p ) { + return p; + }, + swing: function( p ) { + return 0.5 - Math.cos( p * Math.PI ) / 2; + }, + _default: "swing" +}; + +jQuery.fx = Tween.prototype.init; + +// Back compat <1.8 extension point +jQuery.fx.step = {}; + + + + +var + fxNow, inProgress, + rfxtypes = /^(?:toggle|show|hide)$/, + rrun = /queueHooks$/; + +function schedule() { + if ( inProgress ) { + if ( document.hidden === false && window.requestAnimationFrame ) { + window.requestAnimationFrame( schedule ); + } else { + window.setTimeout( schedule, jQuery.fx.interval ); + } + + jQuery.fx.tick(); + } +} + +// Animations created synchronously will run synchronously +function createFxNow() { + window.setTimeout( function() { + fxNow = undefined; + } ); + return ( fxNow = Date.now() ); +} + +// Generate parameters to create a standard animation +function genFx( type, includeWidth ) { + var which, + i = 0, + attrs = { height: type }; + + // If we include width, step value is 1 to do all cssExpand values, + // otherwise step value is 2 to skip over Left and Right + includeWidth = includeWidth ? 1 : 0; + for ( ; i < 4; i += 2 - includeWidth ) { + which = cssExpand[ i ]; + attrs[ "margin" + which ] = attrs[ "padding" + which ] = type; + } + + if ( includeWidth ) { + attrs.opacity = attrs.width = type; + } + + return attrs; +} + +function createTween( value, prop, animation ) { + var tween, + collection = ( Animation.tweeners[ prop ] || [] ).concat( Animation.tweeners[ "*" ] ), + index = 0, + length = collection.length; + for ( ; index < length; index++ ) { + if ( ( tween = collection[ index ].call( animation, prop, value ) ) ) { + + // We're done with this property + return tween; + } + } +} + +function defaultPrefilter( elem, props, opts ) { + var prop, value, toggle, hooks, oldfire, propTween, restoreDisplay, display, + isBox = "width" in props || "height" in props, + anim = this, + orig = {}, + style = elem.style, + hidden = elem.nodeType && isHiddenWithinTree( elem ), + dataShow = dataPriv.get( elem, "fxshow" ); + + // Queue-skipping animations hijack the fx hooks + if ( !opts.queue ) { + hooks = jQuery._queueHooks( elem, "fx" ); + if ( hooks.unqueued == null ) { + hooks.unqueued = 0; + oldfire = hooks.empty.fire; + hooks.empty.fire = function() { + if ( !hooks.unqueued ) { + oldfire(); + } + }; + } + hooks.unqueued++; + + anim.always( function() { + + // Ensure the complete handler is called before this completes + anim.always( function() { + hooks.unqueued--; + if ( !jQuery.queue( elem, "fx" ).length ) { + hooks.empty.fire(); + } + } ); + } ); + } + + // Detect show/hide animations + for ( prop in props ) { + value = props[ prop ]; + if ( rfxtypes.test( value ) ) { + delete props[ prop ]; + toggle = toggle || value === "toggle"; + if ( value === ( hidden ? "hide" : "show" ) ) { + + // Pretend to be hidden if this is a "show" and + // there is still data from a stopped show/hide + if ( value === "show" && dataShow && dataShow[ prop ] !== undefined ) { + hidden = true; + + // Ignore all other no-op show/hide data + } else { + continue; + } + } + orig[ prop ] = dataShow && dataShow[ prop ] || jQuery.style( elem, prop ); + } + } + + // Bail out if this is a no-op like .hide().hide() + propTween = !jQuery.isEmptyObject( props ); + if ( !propTween && jQuery.isEmptyObject( orig ) ) { + return; + } + + // Restrict "overflow" and "display" styles during box animations + if ( isBox && elem.nodeType === 1 ) { + + // Support: IE <=9 - 11, Edge 12 - 15 + // Record all 3 overflow attributes because IE does not infer the shorthand + // from identically-valued overflowX and overflowY and Edge just mirrors + // the overflowX value there. + opts.overflow = [ style.overflow, style.overflowX, style.overflowY ]; + + // Identify a display type, preferring old show/hide data over the CSS cascade + restoreDisplay = dataShow && dataShow.display; + if ( restoreDisplay == null ) { + restoreDisplay = dataPriv.get( elem, "display" ); + } + display = jQuery.css( elem, "display" ); + if ( display === "none" ) { + if ( restoreDisplay ) { + display = restoreDisplay; + } else { + + // Get nonempty value(s) by temporarily forcing visibility + showHide( [ elem ], true ); + restoreDisplay = elem.style.display || restoreDisplay; + display = jQuery.css( elem, "display" ); + showHide( [ elem ] ); + } + } + + // Animate inline elements as inline-block + if ( display === "inline" || display === "inline-block" && restoreDisplay != null ) { + if ( jQuery.css( elem, "float" ) === "none" ) { + + // Restore the original display value at the end of pure show/hide animations + if ( !propTween ) { + anim.done( function() { + style.display = restoreDisplay; + } ); + if ( restoreDisplay == null ) { + display = style.display; + restoreDisplay = display === "none" ? "" : display; + } + } + style.display = "inline-block"; + } + } + } + + if ( opts.overflow ) { + style.overflow = "hidden"; + anim.always( function() { + style.overflow = opts.overflow[ 0 ]; + style.overflowX = opts.overflow[ 1 ]; + style.overflowY = opts.overflow[ 2 ]; + } ); + } + + // Implement show/hide animations + propTween = false; + for ( prop in orig ) { + + // General show/hide setup for this element animation + if ( !propTween ) { + if ( dataShow ) { + if ( "hidden" in dataShow ) { + hidden = dataShow.hidden; + } + } else { + dataShow = dataPriv.access( elem, "fxshow", { display: restoreDisplay } ); + } + + // Store hidden/visible for toggle so `.stop().toggle()` "reverses" + if ( toggle ) { + dataShow.hidden = !hidden; + } + + // Show elements before animating them + if ( hidden ) { + showHide( [ elem ], true ); + } + + /* eslint-disable no-loop-func */ + + anim.done( function() { + + /* eslint-enable no-loop-func */ + + // The final step of a "hide" animation is actually hiding the element + if ( !hidden ) { + showHide( [ elem ] ); + } + dataPriv.remove( elem, "fxshow" ); + for ( prop in orig ) { + jQuery.style( elem, prop, orig[ prop ] ); + } + } ); + } + + // Per-property setup + propTween = createTween( hidden ? dataShow[ prop ] : 0, prop, anim ); + if ( !( prop in dataShow ) ) { + dataShow[ prop ] = propTween.start; + if ( hidden ) { + propTween.end = propTween.start; + propTween.start = 0; + } + } + } +} + +function propFilter( props, specialEasing ) { + var index, name, easing, value, hooks; + + // camelCase, specialEasing and expand cssHook pass + for ( index in props ) { + name = camelCase( index ); + easing = specialEasing[ name ]; + value = props[ index ]; + if ( Array.isArray( value ) ) { + easing = value[ 1 ]; + value = props[ index ] = value[ 0 ]; + } + + if ( index !== name ) { + props[ name ] = value; + delete props[ index ]; + } + + hooks = jQuery.cssHooks[ name ]; + if ( hooks && "expand" in hooks ) { + value = hooks.expand( value ); + delete props[ name ]; + + // Not quite $.extend, this won't overwrite existing keys. + // Reusing 'index' because we have the correct "name" + for ( index in value ) { + if ( !( index in props ) ) { + props[ index ] = value[ index ]; + specialEasing[ index ] = easing; + } + } + } else { + specialEasing[ name ] = easing; + } + } +} + +function Animation( elem, properties, options ) { + var result, + stopped, + index = 0, + length = Animation.prefilters.length, + deferred = jQuery.Deferred().always( function() { + + // Don't match elem in the :animated selector + delete tick.elem; + } ), + tick = function() { + if ( stopped ) { + return false; + } + var currentTime = fxNow || createFxNow(), + remaining = Math.max( 0, animation.startTime + animation.duration - currentTime ), + + // Support: Android 2.3 only + // Archaic crash bug won't allow us to use `1 - ( 0.5 || 0 )` (#12497) + temp = remaining / animation.duration || 0, + percent = 1 - temp, + index = 0, + length = animation.tweens.length; + + for ( ; index < length; index++ ) { + animation.tweens[ index ].run( percent ); + } + + deferred.notifyWith( elem, [ animation, percent, remaining ] ); + + // If there's more to do, yield + if ( percent < 1 && length ) { + return remaining; + } + + // If this was an empty animation, synthesize a final progress notification + if ( !length ) { + deferred.notifyWith( elem, [ animation, 1, 0 ] ); + } + + // Resolve the animation and report its conclusion + deferred.resolveWith( elem, [ animation ] ); + return false; + }, + animation = deferred.promise( { + elem: elem, + props: jQuery.extend( {}, properties ), + opts: jQuery.extend( true, { + specialEasing: {}, + easing: jQuery.easing._default + }, options ), + originalProperties: properties, + originalOptions: options, + startTime: fxNow || createFxNow(), + duration: options.duration, + tweens: [], + createTween: function( prop, end ) { + var tween = jQuery.Tween( elem, animation.opts, prop, end, + animation.opts.specialEasing[ prop ] || animation.opts.easing ); + animation.tweens.push( tween ); + return tween; + }, + stop: function( gotoEnd ) { + var index = 0, + + // If we are going to the end, we want to run all the tweens + // otherwise we skip this part + length = gotoEnd ? animation.tweens.length : 0; + if ( stopped ) { + return this; + } + stopped = true; + for ( ; index < length; index++ ) { + animation.tweens[ index ].run( 1 ); + } + + // Resolve when we played the last frame; otherwise, reject + if ( gotoEnd ) { + deferred.notifyWith( elem, [ animation, 1, 0 ] ); + deferred.resolveWith( elem, [ animation, gotoEnd ] ); + } else { + deferred.rejectWith( elem, [ animation, gotoEnd ] ); + } + return this; + } + } ), + props = animation.props; + + propFilter( props, animation.opts.specialEasing ); + + for ( ; index < length; index++ ) { + result = Animation.prefilters[ index ].call( animation, elem, props, animation.opts ); + if ( result ) { + if ( isFunction( result.stop ) ) { + jQuery._queueHooks( animation.elem, animation.opts.queue ).stop = + result.stop.bind( result ); + } + return result; + } + } + + jQuery.map( props, createTween, animation ); + + if ( isFunction( animation.opts.start ) ) { + animation.opts.start.call( elem, animation ); + } + + // Attach callbacks from options + animation + .progress( animation.opts.progress ) + .done( animation.opts.done, animation.opts.complete ) + .fail( animation.opts.fail ) + .always( animation.opts.always ); + + jQuery.fx.timer( + jQuery.extend( tick, { + elem: elem, + anim: animation, + queue: animation.opts.queue + } ) + ); + + return animation; +} + +jQuery.Animation = jQuery.extend( Animation, { + + tweeners: { + "*": [ function( prop, value ) { + var tween = this.createTween( prop, value ); + adjustCSS( tween.elem, prop, rcssNum.exec( value ), tween ); + return tween; + } ] + }, + + tweener: function( props, callback ) { + if ( isFunction( props ) ) { + callback = props; + props = [ "*" ]; + } else { + props = props.match( rnothtmlwhite ); + } + + var prop, + index = 0, + length = props.length; + + for ( ; index < length; index++ ) { + prop = props[ index ]; + Animation.tweeners[ prop ] = Animation.tweeners[ prop ] || []; + Animation.tweeners[ prop ].unshift( callback ); + } + }, + + prefilters: [ defaultPrefilter ], + + prefilter: function( callback, prepend ) { + if ( prepend ) { + Animation.prefilters.unshift( callback ); + } else { + Animation.prefilters.push( callback ); + } + } +} ); + +jQuery.speed = function( speed, easing, fn ) { + var opt = speed && typeof speed === "object" ? jQuery.extend( {}, speed ) : { + complete: fn || !fn && easing || + isFunction( speed ) && speed, + duration: speed, + easing: fn && easing || easing && !isFunction( easing ) && easing + }; + + // Go to the end state if fx are off + if ( jQuery.fx.off ) { + opt.duration = 0; + + } else { + if ( typeof opt.duration !== "number" ) { + if ( opt.duration in jQuery.fx.speeds ) { + opt.duration = jQuery.fx.speeds[ opt.duration ]; + + } else { + opt.duration = jQuery.fx.speeds._default; + } + } + } + + // Normalize opt.queue - true/undefined/null -> "fx" + if ( opt.queue == null || opt.queue === true ) { + opt.queue = "fx"; + } + + // Queueing + opt.old = opt.complete; + + opt.complete = function() { + if ( isFunction( opt.old ) ) { + opt.old.call( this ); + } + + if ( opt.queue ) { + jQuery.dequeue( this, opt.queue ); + } + }; + + return opt; +}; + +jQuery.fn.extend( { + fadeTo: function( speed, to, easing, callback ) { + + // Show any hidden elements after setting opacity to 0 + return this.filter( isHiddenWithinTree ).css( "opacity", 0 ).show() + + // Animate to the value specified + .end().animate( { opacity: to }, speed, easing, callback ); + }, + animate: function( prop, speed, easing, callback ) { + var empty = jQuery.isEmptyObject( prop ), + optall = jQuery.speed( speed, easing, callback ), + doAnimation = function() { + + // Operate on a copy of prop so per-property easing won't be lost + var anim = Animation( this, jQuery.extend( {}, prop ), optall ); + + // Empty animations, or finishing resolves immediately + if ( empty || dataPriv.get( this, "finish" ) ) { + anim.stop( true ); + } + }; + + doAnimation.finish = doAnimation; + + return empty || optall.queue === false ? + this.each( doAnimation ) : + this.queue( optall.queue, doAnimation ); + }, + stop: function( type, clearQueue, gotoEnd ) { + var stopQueue = function( hooks ) { + var stop = hooks.stop; + delete hooks.stop; + stop( gotoEnd ); + }; + + if ( typeof type !== "string" ) { + gotoEnd = clearQueue; + clearQueue = type; + type = undefined; + } + if ( clearQueue ) { + this.queue( type || "fx", [] ); + } + + return this.each( function() { + var dequeue = true, + index = type != null && type + "queueHooks", + timers = jQuery.timers, + data = dataPriv.get( this ); + + if ( index ) { + if ( data[ index ] && data[ index ].stop ) { + stopQueue( data[ index ] ); + } + } else { + for ( index in data ) { + if ( data[ index ] && data[ index ].stop && rrun.test( index ) ) { + stopQueue( data[ index ] ); + } + } + } + + for ( index = timers.length; index--; ) { + if ( timers[ index ].elem === this && + ( type == null || timers[ index ].queue === type ) ) { + + timers[ index ].anim.stop( gotoEnd ); + dequeue = false; + timers.splice( index, 1 ); + } + } + + // Start the next in the queue if the last step wasn't forced. + // Timers currently will call their complete callbacks, which + // will dequeue but only if they were gotoEnd. + if ( dequeue || !gotoEnd ) { + jQuery.dequeue( this, type ); + } + } ); + }, + finish: function( type ) { + if ( type !== false ) { + type = type || "fx"; + } + return this.each( function() { + var index, + data = dataPriv.get( this ), + queue = data[ type + "queue" ], + hooks = data[ type + "queueHooks" ], + timers = jQuery.timers, + length = queue ? queue.length : 0; + + // Enable finishing flag on private data + data.finish = true; + + // Empty the queue first + jQuery.queue( this, type, [] ); + + if ( hooks && hooks.stop ) { + hooks.stop.call( this, true ); + } + + // Look for any active animations, and finish them + for ( index = timers.length; index--; ) { + if ( timers[ index ].elem === this && timers[ index ].queue === type ) { + timers[ index ].anim.stop( true ); + timers.splice( index, 1 ); + } + } + + // Look for any animations in the old queue and finish them + for ( index = 0; index < length; index++ ) { + if ( queue[ index ] && queue[ index ].finish ) { + queue[ index ].finish.call( this ); + } + } + + // Turn off finishing flag + delete data.finish; + } ); + } +} ); + +jQuery.each( [ "toggle", "show", "hide" ], function( _i, name ) { + var cssFn = jQuery.fn[ name ]; + jQuery.fn[ name ] = function( speed, easing, callback ) { + return speed == null || typeof speed === "boolean" ? + cssFn.apply( this, arguments ) : + this.animate( genFx( name, true ), speed, easing, callback ); + }; +} ); + +// Generate shortcuts for custom animations +jQuery.each( { + slideDown: genFx( "show" ), + slideUp: genFx( "hide" ), + slideToggle: genFx( "toggle" ), + fadeIn: { opacity: "show" }, + fadeOut: { opacity: "hide" }, + fadeToggle: { opacity: "toggle" } +}, function( name, props ) { + jQuery.fn[ name ] = function( speed, easing, callback ) { + return this.animate( props, speed, easing, callback ); + }; +} ); + +jQuery.timers = []; +jQuery.fx.tick = function() { + var timer, + i = 0, + timers = jQuery.timers; + + fxNow = Date.now(); + + for ( ; i < timers.length; i++ ) { + timer = timers[ i ]; + + // Run the timer and safely remove it when done (allowing for external removal) + if ( !timer() && timers[ i ] === timer ) { + timers.splice( i--, 1 ); + } + } + + if ( !timers.length ) { + jQuery.fx.stop(); + } + fxNow = undefined; +}; + +jQuery.fx.timer = function( timer ) { + jQuery.timers.push( timer ); + jQuery.fx.start(); +}; + +jQuery.fx.interval = 13; +jQuery.fx.start = function() { + if ( inProgress ) { + return; + } + + inProgress = true; + schedule(); +}; + +jQuery.fx.stop = function() { + inProgress = null; +}; + +jQuery.fx.speeds = { + slow: 600, + fast: 200, + + // Default speed + _default: 400 +}; + + +// Based off of the plugin by Clint Helfers, with permission. +// https://web.archive.org/web/20100324014747/http://blindsignals.com/index.php/2009/07/jquery-delay/ +jQuery.fn.delay = function( time, type ) { + time = jQuery.fx ? jQuery.fx.speeds[ time ] || time : time; + type = type || "fx"; + + return this.queue( type, function( next, hooks ) { + var timeout = window.setTimeout( next, time ); + hooks.stop = function() { + window.clearTimeout( timeout ); + }; + } ); +}; + + +( function() { + var input = document.createElement( "input" ), + select = document.createElement( "select" ), + opt = select.appendChild( document.createElement( "option" ) ); + + input.type = "checkbox"; + + // Support: Android <=4.3 only + // Default value for a checkbox should be "on" + support.checkOn = input.value !== ""; + + // Support: IE <=11 only + // Must access selectedIndex to make default options select + support.optSelected = opt.selected; + + // Support: IE <=11 only + // An input loses its value after becoming a radio + input = document.createElement( "input" ); + input.value = "t"; + input.type = "radio"; + support.radioValue = input.value === "t"; +} )(); + + +var boolHook, + attrHandle = jQuery.expr.attrHandle; + +jQuery.fn.extend( { + attr: function( name, value ) { + return access( this, jQuery.attr, name, value, arguments.length > 1 ); + }, + + removeAttr: function( name ) { + return this.each( function() { + jQuery.removeAttr( this, name ); + } ); + } +} ); + +jQuery.extend( { + attr: function( elem, name, value ) { + var ret, hooks, + nType = elem.nodeType; + + // Don't get/set attributes on text, comment and attribute nodes + if ( nType === 3 || nType === 8 || nType === 2 ) { + return; + } + + // Fallback to prop when attributes are not supported + if ( typeof elem.getAttribute === "undefined" ) { + return jQuery.prop( elem, name, value ); + } + + // Attribute hooks are determined by the lowercase version + // Grab necessary hook if one is defined + if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) { + hooks = jQuery.attrHooks[ name.toLowerCase() ] || + ( jQuery.expr.match.bool.test( name ) ? boolHook : undefined ); + } + + if ( value !== undefined ) { + if ( value === null ) { + jQuery.removeAttr( elem, name ); + return; + } + + if ( hooks && "set" in hooks && + ( ret = hooks.set( elem, value, name ) ) !== undefined ) { + return ret; + } + + elem.setAttribute( name, value + "" ); + return value; + } + + if ( hooks && "get" in hooks && ( ret = hooks.get( elem, name ) ) !== null ) { + return ret; + } + + ret = jQuery.find.attr( elem, name ); + + // Non-existent attributes return null, we normalize to undefined + return ret == null ? undefined : ret; + }, + + attrHooks: { + type: { + set: function( elem, value ) { + if ( !support.radioValue && value === "radio" && + nodeName( elem, "input" ) ) { + var val = elem.value; + elem.setAttribute( "type", value ); + if ( val ) { + elem.value = val; + } + return value; + } + } + } + }, + + removeAttr: function( elem, value ) { + var name, + i = 0, + + // Attribute names can contain non-HTML whitespace characters + // https://html.spec.whatwg.org/multipage/syntax.html#attributes-2 + attrNames = value && value.match( rnothtmlwhite ); + + if ( attrNames && elem.nodeType === 1 ) { + while ( ( name = attrNames[ i++ ] ) ) { + elem.removeAttribute( name ); + } + } + } +} ); + +// Hooks for boolean attributes +boolHook = { + set: function( elem, value, name ) { + if ( value === false ) { + + // Remove boolean attributes when set to false + jQuery.removeAttr( elem, name ); + } else { + elem.setAttribute( name, name ); + } + return name; + } +}; + +jQuery.each( jQuery.expr.match.bool.source.match( /\w+/g ), function( _i, name ) { + var getter = attrHandle[ name ] || jQuery.find.attr; + + attrHandle[ name ] = function( elem, name, isXML ) { + var ret, handle, + lowercaseName = name.toLowerCase(); + + if ( !isXML ) { + + // Avoid an infinite loop by temporarily removing this function from the getter + handle = attrHandle[ lowercaseName ]; + attrHandle[ lowercaseName ] = ret; + ret = getter( elem, name, isXML ) != null ? + lowercaseName : + null; + attrHandle[ lowercaseName ] = handle; + } + return ret; + }; +} ); + + + + +var rfocusable = /^(?:input|select|textarea|button)$/i, + rclickable = /^(?:a|area)$/i; + +jQuery.fn.extend( { + prop: function( name, value ) { + return access( this, jQuery.prop, name, value, arguments.length > 1 ); + }, + + removeProp: function( name ) { + return this.each( function() { + delete this[ jQuery.propFix[ name ] || name ]; + } ); + } +} ); + +jQuery.extend( { + prop: function( elem, name, value ) { + var ret, hooks, + nType = elem.nodeType; + + // Don't get/set properties on text, comment and attribute nodes + if ( nType === 3 || nType === 8 || nType === 2 ) { + return; + } + + if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) { + + // Fix name and attach hooks + name = jQuery.propFix[ name ] || name; + hooks = jQuery.propHooks[ name ]; + } + + if ( value !== undefined ) { + if ( hooks && "set" in hooks && + ( ret = hooks.set( elem, value, name ) ) !== undefined ) { + return ret; + } + + return ( elem[ name ] = value ); + } + + if ( hooks && "get" in hooks && ( ret = hooks.get( elem, name ) ) !== null ) { + return ret; + } + + return elem[ name ]; + }, + + propHooks: { + tabIndex: { + get: function( elem ) { + + // Support: IE <=9 - 11 only + // elem.tabIndex doesn't always return the + // correct value when it hasn't been explicitly set + // https://web.archive.org/web/20141116233347/http://fluidproject.org/blog/2008/01/09/getting-setting-and-removing-tabindex-values-with-javascript/ + // Use proper attribute retrieval(#12072) + var tabindex = jQuery.find.attr( elem, "tabindex" ); + + if ( tabindex ) { + return parseInt( tabindex, 10 ); + } + + if ( + rfocusable.test( elem.nodeName ) || + rclickable.test( elem.nodeName ) && + elem.href + ) { + return 0; + } + + return -1; + } + } + }, + + propFix: { + "for": "htmlFor", + "class": "className" + } +} ); + +// Support: IE <=11 only +// Accessing the selectedIndex property +// forces the browser to respect setting selected +// on the option +// The getter ensures a default option is selected +// when in an optgroup +// eslint rule "no-unused-expressions" is disabled for this code +// since it considers such accessions noop +if ( !support.optSelected ) { + jQuery.propHooks.selected = { + get: function( elem ) { + + /* eslint no-unused-expressions: "off" */ + + var parent = elem.parentNode; + if ( parent && parent.parentNode ) { + parent.parentNode.selectedIndex; + } + return null; + }, + set: function( elem ) { + + /* eslint no-unused-expressions: "off" */ + + var parent = elem.parentNode; + if ( parent ) { + parent.selectedIndex; + + if ( parent.parentNode ) { + parent.parentNode.selectedIndex; + } + } + } + }; +} + +jQuery.each( [ + "tabIndex", + "readOnly", + "maxLength", + "cellSpacing", + "cellPadding", + "rowSpan", + "colSpan", + "useMap", + "frameBorder", + "contentEditable" +], function() { + jQuery.propFix[ this.toLowerCase() ] = this; +} ); + + + + + // Strip and collapse whitespace according to HTML spec + // https://infra.spec.whatwg.org/#strip-and-collapse-ascii-whitespace + function stripAndCollapse( value ) { + var tokens = value.match( rnothtmlwhite ) || []; + return tokens.join( " " ); + } + + +function getClass( elem ) { + return elem.getAttribute && elem.getAttribute( "class" ) || ""; +} + +function classesToArray( value ) { + if ( Array.isArray( value ) ) { + return value; + } + if ( typeof value === "string" ) { + return value.match( rnothtmlwhite ) || []; + } + return []; +} + +jQuery.fn.extend( { + addClass: function( value ) { + var classes, elem, cur, curValue, clazz, j, finalValue, + i = 0; + + if ( isFunction( value ) ) { + return this.each( function( j ) { + jQuery( this ).addClass( value.call( this, j, getClass( this ) ) ); + } ); + } + + classes = classesToArray( value ); + + if ( classes.length ) { + while ( ( elem = this[ i++ ] ) ) { + curValue = getClass( elem ); + cur = elem.nodeType === 1 && ( " " + stripAndCollapse( curValue ) + " " ); + + if ( cur ) { + j = 0; + while ( ( clazz = classes[ j++ ] ) ) { + if ( cur.indexOf( " " + clazz + " " ) < 0 ) { + cur += clazz + " "; + } + } + + // Only assign if different to avoid unneeded rendering. + finalValue = stripAndCollapse( cur ); + if ( curValue !== finalValue ) { + elem.setAttribute( "class", finalValue ); + } + } + } + } + + return this; + }, + + removeClass: function( value ) { + var classes, elem, cur, curValue, clazz, j, finalValue, + i = 0; + + if ( isFunction( value ) ) { + return this.each( function( j ) { + jQuery( this ).removeClass( value.call( this, j, getClass( this ) ) ); + } ); + } + + if ( !arguments.length ) { + return this.attr( "class", "" ); + } + + classes = classesToArray( value ); + + if ( classes.length ) { + while ( ( elem = this[ i++ ] ) ) { + curValue = getClass( elem ); + + // This expression is here for better compressibility (see addClass) + cur = elem.nodeType === 1 && ( " " + stripAndCollapse( curValue ) + " " ); + + if ( cur ) { + j = 0; + while ( ( clazz = classes[ j++ ] ) ) { + + // Remove *all* instances + while ( cur.indexOf( " " + clazz + " " ) > -1 ) { + cur = cur.replace( " " + clazz + " ", " " ); + } + } + + // Only assign if different to avoid unneeded rendering. + finalValue = stripAndCollapse( cur ); + if ( curValue !== finalValue ) { + elem.setAttribute( "class", finalValue ); + } + } + } + } + + return this; + }, + + toggleClass: function( value, stateVal ) { + var type = typeof value, + isValidValue = type === "string" || Array.isArray( value ); + + if ( typeof stateVal === "boolean" && isValidValue ) { + return stateVal ? this.addClass( value ) : this.removeClass( value ); + } + + if ( isFunction( value ) ) { + return this.each( function( i ) { + jQuery( this ).toggleClass( + value.call( this, i, getClass( this ), stateVal ), + stateVal + ); + } ); + } + + return this.each( function() { + var className, i, self, classNames; + + if ( isValidValue ) { + + // Toggle individual class names + i = 0; + self = jQuery( this ); + classNames = classesToArray( value ); + + while ( ( className = classNames[ i++ ] ) ) { + + // Check each className given, space separated list + if ( self.hasClass( className ) ) { + self.removeClass( className ); + } else { + self.addClass( className ); + } + } + + // Toggle whole class name + } else if ( value === undefined || type === "boolean" ) { + className = getClass( this ); + if ( className ) { + + // Store className if set + dataPriv.set( this, "__className__", className ); + } + + // If the element has a class name or if we're passed `false`, + // then remove the whole classname (if there was one, the above saved it). + // Otherwise bring back whatever was previously saved (if anything), + // falling back to the empty string if nothing was stored. + if ( this.setAttribute ) { + this.setAttribute( "class", + className || value === false ? + "" : + dataPriv.get( this, "__className__" ) || "" + ); + } + } + } ); + }, + + hasClass: function( selector ) { + var className, elem, + i = 0; + + className = " " + selector + " "; + while ( ( elem = this[ i++ ] ) ) { + if ( elem.nodeType === 1 && + ( " " + stripAndCollapse( getClass( elem ) ) + " " ).indexOf( className ) > -1 ) { + return true; + } + } + + return false; + } +} ); + + + + +var rreturn = /\r/g; + +jQuery.fn.extend( { + val: function( value ) { + var hooks, ret, valueIsFunction, + elem = this[ 0 ]; + + if ( !arguments.length ) { + if ( elem ) { + hooks = jQuery.valHooks[ elem.type ] || + jQuery.valHooks[ elem.nodeName.toLowerCase() ]; + + if ( hooks && + "get" in hooks && + ( ret = hooks.get( elem, "value" ) ) !== undefined + ) { + return ret; + } + + ret = elem.value; + + // Handle most common string cases + if ( typeof ret === "string" ) { + return ret.replace( rreturn, "" ); + } + + // Handle cases where value is null/undef or number + return ret == null ? "" : ret; + } + + return; + } + + valueIsFunction = isFunction( value ); + + return this.each( function( i ) { + var val; + + if ( this.nodeType !== 1 ) { + return; + } + + if ( valueIsFunction ) { + val = value.call( this, i, jQuery( this ).val() ); + } else { + val = value; + } + + // Treat null/undefined as ""; convert numbers to string + if ( val == null ) { + val = ""; + + } else if ( typeof val === "number" ) { + val += ""; + + } else if ( Array.isArray( val ) ) { + val = jQuery.map( val, function( value ) { + return value == null ? "" : value + ""; + } ); + } + + hooks = jQuery.valHooks[ this.type ] || jQuery.valHooks[ this.nodeName.toLowerCase() ]; + + // If set returns undefined, fall back to normal setting + if ( !hooks || !( "set" in hooks ) || hooks.set( this, val, "value" ) === undefined ) { + this.value = val; + } + } ); + } +} ); + +jQuery.extend( { + valHooks: { + option: { + get: function( elem ) { + + var val = jQuery.find.attr( elem, "value" ); + return val != null ? + val : + + // Support: IE <=10 - 11 only + // option.text throws exceptions (#14686, #14858) + // Strip and collapse whitespace + // https://html.spec.whatwg.org/#strip-and-collapse-whitespace + stripAndCollapse( jQuery.text( elem ) ); + } + }, + select: { + get: function( elem ) { + var value, option, i, + options = elem.options, + index = elem.selectedIndex, + one = elem.type === "select-one", + values = one ? null : [], + max = one ? index + 1 : options.length; + + if ( index < 0 ) { + i = max; + + } else { + i = one ? index : 0; + } + + // Loop through all the selected options + for ( ; i < max; i++ ) { + option = options[ i ]; + + // Support: IE <=9 only + // IE8-9 doesn't update selected after form reset (#2551) + if ( ( option.selected || i === index ) && + + // Don't return options that are disabled or in a disabled optgroup + !option.disabled && + ( !option.parentNode.disabled || + !nodeName( option.parentNode, "optgroup" ) ) ) { + + // Get the specific value for the option + value = jQuery( option ).val(); + + // We don't need an array for one selects + if ( one ) { + return value; + } + + // Multi-Selects return an array + values.push( value ); + } + } + + return values; + }, + + set: function( elem, value ) { + var optionSet, option, + options = elem.options, + values = jQuery.makeArray( value ), + i = options.length; + + while ( i-- ) { + option = options[ i ]; + + /* eslint-disable no-cond-assign */ + + if ( option.selected = + jQuery.inArray( jQuery.valHooks.option.get( option ), values ) > -1 + ) { + optionSet = true; + } + + /* eslint-enable no-cond-assign */ + } + + // Force browsers to behave consistently when non-matching value is set + if ( !optionSet ) { + elem.selectedIndex = -1; + } + return values; + } + } + } +} ); + +// Radios and checkboxes getter/setter +jQuery.each( [ "radio", "checkbox" ], function() { + jQuery.valHooks[ this ] = { + set: function( elem, value ) { + if ( Array.isArray( value ) ) { + return ( elem.checked = jQuery.inArray( jQuery( elem ).val(), value ) > -1 ); + } + } + }; + if ( !support.checkOn ) { + jQuery.valHooks[ this ].get = function( elem ) { + return elem.getAttribute( "value" ) === null ? "on" : elem.value; + }; + } +} ); + + + + +// Return jQuery for attributes-only inclusion + + +support.focusin = "onfocusin" in window; + + +var rfocusMorph = /^(?:focusinfocus|focusoutblur)$/, + stopPropagationCallback = function( e ) { + e.stopPropagation(); + }; + +jQuery.extend( jQuery.event, { + + trigger: function( event, data, elem, onlyHandlers ) { + + var i, cur, tmp, bubbleType, ontype, handle, special, lastElement, + eventPath = [ elem || document ], + type = hasOwn.call( event, "type" ) ? event.type : event, + namespaces = hasOwn.call( event, "namespace" ) ? event.namespace.split( "." ) : []; + + cur = lastElement = tmp = elem = elem || document; + + // Don't do events on text and comment nodes + if ( elem.nodeType === 3 || elem.nodeType === 8 ) { + return; + } + + // focus/blur morphs to focusin/out; ensure we're not firing them right now + if ( rfocusMorph.test( type + jQuery.event.triggered ) ) { + return; + } + + if ( type.indexOf( "." ) > -1 ) { + + // Namespaced trigger; create a regexp to match event type in handle() + namespaces = type.split( "." ); + type = namespaces.shift(); + namespaces.sort(); + } + ontype = type.indexOf( ":" ) < 0 && "on" + type; + + // Caller can pass in a jQuery.Event object, Object, or just an event type string + event = event[ jQuery.expando ] ? + event : + new jQuery.Event( type, typeof event === "object" && event ); + + // Trigger bitmask: & 1 for native handlers; & 2 for jQuery (always true) + event.isTrigger = onlyHandlers ? 2 : 3; + event.namespace = namespaces.join( "." ); + event.rnamespace = event.namespace ? + new RegExp( "(^|\\.)" + namespaces.join( "\\.(?:.*\\.|)" ) + "(\\.|$)" ) : + null; + + // Clean up the event in case it is being reused + event.result = undefined; + if ( !event.target ) { + event.target = elem; + } + + // Clone any incoming data and prepend the event, creating the handler arg list + data = data == null ? + [ event ] : + jQuery.makeArray( data, [ event ] ); + + // Allow special events to draw outside the lines + special = jQuery.event.special[ type ] || {}; + if ( !onlyHandlers && special.trigger && special.trigger.apply( elem, data ) === false ) { + return; + } + + // Determine event propagation path in advance, per W3C events spec (#9951) + // Bubble up to document, then to window; watch for a global ownerDocument var (#9724) + if ( !onlyHandlers && !special.noBubble && !isWindow( elem ) ) { + + bubbleType = special.delegateType || type; + if ( !rfocusMorph.test( bubbleType + type ) ) { + cur = cur.parentNode; + } + for ( ; cur; cur = cur.parentNode ) { + eventPath.push( cur ); + tmp = cur; + } + + // Only add window if we got to document (e.g., not plain obj or detached DOM) + if ( tmp === ( elem.ownerDocument || document ) ) { + eventPath.push( tmp.defaultView || tmp.parentWindow || window ); + } + } + + // Fire handlers on the event path + i = 0; + while ( ( cur = eventPath[ i++ ] ) && !event.isPropagationStopped() ) { + lastElement = cur; + event.type = i > 1 ? + bubbleType : + special.bindType || type; + + // jQuery handler + handle = ( dataPriv.get( cur, "events" ) || Object.create( null ) )[ event.type ] && + dataPriv.get( cur, "handle" ); + if ( handle ) { + handle.apply( cur, data ); + } + + // Native handler + handle = ontype && cur[ ontype ]; + if ( handle && handle.apply && acceptData( cur ) ) { + event.result = handle.apply( cur, data ); + if ( event.result === false ) { + event.preventDefault(); + } + } + } + event.type = type; + + // If nobody prevented the default action, do it now + if ( !onlyHandlers && !event.isDefaultPrevented() ) { + + if ( ( !special._default || + special._default.apply( eventPath.pop(), data ) === false ) && + acceptData( elem ) ) { + + // Call a native DOM method on the target with the same name as the event. + // Don't do default actions on window, that's where global variables be (#6170) + if ( ontype && isFunction( elem[ type ] ) && !isWindow( elem ) ) { + + // Don't re-trigger an onFOO event when we call its FOO() method + tmp = elem[ ontype ]; + + if ( tmp ) { + elem[ ontype ] = null; + } + + // Prevent re-triggering of the same event, since we already bubbled it above + jQuery.event.triggered = type; + + if ( event.isPropagationStopped() ) { + lastElement.addEventListener( type, stopPropagationCallback ); + } + + elem[ type ](); + + if ( event.isPropagationStopped() ) { + lastElement.removeEventListener( type, stopPropagationCallback ); + } + + jQuery.event.triggered = undefined; + + if ( tmp ) { + elem[ ontype ] = tmp; + } + } + } + } + + return event.result; + }, + + // Piggyback on a donor event to simulate a different one + // Used only for `focus(in | out)` events + simulate: function( type, elem, event ) { + var e = jQuery.extend( + new jQuery.Event(), + event, + { + type: type, + isSimulated: true + } + ); + + jQuery.event.trigger( e, null, elem ); + } + +} ); + +jQuery.fn.extend( { + + trigger: function( type, data ) { + return this.each( function() { + jQuery.event.trigger( type, data, this ); + } ); + }, + triggerHandler: function( type, data ) { + var elem = this[ 0 ]; + if ( elem ) { + return jQuery.event.trigger( type, data, elem, true ); + } + } +} ); + + +// Support: Firefox <=44 +// Firefox doesn't have focus(in | out) events +// Related ticket - https://bugzilla.mozilla.org/show_bug.cgi?id=687787 +// +// Support: Chrome <=48 - 49, Safari <=9.0 - 9.1 +// focus(in | out) events fire after focus & blur events, +// which is spec violation - http://www.w3.org/TR/DOM-Level-3-Events/#events-focusevent-event-order +// Related ticket - https://bugs.chromium.org/p/chromium/issues/detail?id=449857 +if ( !support.focusin ) { + jQuery.each( { focus: "focusin", blur: "focusout" }, function( orig, fix ) { + + // Attach a single capturing handler on the document while someone wants focusin/focusout + var handler = function( event ) { + jQuery.event.simulate( fix, event.target, jQuery.event.fix( event ) ); + }; + + jQuery.event.special[ fix ] = { + setup: function() { + + // Handle: regular nodes (via `this.ownerDocument`), window + // (via `this.document`) & document (via `this`). + var doc = this.ownerDocument || this.document || this, + attaches = dataPriv.access( doc, fix ); + + if ( !attaches ) { + doc.addEventListener( orig, handler, true ); + } + dataPriv.access( doc, fix, ( attaches || 0 ) + 1 ); + }, + teardown: function() { + var doc = this.ownerDocument || this.document || this, + attaches = dataPriv.access( doc, fix ) - 1; + + if ( !attaches ) { + doc.removeEventListener( orig, handler, true ); + dataPriv.remove( doc, fix ); + + } else { + dataPriv.access( doc, fix, attaches ); + } + } + }; + } ); +} +var location = window.location; + +var nonce = { guid: Date.now() }; + +var rquery = ( /\?/ ); + + + +// Cross-browser xml parsing +jQuery.parseXML = function( data ) { + var xml, parserErrorElem; + if ( !data || typeof data !== "string" ) { + return null; + } + + // Support: IE 9 - 11 only + // IE throws on parseFromString with invalid input. + try { + xml = ( new window.DOMParser() ).parseFromString( data, "text/xml" ); + } catch ( e ) {} + + parserErrorElem = xml && xml.getElementsByTagName( "parsererror" )[ 0 ]; + if ( !xml || parserErrorElem ) { + jQuery.error( "Invalid XML: " + ( + parserErrorElem ? + jQuery.map( parserErrorElem.childNodes, function( el ) { + return el.textContent; + } ).join( "\n" ) : + data + ) ); + } + return xml; +}; + + +var + rbracket = /\[\]$/, + rCRLF = /\r?\n/g, + rsubmitterTypes = /^(?:submit|button|image|reset|file)$/i, + rsubmittable = /^(?:input|select|textarea|keygen)/i; + +function buildParams( prefix, obj, traditional, add ) { + var name; + + if ( Array.isArray( obj ) ) { + + // Serialize array item. + jQuery.each( obj, function( i, v ) { + if ( traditional || rbracket.test( prefix ) ) { + + // Treat each array item as a scalar. + add( prefix, v ); + + } else { + + // Item is non-scalar (array or object), encode its numeric index. + buildParams( + prefix + "[" + ( typeof v === "object" && v != null ? i : "" ) + "]", + v, + traditional, + add + ); + } + } ); + + } else if ( !traditional && toType( obj ) === "object" ) { + + // Serialize object item. + for ( name in obj ) { + buildParams( prefix + "[" + name + "]", obj[ name ], traditional, add ); + } + + } else { + + // Serialize scalar item. + add( prefix, obj ); + } +} + +// Serialize an array of form elements or a set of +// key/values into a query string +jQuery.param = function( a, traditional ) { + var prefix, + s = [], + add = function( key, valueOrFunction ) { + + // If value is a function, invoke it and use its return value + var value = isFunction( valueOrFunction ) ? + valueOrFunction() : + valueOrFunction; + + s[ s.length ] = encodeURIComponent( key ) + "=" + + encodeURIComponent( value == null ? "" : value ); + }; + + if ( a == null ) { + return ""; + } + + // If an array was passed in, assume that it is an array of form elements. + if ( Array.isArray( a ) || ( a.jquery && !jQuery.isPlainObject( a ) ) ) { + + // Serialize the form elements + jQuery.each( a, function() { + add( this.name, this.value ); + } ); + + } else { + + // If traditional, encode the "old" way (the way 1.3.2 or older + // did it), otherwise encode params recursively. + for ( prefix in a ) { + buildParams( prefix, a[ prefix ], traditional, add ); + } + } + + // Return the resulting serialization + return s.join( "&" ); +}; + +jQuery.fn.extend( { + serialize: function() { + return jQuery.param( this.serializeArray() ); + }, + serializeArray: function() { + return this.map( function() { + + // Can add propHook for "elements" to filter or add form elements + var elements = jQuery.prop( this, "elements" ); + return elements ? jQuery.makeArray( elements ) : this; + } ).filter( function() { + var type = this.type; + + // Use .is( ":disabled" ) so that fieldset[disabled] works + return this.name && !jQuery( this ).is( ":disabled" ) && + rsubmittable.test( this.nodeName ) && !rsubmitterTypes.test( type ) && + ( this.checked || !rcheckableType.test( type ) ); + } ).map( function( _i, elem ) { + var val = jQuery( this ).val(); + + if ( val == null ) { + return null; + } + + if ( Array.isArray( val ) ) { + return jQuery.map( val, function( val ) { + return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) }; + } ); + } + + return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) }; + } ).get(); + } +} ); + + +var + r20 = /%20/g, + rhash = /#.*$/, + rantiCache = /([?&])_=[^&]*/, + rheaders = /^(.*?):[ \t]*([^\r\n]*)$/mg, + + // #7653, #8125, #8152: local protocol detection + rlocalProtocol = /^(?:about|app|app-storage|.+-extension|file|res|widget):$/, + rnoContent = /^(?:GET|HEAD)$/, + rprotocol = /^\/\//, + + /* Prefilters + * 1) They are useful to introduce custom dataTypes (see ajax/jsonp.js for an example) + * 2) These are called: + * - BEFORE asking for a transport + * - AFTER param serialization (s.data is a string if s.processData is true) + * 3) key is the dataType + * 4) the catchall symbol "*" can be used + * 5) execution will start with transport dataType and THEN continue down to "*" if needed + */ + prefilters = {}, + + /* Transports bindings + * 1) key is the dataType + * 2) the catchall symbol "*" can be used + * 3) selection will start with transport dataType and THEN go to "*" if needed + */ + transports = {}, + + // Avoid comment-prolog char sequence (#10098); must appease lint and evade compression + allTypes = "*/".concat( "*" ), + + // Anchor tag for parsing the document origin + originAnchor = document.createElement( "a" ); + +originAnchor.href = location.href; + +// Base "constructor" for jQuery.ajaxPrefilter and jQuery.ajaxTransport +function addToPrefiltersOrTransports( structure ) { + + // dataTypeExpression is optional and defaults to "*" + return function( dataTypeExpression, func ) { + + if ( typeof dataTypeExpression !== "string" ) { + func = dataTypeExpression; + dataTypeExpression = "*"; + } + + var dataType, + i = 0, + dataTypes = dataTypeExpression.toLowerCase().match( rnothtmlwhite ) || []; + + if ( isFunction( func ) ) { + + // For each dataType in the dataTypeExpression + while ( ( dataType = dataTypes[ i++ ] ) ) { + + // Prepend if requested + if ( dataType[ 0 ] === "+" ) { + dataType = dataType.slice( 1 ) || "*"; + ( structure[ dataType ] = structure[ dataType ] || [] ).unshift( func ); + + // Otherwise append + } else { + ( structure[ dataType ] = structure[ dataType ] || [] ).push( func ); + } + } + } + }; +} + +// Base inspection function for prefilters and transports +function inspectPrefiltersOrTransports( structure, options, originalOptions, jqXHR ) { + + var inspected = {}, + seekingTransport = ( structure === transports ); + + function inspect( dataType ) { + var selected; + inspected[ dataType ] = true; + jQuery.each( structure[ dataType ] || [], function( _, prefilterOrFactory ) { + var dataTypeOrTransport = prefilterOrFactory( options, originalOptions, jqXHR ); + if ( typeof dataTypeOrTransport === "string" && + !seekingTransport && !inspected[ dataTypeOrTransport ] ) { + + options.dataTypes.unshift( dataTypeOrTransport ); + inspect( dataTypeOrTransport ); + return false; + } else if ( seekingTransport ) { + return !( selected = dataTypeOrTransport ); + } + } ); + return selected; + } + + return inspect( options.dataTypes[ 0 ] ) || !inspected[ "*" ] && inspect( "*" ); +} + +// A special extend for ajax options +// that takes "flat" options (not to be deep extended) +// Fixes #9887 +function ajaxExtend( target, src ) { + var key, deep, + flatOptions = jQuery.ajaxSettings.flatOptions || {}; + + for ( key in src ) { + if ( src[ key ] !== undefined ) { + ( flatOptions[ key ] ? target : ( deep || ( deep = {} ) ) )[ key ] = src[ key ]; + } + } + if ( deep ) { + jQuery.extend( true, target, deep ); + } + + return target; +} + +/* Handles responses to an ajax request: + * - finds the right dataType (mediates between content-type and expected dataType) + * - returns the corresponding response + */ +function ajaxHandleResponses( s, jqXHR, responses ) { + + var ct, type, finalDataType, firstDataType, + contents = s.contents, + dataTypes = s.dataTypes; + + // Remove auto dataType and get content-type in the process + while ( dataTypes[ 0 ] === "*" ) { + dataTypes.shift(); + if ( ct === undefined ) { + ct = s.mimeType || jqXHR.getResponseHeader( "Content-Type" ); + } + } + + // Check if we're dealing with a known content-type + if ( ct ) { + for ( type in contents ) { + if ( contents[ type ] && contents[ type ].test( ct ) ) { + dataTypes.unshift( type ); + break; + } + } + } + + // Check to see if we have a response for the expected dataType + if ( dataTypes[ 0 ] in responses ) { + finalDataType = dataTypes[ 0 ]; + } else { + + // Try convertible dataTypes + for ( type in responses ) { + if ( !dataTypes[ 0 ] || s.converters[ type + " " + dataTypes[ 0 ] ] ) { + finalDataType = type; + break; + } + if ( !firstDataType ) { + firstDataType = type; + } + } + + // Or just use first one + finalDataType = finalDataType || firstDataType; + } + + // If we found a dataType + // We add the dataType to the list if needed + // and return the corresponding response + if ( finalDataType ) { + if ( finalDataType !== dataTypes[ 0 ] ) { + dataTypes.unshift( finalDataType ); + } + return responses[ finalDataType ]; + } +} + +/* Chain conversions given the request and the original response + * Also sets the responseXXX fields on the jqXHR instance + */ +function ajaxConvert( s, response, jqXHR, isSuccess ) { + var conv2, current, conv, tmp, prev, + converters = {}, + + // Work with a copy of dataTypes in case we need to modify it for conversion + dataTypes = s.dataTypes.slice(); + + // Create converters map with lowercased keys + if ( dataTypes[ 1 ] ) { + for ( conv in s.converters ) { + converters[ conv.toLowerCase() ] = s.converters[ conv ]; + } + } + + current = dataTypes.shift(); + + // Convert to each sequential dataType + while ( current ) { + + if ( s.responseFields[ current ] ) { + jqXHR[ s.responseFields[ current ] ] = response; + } + + // Apply the dataFilter if provided + if ( !prev && isSuccess && s.dataFilter ) { + response = s.dataFilter( response, s.dataType ); + } + + prev = current; + current = dataTypes.shift(); + + if ( current ) { + + // There's only work to do if current dataType is non-auto + if ( current === "*" ) { + + current = prev; + + // Convert response if prev dataType is non-auto and differs from current + } else if ( prev !== "*" && prev !== current ) { + + // Seek a direct converter + conv = converters[ prev + " " + current ] || converters[ "* " + current ]; + + // If none found, seek a pair + if ( !conv ) { + for ( conv2 in converters ) { + + // If conv2 outputs current + tmp = conv2.split( " " ); + if ( tmp[ 1 ] === current ) { + + // If prev can be converted to accepted input + conv = converters[ prev + " " + tmp[ 0 ] ] || + converters[ "* " + tmp[ 0 ] ]; + if ( conv ) { + + // Condense equivalence converters + if ( conv === true ) { + conv = converters[ conv2 ]; + + // Otherwise, insert the intermediate dataType + } else if ( converters[ conv2 ] !== true ) { + current = tmp[ 0 ]; + dataTypes.unshift( tmp[ 1 ] ); + } + break; + } + } + } + } + + // Apply converter (if not an equivalence) + if ( conv !== true ) { + + // Unless errors are allowed to bubble, catch and return them + if ( conv && s.throws ) { + response = conv( response ); + } else { + try { + response = conv( response ); + } catch ( e ) { + return { + state: "parsererror", + error: conv ? e : "No conversion from " + prev + " to " + current + }; + } + } + } + } + } + } + + return { state: "success", data: response }; +} + +jQuery.extend( { + + // Counter for holding the number of active queries + active: 0, + + // Last-Modified header cache for next request + lastModified: {}, + etag: {}, + + ajaxSettings: { + url: location.href, + type: "GET", + isLocal: rlocalProtocol.test( location.protocol ), + global: true, + processData: true, + async: true, + contentType: "application/x-www-form-urlencoded; charset=UTF-8", + + /* + timeout: 0, + data: null, + dataType: null, + username: null, + password: null, + cache: null, + throws: false, + traditional: false, + headers: {}, + */ + + accepts: { + "*": allTypes, + text: "text/plain", + html: "text/html", + xml: "application/xml, text/xml", + json: "application/json, text/javascript" + }, + + contents: { + xml: /\bxml\b/, + html: /\bhtml/, + json: /\bjson\b/ + }, + + responseFields: { + xml: "responseXML", + text: "responseText", + json: "responseJSON" + }, + + // Data converters + // Keys separate source (or catchall "*") and destination types with a single space + converters: { + + // Convert anything to text + "* text": String, + + // Text to html (true = no transformation) + "text html": true, + + // Evaluate text as a json expression + "text json": JSON.parse, + + // Parse text as xml + "text xml": jQuery.parseXML + }, + + // For options that shouldn't be deep extended: + // you can add your own custom options here if + // and when you create one that shouldn't be + // deep extended (see ajaxExtend) + flatOptions: { + url: true, + context: true + } + }, + + // Creates a full fledged settings object into target + // with both ajaxSettings and settings fields. + // If target is omitted, writes into ajaxSettings. + ajaxSetup: function( target, settings ) { + return settings ? + + // Building a settings object + ajaxExtend( ajaxExtend( target, jQuery.ajaxSettings ), settings ) : + + // Extending ajaxSettings + ajaxExtend( jQuery.ajaxSettings, target ); + }, + + ajaxPrefilter: addToPrefiltersOrTransports( prefilters ), + ajaxTransport: addToPrefiltersOrTransports( transports ), + + // Main method + ajax: function( url, options ) { + + // If url is an object, simulate pre-1.5 signature + if ( typeof url === "object" ) { + options = url; + url = undefined; + } + + // Force options to be an object + options = options || {}; + + var transport, + + // URL without anti-cache param + cacheURL, + + // Response headers + responseHeadersString, + responseHeaders, + + // timeout handle + timeoutTimer, + + // Url cleanup var + urlAnchor, + + // Request state (becomes false upon send and true upon completion) + completed, + + // To know if global events are to be dispatched + fireGlobals, + + // Loop variable + i, + + // uncached part of the url + uncached, + + // Create the final options object + s = jQuery.ajaxSetup( {}, options ), + + // Callbacks context + callbackContext = s.context || s, + + // Context for global events is callbackContext if it is a DOM node or jQuery collection + globalEventContext = s.context && + ( callbackContext.nodeType || callbackContext.jquery ) ? + jQuery( callbackContext ) : + jQuery.event, + + // Deferreds + deferred = jQuery.Deferred(), + completeDeferred = jQuery.Callbacks( "once memory" ), + + // Status-dependent callbacks + statusCode = s.statusCode || {}, + + // Headers (they are sent all at once) + requestHeaders = {}, + requestHeadersNames = {}, + + // Default abort message + strAbort = "canceled", + + // Fake xhr + jqXHR = { + readyState: 0, + + // Builds headers hashtable if needed + getResponseHeader: function( key ) { + var match; + if ( completed ) { + if ( !responseHeaders ) { + responseHeaders = {}; + while ( ( match = rheaders.exec( responseHeadersString ) ) ) { + responseHeaders[ match[ 1 ].toLowerCase() + " " ] = + ( responseHeaders[ match[ 1 ].toLowerCase() + " " ] || [] ) + .concat( match[ 2 ] ); + } + } + match = responseHeaders[ key.toLowerCase() + " " ]; + } + return match == null ? null : match.join( ", " ); + }, + + // Raw string + getAllResponseHeaders: function() { + return completed ? responseHeadersString : null; + }, + + // Caches the header + setRequestHeader: function( name, value ) { + if ( completed == null ) { + name = requestHeadersNames[ name.toLowerCase() ] = + requestHeadersNames[ name.toLowerCase() ] || name; + requestHeaders[ name ] = value; + } + return this; + }, + + // Overrides response content-type header + overrideMimeType: function( type ) { + if ( completed == null ) { + s.mimeType = type; + } + return this; + }, + + // Status-dependent callbacks + statusCode: function( map ) { + var code; + if ( map ) { + if ( completed ) { + + // Execute the appropriate callbacks + jqXHR.always( map[ jqXHR.status ] ); + } else { + + // Lazy-add the new callbacks in a way that preserves old ones + for ( code in map ) { + statusCode[ code ] = [ statusCode[ code ], map[ code ] ]; + } + } + } + return this; + }, + + // Cancel the request + abort: function( statusText ) { + var finalText = statusText || strAbort; + if ( transport ) { + transport.abort( finalText ); + } + done( 0, finalText ); + return this; + } + }; + + // Attach deferreds + deferred.promise( jqXHR ); + + // Add protocol if not provided (prefilters might expect it) + // Handle falsy url in the settings object (#10093: consistency with old signature) + // We also use the url parameter if available + s.url = ( ( url || s.url || location.href ) + "" ) + .replace( rprotocol, location.protocol + "//" ); + + // Alias method option to type as per ticket #12004 + s.type = options.method || options.type || s.method || s.type; + + // Extract dataTypes list + s.dataTypes = ( s.dataType || "*" ).toLowerCase().match( rnothtmlwhite ) || [ "" ]; + + // A cross-domain request is in order when the origin doesn't match the current origin. + if ( s.crossDomain == null ) { + urlAnchor = document.createElement( "a" ); + + // Support: IE <=8 - 11, Edge 12 - 15 + // IE throws exception on accessing the href property if url is malformed, + // e.g. http://example.com:80x/ + try { + urlAnchor.href = s.url; + + // Support: IE <=8 - 11 only + // Anchor's host property isn't correctly set when s.url is relative + urlAnchor.href = urlAnchor.href; + s.crossDomain = originAnchor.protocol + "//" + originAnchor.host !== + urlAnchor.protocol + "//" + urlAnchor.host; + } catch ( e ) { + + // If there is an error parsing the URL, assume it is crossDomain, + // it can be rejected by the transport if it is invalid + s.crossDomain = true; + } + } + + // Convert data if not already a string + if ( s.data && s.processData && typeof s.data !== "string" ) { + s.data = jQuery.param( s.data, s.traditional ); + } + + // Apply prefilters + inspectPrefiltersOrTransports( prefilters, s, options, jqXHR ); + + // If request was aborted inside a prefilter, stop there + if ( completed ) { + return jqXHR; + } + + // We can fire global events as of now if asked to + // Don't fire events if jQuery.event is undefined in an AMD-usage scenario (#15118) + fireGlobals = jQuery.event && s.global; + + // Watch for a new set of requests + if ( fireGlobals && jQuery.active++ === 0 ) { + jQuery.event.trigger( "ajaxStart" ); + } + + // Uppercase the type + s.type = s.type.toUpperCase(); + + // Determine if request has content + s.hasContent = !rnoContent.test( s.type ); + + // Save the URL in case we're toying with the If-Modified-Since + // and/or If-None-Match header later on + // Remove hash to simplify url manipulation + cacheURL = s.url.replace( rhash, "" ); + + // More options handling for requests with no content + if ( !s.hasContent ) { + + // Remember the hash so we can put it back + uncached = s.url.slice( cacheURL.length ); + + // If data is available and should be processed, append data to url + if ( s.data && ( s.processData || typeof s.data === "string" ) ) { + cacheURL += ( rquery.test( cacheURL ) ? "&" : "?" ) + s.data; + + // #9682: remove data so that it's not used in an eventual retry + delete s.data; + } + + // Add or update anti-cache param if needed + if ( s.cache === false ) { + cacheURL = cacheURL.replace( rantiCache, "$1" ); + uncached = ( rquery.test( cacheURL ) ? "&" : "?" ) + "_=" + ( nonce.guid++ ) + + uncached; + } + + // Put hash and anti-cache on the URL that will be requested (gh-1732) + s.url = cacheURL + uncached; + + // Change '%20' to '+' if this is encoded form body content (gh-2658) + } else if ( s.data && s.processData && + ( s.contentType || "" ).indexOf( "application/x-www-form-urlencoded" ) === 0 ) { + s.data = s.data.replace( r20, "+" ); + } + + // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode. + if ( s.ifModified ) { + if ( jQuery.lastModified[ cacheURL ] ) { + jqXHR.setRequestHeader( "If-Modified-Since", jQuery.lastModified[ cacheURL ] ); + } + if ( jQuery.etag[ cacheURL ] ) { + jqXHR.setRequestHeader( "If-None-Match", jQuery.etag[ cacheURL ] ); + } + } + + // Set the correct header, if data is being sent + if ( s.data && s.hasContent && s.contentType !== false || options.contentType ) { + jqXHR.setRequestHeader( "Content-Type", s.contentType ); + } + + // Set the Accepts header for the server, depending on the dataType + jqXHR.setRequestHeader( + "Accept", + s.dataTypes[ 0 ] && s.accepts[ s.dataTypes[ 0 ] ] ? + s.accepts[ s.dataTypes[ 0 ] ] + + ( s.dataTypes[ 0 ] !== "*" ? ", " + allTypes + "; q=0.01" : "" ) : + s.accepts[ "*" ] + ); + + // Check for headers option + for ( i in s.headers ) { + jqXHR.setRequestHeader( i, s.headers[ i ] ); + } + + // Allow custom headers/mimetypes and early abort + if ( s.beforeSend && + ( s.beforeSend.call( callbackContext, jqXHR, s ) === false || completed ) ) { + + // Abort if not done already and return + return jqXHR.abort(); + } + + // Aborting is no longer a cancellation + strAbort = "abort"; + + // Install callbacks on deferreds + completeDeferred.add( s.complete ); + jqXHR.done( s.success ); + jqXHR.fail( s.error ); + + // Get transport + transport = inspectPrefiltersOrTransports( transports, s, options, jqXHR ); + + // If no transport, we auto-abort + if ( !transport ) { + done( -1, "No Transport" ); + } else { + jqXHR.readyState = 1; + + // Send global event + if ( fireGlobals ) { + globalEventContext.trigger( "ajaxSend", [ jqXHR, s ] ); + } + + // If request was aborted inside ajaxSend, stop there + if ( completed ) { + return jqXHR; + } + + // Timeout + if ( s.async && s.timeout > 0 ) { + timeoutTimer = window.setTimeout( function() { + jqXHR.abort( "timeout" ); + }, s.timeout ); + } + + try { + completed = false; + transport.send( requestHeaders, done ); + } catch ( e ) { + + // Rethrow post-completion exceptions + if ( completed ) { + throw e; + } + + // Propagate others as results + done( -1, e ); + } + } + + // Callback for when everything is done + function done( status, nativeStatusText, responses, headers ) { + var isSuccess, success, error, response, modified, + statusText = nativeStatusText; + + // Ignore repeat invocations + if ( completed ) { + return; + } + + completed = true; + + // Clear timeout if it exists + if ( timeoutTimer ) { + window.clearTimeout( timeoutTimer ); + } + + // Dereference transport for early garbage collection + // (no matter how long the jqXHR object will be used) + transport = undefined; + + // Cache response headers + responseHeadersString = headers || ""; + + // Set readyState + jqXHR.readyState = status > 0 ? 4 : 0; + + // Determine if successful + isSuccess = status >= 200 && status < 300 || status === 304; + + // Get response data + if ( responses ) { + response = ajaxHandleResponses( s, jqXHR, responses ); + } + + // Use a noop converter for missing script but not if jsonp + if ( !isSuccess && + jQuery.inArray( "script", s.dataTypes ) > -1 && + jQuery.inArray( "json", s.dataTypes ) < 0 ) { + s.converters[ "text script" ] = function() {}; + } + + // Convert no matter what (that way responseXXX fields are always set) + response = ajaxConvert( s, response, jqXHR, isSuccess ); + + // If successful, handle type chaining + if ( isSuccess ) { + + // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode. + if ( s.ifModified ) { + modified = jqXHR.getResponseHeader( "Last-Modified" ); + if ( modified ) { + jQuery.lastModified[ cacheURL ] = modified; + } + modified = jqXHR.getResponseHeader( "etag" ); + if ( modified ) { + jQuery.etag[ cacheURL ] = modified; + } + } + + // if no content + if ( status === 204 || s.type === "HEAD" ) { + statusText = "nocontent"; + + // if not modified + } else if ( status === 304 ) { + statusText = "notmodified"; + + // If we have data, let's convert it + } else { + statusText = response.state; + success = response.data; + error = response.error; + isSuccess = !error; + } + } else { + + // Extract error from statusText and normalize for non-aborts + error = statusText; + if ( status || !statusText ) { + statusText = "error"; + if ( status < 0 ) { + status = 0; + } + } + } + + // Set data for the fake xhr object + jqXHR.status = status; + jqXHR.statusText = ( nativeStatusText || statusText ) + ""; + + // Success/Error + if ( isSuccess ) { + deferred.resolveWith( callbackContext, [ success, statusText, jqXHR ] ); + } else { + deferred.rejectWith( callbackContext, [ jqXHR, statusText, error ] ); + } + + // Status-dependent callbacks + jqXHR.statusCode( statusCode ); + statusCode = undefined; + + if ( fireGlobals ) { + globalEventContext.trigger( isSuccess ? "ajaxSuccess" : "ajaxError", + [ jqXHR, s, isSuccess ? success : error ] ); + } + + // Complete + completeDeferred.fireWith( callbackContext, [ jqXHR, statusText ] ); + + if ( fireGlobals ) { + globalEventContext.trigger( "ajaxComplete", [ jqXHR, s ] ); + + // Handle the global AJAX counter + if ( !( --jQuery.active ) ) { + jQuery.event.trigger( "ajaxStop" ); + } + } + } + + return jqXHR; + }, + + getJSON: function( url, data, callback ) { + return jQuery.get( url, data, callback, "json" ); + }, + + getScript: function( url, callback ) { + return jQuery.get( url, undefined, callback, "script" ); + } +} ); + +jQuery.each( [ "get", "post" ], function( _i, method ) { + jQuery[ method ] = function( url, data, callback, type ) { + + // Shift arguments if data argument was omitted + if ( isFunction( data ) ) { + type = type || callback; + callback = data; + data = undefined; + } + + // The url can be an options object (which then must have .url) + return jQuery.ajax( jQuery.extend( { + url: url, + type: method, + dataType: type, + data: data, + success: callback + }, jQuery.isPlainObject( url ) && url ) ); + }; +} ); + +jQuery.ajaxPrefilter( function( s ) { + var i; + for ( i in s.headers ) { + if ( i.toLowerCase() === "content-type" ) { + s.contentType = s.headers[ i ] || ""; + } + } +} ); + + +jQuery._evalUrl = function( url, options, doc ) { + return jQuery.ajax( { + url: url, + + // Make this explicit, since user can override this through ajaxSetup (#11264) + type: "GET", + dataType: "script", + cache: true, + async: false, + global: false, + + // Only evaluate the response if it is successful (gh-4126) + // dataFilter is not invoked for failure responses, so using it instead + // of the default converter is kludgy but it works. + converters: { + "text script": function() {} + }, + dataFilter: function( response ) { + jQuery.globalEval( response, options, doc ); + } + } ); +}; + + +jQuery.fn.extend( { + wrapAll: function( html ) { + var wrap; + + if ( this[ 0 ] ) { + if ( isFunction( html ) ) { + html = html.call( this[ 0 ] ); + } + + // The elements to wrap the target around + wrap = jQuery( html, this[ 0 ].ownerDocument ).eq( 0 ).clone( true ); + + if ( this[ 0 ].parentNode ) { + wrap.insertBefore( this[ 0 ] ); + } + + wrap.map( function() { + var elem = this; + + while ( elem.firstElementChild ) { + elem = elem.firstElementChild; + } + + return elem; + } ).append( this ); + } + + return this; + }, + + wrapInner: function( html ) { + if ( isFunction( html ) ) { + return this.each( function( i ) { + jQuery( this ).wrapInner( html.call( this, i ) ); + } ); + } + + return this.each( function() { + var self = jQuery( this ), + contents = self.contents(); + + if ( contents.length ) { + contents.wrapAll( html ); + + } else { + self.append( html ); + } + } ); + }, + + wrap: function( html ) { + var htmlIsFunction = isFunction( html ); + + return this.each( function( i ) { + jQuery( this ).wrapAll( htmlIsFunction ? html.call( this, i ) : html ); + } ); + }, + + unwrap: function( selector ) { + this.parent( selector ).not( "body" ).each( function() { + jQuery( this ).replaceWith( this.childNodes ); + } ); + return this; + } +} ); + + +jQuery.expr.pseudos.hidden = function( elem ) { + return !jQuery.expr.pseudos.visible( elem ); +}; +jQuery.expr.pseudos.visible = function( elem ) { + return !!( elem.offsetWidth || elem.offsetHeight || elem.getClientRects().length ); +}; + + + + +jQuery.ajaxSettings.xhr = function() { + try { + return new window.XMLHttpRequest(); + } catch ( e ) {} +}; + +var xhrSuccessStatus = { + + // File protocol always yields status code 0, assume 200 + 0: 200, + + // Support: IE <=9 only + // #1450: sometimes IE returns 1223 when it should be 204 + 1223: 204 + }, + xhrSupported = jQuery.ajaxSettings.xhr(); + +support.cors = !!xhrSupported && ( "withCredentials" in xhrSupported ); +support.ajax = xhrSupported = !!xhrSupported; + +jQuery.ajaxTransport( function( options ) { + var callback, errorCallback; + + // Cross domain only allowed if supported through XMLHttpRequest + if ( support.cors || xhrSupported && !options.crossDomain ) { + return { + send: function( headers, complete ) { + var i, + xhr = options.xhr(); + + xhr.open( + options.type, + options.url, + options.async, + options.username, + options.password + ); + + // Apply custom fields if provided + if ( options.xhrFields ) { + for ( i in options.xhrFields ) { + xhr[ i ] = options.xhrFields[ i ]; + } + } + + // Override mime type if needed + if ( options.mimeType && xhr.overrideMimeType ) { + xhr.overrideMimeType( options.mimeType ); + } + + // X-Requested-With header + // For cross-domain requests, seeing as conditions for a preflight are + // akin to a jigsaw puzzle, we simply never set it to be sure. + // (it can always be set on a per-request basis or even using ajaxSetup) + // For same-domain requests, won't change header if already provided. + if ( !options.crossDomain && !headers[ "X-Requested-With" ] ) { + headers[ "X-Requested-With" ] = "XMLHttpRequest"; + } + + // Set headers + for ( i in headers ) { + xhr.setRequestHeader( i, headers[ i ] ); + } + + // Callback + callback = function( type ) { + return function() { + if ( callback ) { + callback = errorCallback = xhr.onload = + xhr.onerror = xhr.onabort = xhr.ontimeout = + xhr.onreadystatechange = null; + + if ( type === "abort" ) { + xhr.abort(); + } else if ( type === "error" ) { + + // Support: IE <=9 only + // On a manual native abort, IE9 throws + // errors on any property access that is not readyState + if ( typeof xhr.status !== "number" ) { + complete( 0, "error" ); + } else { + complete( + + // File: protocol always yields status 0; see #8605, #14207 + xhr.status, + xhr.statusText + ); + } + } else { + complete( + xhrSuccessStatus[ xhr.status ] || xhr.status, + xhr.statusText, + + // Support: IE <=9 only + // IE9 has no XHR2 but throws on binary (trac-11426) + // For XHR2 non-text, let the caller handle it (gh-2498) + ( xhr.responseType || "text" ) !== "text" || + typeof xhr.responseText !== "string" ? + { binary: xhr.response } : + { text: xhr.responseText }, + xhr.getAllResponseHeaders() + ); + } + } + }; + }; + + // Listen to events + xhr.onload = callback(); + errorCallback = xhr.onerror = xhr.ontimeout = callback( "error" ); + + // Support: IE 9 only + // Use onreadystatechange to replace onabort + // to handle uncaught aborts + if ( xhr.onabort !== undefined ) { + xhr.onabort = errorCallback; + } else { + xhr.onreadystatechange = function() { + + // Check readyState before timeout as it changes + if ( xhr.readyState === 4 ) { + + // Allow onerror to be called first, + // but that will not handle a native abort + // Also, save errorCallback to a variable + // as xhr.onerror cannot be accessed + window.setTimeout( function() { + if ( callback ) { + errorCallback(); + } + } ); + } + }; + } + + // Create the abort callback + callback = callback( "abort" ); + + try { + + // Do send the request (this may raise an exception) + xhr.send( options.hasContent && options.data || null ); + } catch ( e ) { + + // #14683: Only rethrow if this hasn't been notified as an error yet + if ( callback ) { + throw e; + } + } + }, + + abort: function() { + if ( callback ) { + callback(); + } + } + }; + } +} ); + + + + +// Prevent auto-execution of scripts when no explicit dataType was provided (See gh-2432) +jQuery.ajaxPrefilter( function( s ) { + if ( s.crossDomain ) { + s.contents.script = false; + } +} ); + +// Install script dataType +jQuery.ajaxSetup( { + accepts: { + script: "text/javascript, application/javascript, " + + "application/ecmascript, application/x-ecmascript" + }, + contents: { + script: /\b(?:java|ecma)script\b/ + }, + converters: { + "text script": function( text ) { + jQuery.globalEval( text ); + return text; + } + } +} ); + +// Handle cache's special case and crossDomain +jQuery.ajaxPrefilter( "script", function( s ) { + if ( s.cache === undefined ) { + s.cache = false; + } + if ( s.crossDomain ) { + s.type = "GET"; + } +} ); + +// Bind script tag hack transport +jQuery.ajaxTransport( "script", function( s ) { + + // This transport only deals with cross domain or forced-by-attrs requests + if ( s.crossDomain || s.scriptAttrs ) { + var script, callback; + return { + send: function( _, complete ) { + script = jQuery( "<script>" ) + .attr( s.scriptAttrs || {} ) + .prop( { charset: s.scriptCharset, src: s.url } ) + .on( "load error", callback = function( evt ) { + script.remove(); + callback = null; + if ( evt ) { + complete( evt.type === "error" ? 404 : 200, evt.type ); + } + } ); + + // Use native DOM manipulation to avoid our domManip AJAX trickery + document.head.appendChild( script[ 0 ] ); + }, + abort: function() { + if ( callback ) { + callback(); + } + } + }; + } +} ); + + + + +var oldCallbacks = [], + rjsonp = /(=)\?(?=&|$)|\?\?/; + +// Default jsonp settings +jQuery.ajaxSetup( { + jsonp: "callback", + jsonpCallback: function() { + var callback = oldCallbacks.pop() || ( jQuery.expando + "_" + ( nonce.guid++ ) ); + this[ callback ] = true; + return callback; + } +} ); + +// Detect, normalize options and install callbacks for jsonp requests +jQuery.ajaxPrefilter( "json jsonp", function( s, originalSettings, jqXHR ) { + + var callbackName, overwritten, responseContainer, + jsonProp = s.jsonp !== false && ( rjsonp.test( s.url ) ? + "url" : + typeof s.data === "string" && + ( s.contentType || "" ) + .indexOf( "application/x-www-form-urlencoded" ) === 0 && + rjsonp.test( s.data ) && "data" + ); + + // Handle iff the expected data type is "jsonp" or we have a parameter to set + if ( jsonProp || s.dataTypes[ 0 ] === "jsonp" ) { + + // Get callback name, remembering preexisting value associated with it + callbackName = s.jsonpCallback = isFunction( s.jsonpCallback ) ? + s.jsonpCallback() : + s.jsonpCallback; + + // Insert callback into url or form data + if ( jsonProp ) { + s[ jsonProp ] = s[ jsonProp ].replace( rjsonp, "$1" + callbackName ); + } else if ( s.jsonp !== false ) { + s.url += ( rquery.test( s.url ) ? "&" : "?" ) + s.jsonp + "=" + callbackName; + } + + // Use data converter to retrieve json after script execution + s.converters[ "script json" ] = function() { + if ( !responseContainer ) { + jQuery.error( callbackName + " was not called" ); + } + return responseContainer[ 0 ]; + }; + + // Force json dataType + s.dataTypes[ 0 ] = "json"; + + // Install callback + overwritten = window[ callbackName ]; + window[ callbackName ] = function() { + responseContainer = arguments; + }; + + // Clean-up function (fires after converters) + jqXHR.always( function() { + + // If previous value didn't exist - remove it + if ( overwritten === undefined ) { + jQuery( window ).removeProp( callbackName ); + + // Otherwise restore preexisting value + } else { + window[ callbackName ] = overwritten; + } + + // Save back as free + if ( s[ callbackName ] ) { + + // Make sure that re-using the options doesn't screw things around + s.jsonpCallback = originalSettings.jsonpCallback; + + // Save the callback name for future use + oldCallbacks.push( callbackName ); + } + + // Call if it was a function and we have a response + if ( responseContainer && isFunction( overwritten ) ) { + overwritten( responseContainer[ 0 ] ); + } + + responseContainer = overwritten = undefined; + } ); + + // Delegate to script + return "script"; + } +} ); + + + + +// Support: Safari 8 only +// In Safari 8 documents created via document.implementation.createHTMLDocument +// collapse sibling forms: the second one becomes a child of the first one. +// Because of that, this security measure has to be disabled in Safari 8. +// https://bugs.webkit.org/show_bug.cgi?id=137337 +support.createHTMLDocument = ( function() { + var body = document.implementation.createHTMLDocument( "" ).body; + body.innerHTML = "<form></form><form></form>"; + return body.childNodes.length === 2; +} )(); + + +// Argument "data" should be string of html +// context (optional): If specified, the fragment will be created in this context, +// defaults to document +// keepScripts (optional): If true, will include scripts passed in the html string +jQuery.parseHTML = function( data, context, keepScripts ) { + if ( typeof data !== "string" ) { + return []; + } + if ( typeof context === "boolean" ) { + keepScripts = context; + context = false; + } + + var base, parsed, scripts; + + if ( !context ) { + + // Stop scripts or inline event handlers from being executed immediately + // by using document.implementation + if ( support.createHTMLDocument ) { + context = document.implementation.createHTMLDocument( "" ); + + // Set the base href for the created document + // so any parsed elements with URLs + // are based on the document's URL (gh-2965) + base = context.createElement( "base" ); + base.href = document.location.href; + context.head.appendChild( base ); + } else { + context = document; + } + } + + parsed = rsingleTag.exec( data ); + scripts = !keepScripts && []; + + // Single tag + if ( parsed ) { + return [ context.createElement( parsed[ 1 ] ) ]; + } + + parsed = buildFragment( [ data ], context, scripts ); + + if ( scripts && scripts.length ) { + jQuery( scripts ).remove(); + } + + return jQuery.merge( [], parsed.childNodes ); +}; + + +/** + * Load a url into a page + */ +jQuery.fn.load = function( url, params, callback ) { + var selector, type, response, + self = this, + off = url.indexOf( " " ); + + if ( off > -1 ) { + selector = stripAndCollapse( url.slice( off ) ); + url = url.slice( 0, off ); + } + + // If it's a function + if ( isFunction( params ) ) { + + // We assume that it's the callback + callback = params; + params = undefined; + + // Otherwise, build a param string + } else if ( params && typeof params === "object" ) { + type = "POST"; + } + + // If we have elements to modify, make the request + if ( self.length > 0 ) { + jQuery.ajax( { + url: url, + + // If "type" variable is undefined, then "GET" method will be used. + // Make value of this field explicit since + // user can override it through ajaxSetup method + type: type || "GET", + dataType: "html", + data: params + } ).done( function( responseText ) { + + // Save response for use in complete callback + response = arguments; + + self.html( selector ? + + // If a selector was specified, locate the right elements in a dummy div + // Exclude scripts to avoid IE 'Permission Denied' errors + jQuery( "<div>" ).append( jQuery.parseHTML( responseText ) ).find( selector ) : + + // Otherwise use the full result + responseText ); + + // If the request succeeds, this function gets "data", "status", "jqXHR" + // but they are ignored because response was set above. + // If it fails, this function gets "jqXHR", "status", "error" + } ).always( callback && function( jqXHR, status ) { + self.each( function() { + callback.apply( this, response || [ jqXHR.responseText, status, jqXHR ] ); + } ); + } ); + } + + return this; +}; + + + + +jQuery.expr.pseudos.animated = function( elem ) { + return jQuery.grep( jQuery.timers, function( fn ) { + return elem === fn.elem; + } ).length; +}; + + + + +jQuery.offset = { + setOffset: function( elem, options, i ) { + var curPosition, curLeft, curCSSTop, curTop, curOffset, curCSSLeft, calculatePosition, + position = jQuery.css( elem, "position" ), + curElem = jQuery( elem ), + props = {}; + + // Set position first, in-case top/left are set even on static elem + if ( position === "static" ) { + elem.style.position = "relative"; + } + + curOffset = curElem.offset(); + curCSSTop = jQuery.css( elem, "top" ); + curCSSLeft = jQuery.css( elem, "left" ); + calculatePosition = ( position === "absolute" || position === "fixed" ) && + ( curCSSTop + curCSSLeft ).indexOf( "auto" ) > -1; + + // Need to be able to calculate position if either + // top or left is auto and position is either absolute or fixed + if ( calculatePosition ) { + curPosition = curElem.position(); + curTop = curPosition.top; + curLeft = curPosition.left; + + } else { + curTop = parseFloat( curCSSTop ) || 0; + curLeft = parseFloat( curCSSLeft ) || 0; + } + + if ( isFunction( options ) ) { + + // Use jQuery.extend here to allow modification of coordinates argument (gh-1848) + options = options.call( elem, i, jQuery.extend( {}, curOffset ) ); + } + + if ( options.top != null ) { + props.top = ( options.top - curOffset.top ) + curTop; + } + if ( options.left != null ) { + props.left = ( options.left - curOffset.left ) + curLeft; + } + + if ( "using" in options ) { + options.using.call( elem, props ); + + } else { + curElem.css( props ); + } + } +}; + +jQuery.fn.extend( { + + // offset() relates an element's border box to the document origin + offset: function( options ) { + + // Preserve chaining for setter + if ( arguments.length ) { + return options === undefined ? + this : + this.each( function( i ) { + jQuery.offset.setOffset( this, options, i ); + } ); + } + + var rect, win, + elem = this[ 0 ]; + + if ( !elem ) { + return; + } + + // Return zeros for disconnected and hidden (display: none) elements (gh-2310) + // Support: IE <=11 only + // Running getBoundingClientRect on a + // disconnected node in IE throws an error + if ( !elem.getClientRects().length ) { + return { top: 0, left: 0 }; + } + + // Get document-relative position by adding viewport scroll to viewport-relative gBCR + rect = elem.getBoundingClientRect(); + win = elem.ownerDocument.defaultView; + return { + top: rect.top + win.pageYOffset, + left: rect.left + win.pageXOffset + }; + }, + + // position() relates an element's margin box to its offset parent's padding box + // This corresponds to the behavior of CSS absolute positioning + position: function() { + if ( !this[ 0 ] ) { + return; + } + + var offsetParent, offset, doc, + elem = this[ 0 ], + parentOffset = { top: 0, left: 0 }; + + // position:fixed elements are offset from the viewport, which itself always has zero offset + if ( jQuery.css( elem, "position" ) === "fixed" ) { + + // Assume position:fixed implies availability of getBoundingClientRect + offset = elem.getBoundingClientRect(); + + } else { + offset = this.offset(); + + // Account for the *real* offset parent, which can be the document or its root element + // when a statically positioned element is identified + doc = elem.ownerDocument; + offsetParent = elem.offsetParent || doc.documentElement; + while ( offsetParent && + ( offsetParent === doc.body || offsetParent === doc.documentElement ) && + jQuery.css( offsetParent, "position" ) === "static" ) { + + offsetParent = offsetParent.parentNode; + } + if ( offsetParent && offsetParent !== elem && offsetParent.nodeType === 1 ) { + + // Incorporate borders into its offset, since they are outside its content origin + parentOffset = jQuery( offsetParent ).offset(); + parentOffset.top += jQuery.css( offsetParent, "borderTopWidth", true ); + parentOffset.left += jQuery.css( offsetParent, "borderLeftWidth", true ); + } + } + + // Subtract parent offsets and element margins + return { + top: offset.top - parentOffset.top - jQuery.css( elem, "marginTop", true ), + left: offset.left - parentOffset.left - jQuery.css( elem, "marginLeft", true ) + }; + }, + + // This method will return documentElement in the following cases: + // 1) For the element inside the iframe without offsetParent, this method will return + // documentElement of the parent window + // 2) For the hidden or detached element + // 3) For body or html element, i.e. in case of the html node - it will return itself + // + // but those exceptions were never presented as a real life use-cases + // and might be considered as more preferable results. + // + // This logic, however, is not guaranteed and can change at any point in the future + offsetParent: function() { + return this.map( function() { + var offsetParent = this.offsetParent; + + while ( offsetParent && jQuery.css( offsetParent, "position" ) === "static" ) { + offsetParent = offsetParent.offsetParent; + } + + return offsetParent || documentElement; + } ); + } +} ); + +// Create scrollLeft and scrollTop methods +jQuery.each( { scrollLeft: "pageXOffset", scrollTop: "pageYOffset" }, function( method, prop ) { + var top = "pageYOffset" === prop; + + jQuery.fn[ method ] = function( val ) { + return access( this, function( elem, method, val ) { + + // Coalesce documents and windows + var win; + if ( isWindow( elem ) ) { + win = elem; + } else if ( elem.nodeType === 9 ) { + win = elem.defaultView; + } + + if ( val === undefined ) { + return win ? win[ prop ] : elem[ method ]; + } + + if ( win ) { + win.scrollTo( + !top ? val : win.pageXOffset, + top ? val : win.pageYOffset + ); + + } else { + elem[ method ] = val; + } + }, method, val, arguments.length ); + }; +} ); + +// Support: Safari <=7 - 9.1, Chrome <=37 - 49 +// Add the top/left cssHooks using jQuery.fn.position +// Webkit bug: https://bugs.webkit.org/show_bug.cgi?id=29084 +// Blink bug: https://bugs.chromium.org/p/chromium/issues/detail?id=589347 +// getComputedStyle returns percent when specified for top/left/bottom/right; +// rather than make the css module depend on the offset module, just check for it here +jQuery.each( [ "top", "left" ], function( _i, prop ) { + jQuery.cssHooks[ prop ] = addGetHookIf( support.pixelPosition, + function( elem, computed ) { + if ( computed ) { + computed = curCSS( elem, prop ); + + // If curCSS returns percentage, fallback to offset + return rnumnonpx.test( computed ) ? + jQuery( elem ).position()[ prop ] + "px" : + computed; + } + } + ); +} ); + + +// Create innerHeight, innerWidth, height, width, outerHeight and outerWidth methods +jQuery.each( { Height: "height", Width: "width" }, function( name, type ) { + jQuery.each( { + padding: "inner" + name, + content: type, + "": "outer" + name + }, function( defaultExtra, funcName ) { + + // Margin is only for outerHeight, outerWidth + jQuery.fn[ funcName ] = function( margin, value ) { + var chainable = arguments.length && ( defaultExtra || typeof margin !== "boolean" ), + extra = defaultExtra || ( margin === true || value === true ? 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\ No newline at end of file diff --git a/docs/index.html b/docs/index.html index eb3fe7f9..2917f012 100644 --- a/docs/index.html +++ b/docs/index.html @@ -4,14 +4,25 @@ <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> -<meta name="viewport" content="width=device-width, initial-scale=1.0"> +<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"> +<meta name="description" content="Calculation routines based on the FOCUS Kinetics Report (2006, + 2014). Includes a function for conveniently defining differential equation + models, model solution based on eigenvalues if possible or using numerical + solvers. If a C compiler (on windows: Rtools) is installed, differential + equation models are solved using automatically generated C functions. + Heteroscedasticity can be taken into account using variance by variable or + two-component error models as described by Ranke and Meinecke (2018) + <doi:10.3390/environments6120124>. Hierarchical degradation models can + be fitted using nonlinear mixed-effects model packages as a back end as + described by Ranke et al. (2021) <doi:10.3390/environments8080071>. 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Includes a function for conveniently defining differential equation models, model solution based on eigenvalues if possible or using numerical @@ -29,120 +40,77 @@ <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> <![endif]--> </head> -<body data-spy="scroll" data-target="#toc"> +<body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - <div class="container template-home"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - <span class="sr-only">Toggle navigation</span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - <span class="icon-bar"></span> - </button> - <span class="navbar-brand"> - <a class="navbar-link" href="index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" 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class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.2.6</span> - </span> - </div> + <nav class="navbar fixed-top navbar-default navbar-expand-lg bg-light"><div class="container"> + + <a class="navbar-brand me-2" href="../index.html">mkin</a> + + <small class="nav-text text-default me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="Released version">1.2.6</small> + + + <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation"> + <span class="navbar-toggler-icon"></span> + </button> - <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"><li> - <a href="../reference/index.html">Reference</a> + <div id="navbar" class="collapse navbar-collapse ms-3"> + <ul class="navbar-nav me-auto"><li class="nav-item"> + <a class="nav-link" href="../reference/index.html">Reference</a> </li> 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with residue data on dimethenamid and dimethenamid-P</a> - </li> - <li> - <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> - <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> - </li> - <li> - <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> - </li> - <li class="divider"> - <li class="dropdown-header">Performance</li> - <li> - <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model 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href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> + <a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> + <a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Performance</h6> + <a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a class="dropdown-item" href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + <a class="dropdown-item" href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6> + <a class="dropdown-item" href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a class="dropdown-item" href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </div> +</li> +<li class="active nav-item"> + <a class="nav-link" href="../news/index.html">News</a> </li> - </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - + </ul></div> - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1 data-toc-skip>Changelog <small></small></h1> + + </div> +</nav><div class="container template-news"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Changelog</h1> <small>Source: <a href="https://github.com/jranke/mkin/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small> </div> <div class="section level2"> -<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> +<h2 class="pkg-version" data-toc-text="1.2.6" id="mkin-126">mkin 1.2.6<a class="anchor" aria-label="anchor" href="#mkin-126"></a></h2> <ul><li>‘inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd’: Fix an erroneous call to the ‘endpoints()’ function</li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.2.5" id="mkin-125-2023-08-09">mkin 1.2.5 (2023-08-09)<a class="anchor" aria-label="anchor" href="#mkin-125-2023-08-09"></a></h2> +<h2 class="pkg-version" data-toc-text="1.2.5" id="mkin-125-2023-08-09">mkin 1.2.5 (2023-08-09)<a class="anchor" aria-label="anchor" href="#mkin-125-2023-08-09"></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-124-2023-05-19">mkin 1.2.4 (2023-05-19)<a class="anchor" aria-label="anchor" href="#mkin-124-2023-05-19"></a></h2> +<h2 class="pkg-version" data-toc-text="1.2.4" id="mkin-124-2023-05-19">mkin 1.2.4 (2023-05-19)<a class="anchor" aria-label="anchor" href="#mkin-124-2023-05-19"></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> +<h2 class="pkg-version" 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-123-2023-04-17">mkin 1.2.3 (2023-04-17)<a class="anchor" aria-label="anchor" href="#mkin-123-2023-04-17"></a></h2> +<h2 class="pkg-version" 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> @@ -134,7 +99,7 @@ <li><p>‘R/mkinerrmin.R’: Fix typo in subset (use of = instead of ==), thanks to Sebastian Meyer for spotting this during his work on R 4.3.0.</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.2.2" id="mkin-122-unreleased">mkin 1.2.2 (unreleased)<a class="anchor" aria-label="anchor" href="#mkin-122-unreleased"></a></h2> +<h2 class="pkg-version" data-toc-text="1.2.2" id="mkin-122-unreleased">mkin 1.2.2 (unreleased)<a class="anchor" aria-label="anchor" href="#mkin-122-unreleased"></a></h2> <ul><li><p>‘inst/rmarkdown/templates/hierarchical_kinetics’: R markdown template to facilitate the application of hierarchical kinetic models.</p></li> <li><p>‘inst/testdata/{cyantraniliprole_soil_efsa_2014,lambda-cyhalothrin_soil_efsa_2014}.xlsx’: Example spreadsheets for use with ‘read_spreadsheet()’.</p></li> <li><p>‘R/mhmkin.R’: Allow an ‘illparms.mhmkin’ object or a list with suitable dimensions as value of the argument ‘no_random_effects’, making it possible to exclude random effects that were ill-defined in simpler variants of the set of degradation models. Remove the possibility to exclude random effects based on separate fits, as it did not work well.</p></li> @@ -145,7 +110,7 @@ <li><p>‘R/intervals.R’: Include correlations of random effects in the model in case there are any.</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.2.1" id="mkin-121-2022-11-19">mkin 1.2.1 (2022-11-19)<a class="anchor" aria-label="anchor" href="#mkin-121-2022-11-19"></a></h2> +<h2 class="pkg-version" data-toc-text="1.2.1" id="mkin-121-2022-11-19">mkin 1.2.1 (2022-11-19)<a class="anchor" aria-label="anchor" href="#mkin-121-2022-11-19"></a></h2> <ul><li><p>‘{data,R}/ds_mixed.rda’: Include the test data in the package instead of generating it in ‘tests/testthat/setup_script.R’. Refactor the generating code to make it consistent and update tests.</p></li> <li><p>‘tests/testthat/setup_script.R’: Excluded another ill-defined random effect for the DFOP fit with ‘saem’, in an attempt to avoid a platform dependence that surfaced on Fedora systems on the CRAN check farm</p></li> <li><p>‘tests/testthat/test_mixed.R’: Round parameters found by saemix to two significant digits before printing, to also help to avoid platform dependence of tests</p></li> @@ -154,7 +119,7 @@ <li><p>‘R/loglik.mkinfit.R’: Add ‘nobs’ attribute to the resulting ‘logLik’ object, in order to make test_AIC.R succeed on current R-devel</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.2.0" id="mkin-120-2022-11-17">mkin 1.2.0 (2022-11-17)<a class="anchor" aria-label="anchor" href="#mkin-120-2022-11-17"></a></h2> +<h2 class="pkg-version" data-toc-text="1.2.0" id="mkin-120-2022-11-17">mkin 1.2.0 (2022-11-17)<a class="anchor" aria-label="anchor" href="#mkin-120-2022-11-17"></a></h2> <ul><li><p>‘R/saem.R’: ‘logLik’, ‘update’ and ‘anova’ methods for ‘saem.mmkin’ objects.</p></li> <li><p>‘R/saem.R’: Automatic estimation of start parameters for random effects for the case of mkin transformations, nicely improving convergence and reducing problems with iterative ODE solutions.</p></li> <li><p>‘R/status.R’: New generic to show status information for fit array objects with methods for ‘mmkin’, ‘mhmkin’ and ‘multistart’ objects.</p></li> @@ -168,7 +133,7 @@ <li><p>‘R/tex_listings.R’: Conveniently include summaries of fit objects in R markdown documents that are compiled to LaTeX.</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.1.1" id="mkin-111-2022-07-12">mkin 1.1.1 (2022-07-12)<a class="anchor" aria-label="anchor" href="#mkin-111-2022-07-12"></a></h2> +<h2 class="pkg-version" data-toc-text="1.1.1" id="mkin-111-2022-07-12">mkin 1.1.1 (2022-07-12)<a class="anchor" aria-label="anchor" href="#mkin-111-2022-07-12"></a></h2> <ul><li><p>’R/{mkinmod,mkinpredict}.R: Store DLL information in mkinmod objects and use that information in mkinpredict to avoid a performance regression brought by a bugfix in R 4.2.x. Thanks to Tomas Kalibera for his analysis of the problem on the r-package-devel list and his suggestion on how to fix it.</p></li> <li><p>‘vignettes/FOCUS_L.rmd’: Remove an outdated note referring to a failure to calculate the covariance matrix for DFOP with the L2 dataset. Since 0.9.45.5 the covariance matrix is available</p></li> <li><p>‘vignettes/web_only/benchmarks.rmd’: Add the first benchmark data using my laptop system, therefore add the CPU when showing the benchmark results.</p></li> @@ -180,7 +145,7 @@ <li><p>‘plot.mkinfit’: Respect argument ‘maxabs’ for residual plots, and make it possible to give ylim as a list, for row layouts</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.1.0" id="mkin-110-2022-03-14">mkin 1.1.0 (2022-03-14)<a class="anchor" aria-label="anchor" href="#mkin-110-2022-03-14"></a></h2> +<h2 class="pkg-version" data-toc-text="1.1.0" id="mkin-110-2022-03-14">mkin 1.1.0 (2022-03-14)<a class="anchor" aria-label="anchor" href="#mkin-110-2022-03-14"></a></h2> <div class="section level3"> <h3 id="mixed-effects-models-1-1-0">Mixed-effects models<a class="anchor" aria-label="anchor" href="#mixed-effects-models-1-1-0"></a></h3> <ul><li><p>Reintroduce the interface to saemix version 3.0 (now on CRAN), in particular the generic function ‘saem’ with a generator ‘saem.mmkin’, currently using ‘saemix_model’ and ‘saemix_data’, summary and plot methods</p></li> @@ -191,25 +156,25 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.0.5" id="mkin-105-2021-09-15">mkin 1.0.5 (2021-09-15)<a class="anchor" aria-label="anchor" href="#mkin-105-2021-09-15"></a></h2> +<h2 class="pkg-version" data-toc-text="1.0.5" id="mkin-105-2021-09-15">mkin 1.0.5 (2021-09-15)<a class="anchor" aria-label="anchor" href="#mkin-105-2021-09-15"></a></h2> <ul><li>‘dimethenamid_2018’: Correct the data for the Borstel soil. The five observations from Staudenmaier (2013) that were previously stored as “Borstel 2” are actually just a subset of the 16 observations in “Borstel 1” which is now simply “Borstel”</li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.0.4" id="mkin-104-2021-04-20">mkin 1.0.4 (2021-04-20)<a class="anchor" aria-label="anchor" href="#mkin-104-2021-04-20"></a></h2> +<h2 class="pkg-version" data-toc-text="1.0.4" id="mkin-104-2021-04-20">mkin 1.0.4 (2021-04-20)<a class="anchor" aria-label="anchor" href="#mkin-104-2021-04-20"></a></h2> <ul><li><p>All plotting functions setting graphical parameters: Use on.exit() for resetting graphical parameters</p></li> <li><p>‘plot.mkinfit’: Use xlab and xlim for the residual plot if show_residuals is TRUE</p></li> <li><p>‘mmkin’: Use cores = 1 per default on Windows to make it easier for first time users</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.0.3" id="mkin-103-2021-02-15">mkin 1.0.3 (2021-02-15)<a class="anchor" aria-label="anchor" href="#mkin-103-2021-02-15"></a></h2> +<h2 class="pkg-version" data-toc-text="1.0.3" id="mkin-103-2021-02-15">mkin 1.0.3 (2021-02-15)<a class="anchor" aria-label="anchor" href="#mkin-103-2021-02-15"></a></h2> <ul><li>Review and update README, the ‘Introduction to mkin’ vignette and some of the help pages</li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.0.2" id="mkin-102-unreleased">mkin 1.0.2 (Unreleased)<a class="anchor" aria-label="anchor" href="#mkin-102-unreleased"></a></h2> +<h2 class="pkg-version" data-toc-text="1.0.2" id="mkin-102-unreleased">mkin 1.0.2 (Unreleased)<a class="anchor" aria-label="anchor" href="#mkin-102-unreleased"></a></h2> <ul><li>‘mkinfit’: Keep model names stored in ‘mkinmod’ objects, avoiding their loss in ‘gmkin’</li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.0.1" id="mkin-101-2021-02-10">mkin 1.0.1 (2021-02-10)<a class="anchor" aria-label="anchor" href="#mkin-101-2021-02-10"></a></h2> +<h2 class="pkg-version" data-toc-text="1.0.1" id="mkin-101-2021-02-10">mkin 1.0.1 (2021-02-10)<a class="anchor" aria-label="anchor" href="#mkin-101-2021-02-10"></a></h2> <ul><li><p>‘confint.mmkin’, ‘nlme.mmkin’, ‘transform_odeparms’: Fix example code in dontrun sections that failed with current defaults</p></li> <li><p>‘logLik.mkinfit’: Improve example code to avoid warnings and show convenient syntax</p></li> <li><p>‘mkinresplot’: Re-add Katrin Lindenberger as coauthor who was accidentally removed long ago</p></li> @@ -217,7 +182,7 @@ <li><p>Increase test tolerance for some parameter comparisons that also proved to be platform dependent</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="1.0.0" id="mkin-100-2021-02-03">mkin 1.0.0 (2021-02-03)<a class="anchor" aria-label="anchor" href="#mkin-100-2021-02-03"></a></h2> +<h2 class="pkg-version" data-toc-text="1.0.0" id="mkin-100-2021-02-03">mkin 1.0.0 (2021-02-03)<a class="anchor" aria-label="anchor" href="#mkin-100-2021-02-03"></a></h2> <div class="section level3"> <h3 id="general-1-0-0">General<a class="anchor" aria-label="anchor" href="#general-1-0-0"></a></h3> <ul><li><p>‘mkinmod’ models gain arguments ‘name’ and ‘dll_dir’ which, in conjunction with a current version of the ‘inline’ package, make it possible to still use the DLL used for fast ODE solutions with ‘deSolve’ after saving and restoring the ‘mkinmod’ object.</p></li> @@ -238,7 +203,7 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.50.3" id="mkin-09503-2020-10-08">mkin 0.9.50.3 (2020-10-08)<a class="anchor" aria-label="anchor" href="#mkin-09503-2020-10-08"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.50.3" id="mkin-09503-2020-10-08">mkin 0.9.50.3 (2020-10-08)<a class="anchor" aria-label="anchor" href="#mkin-09503-2020-10-08"></a></h2> <ul><li><p>‘parms’: Add a method for mmkin objects</p></li> <li><p>‘mmkin’ and ‘confint(method = ’profile’): Use all cores detected by parallel::detectCores() per default</p></li> <li><p>‘confint(method = ’profile’): Choose accuracy based on ‘rel_tol’ argument, relative to the bounds obtained by the quadratic approximation</p></li> @@ -250,22 +215,22 @@ <li><p>‘endpoints’: Back-calculate DT50 value from DT90 also for the biphasic models DFOP, HS and SFORB</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.50.2" id="mkin-09502-2020-05-12">mkin 0.9.50.2 (2020-05-12)<a class="anchor" aria-label="anchor" href="#mkin-09502-2020-05-12"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.50.2" id="mkin-09502-2020-05-12">mkin 0.9.50.2 (2020-05-12)<a class="anchor" aria-label="anchor" href="#mkin-09502-2020-05-12"></a></h2> <ul><li><p>Increase tolerance for a platform specific test results on the Solaris test machine on CRAN</p></li> <li><p>Updates and corrections (using the spelling package) to the documentation</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.50.1" id="mkin-09501-2020-05-11">mkin 0.9.50.1 (2020-05-11)<a class="anchor" aria-label="anchor" href="#mkin-09501-2020-05-11"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.50.1" id="mkin-09501-2020-05-11">mkin 0.9.50.1 (2020-05-11)<a class="anchor" aria-label="anchor" href="#mkin-09501-2020-05-11"></a></h2> <ul><li><p>Support SFORB with formation fractions</p></li> <li><p>‘mkinmod’: Make ‘use_of_ff’ = “max” the default</p></li> <li><p>Improve performance by a) avoiding expensive calls in the cost function like merge() and data.frame(), and b) by implementing analytical solutions for SFO-SFO and DFOP-SFO</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.49.11" id="mkin-094911-2020-04-20">mkin 0.9.49.11 (2020-04-20)<a class="anchor" aria-label="anchor" href="#mkin-094911-2020-04-20"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.49.11" id="mkin-094911-2020-04-20">mkin 0.9.49.11 (2020-04-20)<a class="anchor" aria-label="anchor" href="#mkin-094911-2020-04-20"></a></h2> <ul><li>Increase a test tolerance to make it pass on all CRAN check machines</li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.49.10" id="mkin-094910-2020-04-18">mkin 0.9.49.10 (2020-04-18)<a class="anchor" aria-label="anchor" href="#mkin-094910-2020-04-18"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.49.10" id="mkin-094910-2020-04-18">mkin 0.9.49.10 (2020-04-18)<a class="anchor" aria-label="anchor" href="#mkin-094910-2020-04-18"></a></h2> <ul><li><p>‘nlme.mmkin’: An nlme method for mmkin row objects and an associated S3 class with print, plot, anova and endpoint methods</p></li> <li><p>‘mean_degparms, nlme_data, nlme_function’: Three new functions to facilitate building nlme models from mmkin row objects</p></li> <li><p>‘endpoints’: Don’t return the SFORB list component if it’s empty. This reduces distraction and complies with the documentation</p></li> @@ -274,12 +239,12 @@ <li><p>‘summary.mkinfit’: Add AIC, BIC and log likelihood to the summary</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.49.9" id="mkin-09499-2020-03-31">mkin 0.9.49.9 (2020-03-31)<a class="anchor" aria-label="anchor" href="#mkin-09499-2020-03-31"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.49.9" id="mkin-09499-2020-03-31">mkin 0.9.49.9 (2020-03-31)<a class="anchor" aria-label="anchor" href="#mkin-09499-2020-03-31"></a></h2> <ul><li><p>‘mkinmod’: Use pkgbuild::has_compiler instead of Sys.which(‘gcc’), as the latter will often fail even if Rtools are installed</p></li> <li><p>‘mkinds’: Use roxygen for documenting fields and methods of this R6 class</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.49.8" id="mkin-09498-2020-01-09">mkin 0.9.49.8 (2020-01-09)<a class="anchor" aria-label="anchor" href="#mkin-09498-2020-01-09"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.49.8" id="mkin-09498-2020-01-09">mkin 0.9.49.8 (2020-01-09)<a class="anchor" aria-label="anchor" href="#mkin-09498-2020-01-09"></a></h2> <ul><li><p>‘aw’: Generic function for calculating Akaike weights, methods for mkinfit objects and mmkin columns</p></li> <li><p>‘loftest’: Add a lack-of-fit test</p></li> <li><p>‘plot_res’, ‘plot_sep’ and ‘mkinerrplot’: Add the possibility to show standardized residuals and make it the default for fits with error models other than ‘const’</p></li> @@ -287,12 +252,12 @@ <li><p>‘confint.mkinfit’: Make the quadratic approximation the default, as the likelihood profiling takes a lot of time, especially if the fit has more than three parameters</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.49.7" id="mkin-09497-2019-11-01">mkin 0.9.49.7 (2019-11-01)<a class="anchor" aria-label="anchor" href="#mkin-09497-2019-11-01"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.49.7" id="mkin-09497-2019-11-01">mkin 0.9.49.7 (2019-11-01)<a class="anchor" aria-label="anchor" href="#mkin-09497-2019-11-01"></a></h2> <ul><li><p>Fix a bug introduced in 0.9.49.6 that occurred if the direct optimisation yielded a higher likelihood than the three-step optimisation in the d_3 algorithm, which caused the fitted parameters of the three-step optimisation to be returned instead of the parameters of the direct optimisation</p></li> <li><p>Add a ‘nobs’ method for mkinfit objects, enabling the default ‘BIC’ method from the stats package. Also, add a ‘BIC’ method for mmkin column objects.</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.49.6" id="mkin-09496-2019-10-31">mkin 0.9.49.6 (2019-10-31)<a class="anchor" aria-label="anchor" href="#mkin-09496-2019-10-31"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.49.6" id="mkin-09496-2019-10-31">mkin 0.9.49.6 (2019-10-31)<a class="anchor" aria-label="anchor" href="#mkin-09496-2019-10-31"></a></h2> <ul><li><p>Implement a likelihood ratio test as a method for ‘lrtest’ from the lmtest package</p></li> <li><p>Add an ‘update’ method for mkinfit objects which remembers fitted parameters if appropriate</p></li> <li><p>Add a ‘residuals’ method for mkinfit objects that supports scaling based on the error model</p></li> @@ -308,7 +273,7 @@ <li><p>Support summarizing ‘mkinfit’ objects generated with versions < 0.9.49.5</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.49.5" id="mkin-09495-2019-07-04">mkin 0.9.49.5 (2019-07-04)<a class="anchor" aria-label="anchor" href="#mkin-09495-2019-07-04"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.49.5" id="mkin-09495-2019-07-04">mkin 0.9.49.5 (2019-07-04)<a class="anchor" aria-label="anchor" href="#mkin-09495-2019-07-04"></a></h2> <ul><li><p>Several algorithms for minimization of the negative log-likelihood for non-constant error models (two-component and variance by variable). In the case the error model is constant variance, least squares is used as this is more stable. The default algorithm ‘d_3’ tries direct minimization and a three-step procedure, and returns the model with the highest likelihood.</p></li> <li><p>The argument ‘reweight.method’ to mkinfit and mmkin is now obsolete, use ‘error_model’ and ‘error_model_algorithm’ instead</p></li> <li><p>Add a test that checks if we get the best known AIC for parent only fits to 12 test datasets. Add these test datasets for this purpose.</p></li> @@ -323,7 +288,7 @@ <li><p>Add example datasets obtained from risk assessment reports published by the European Food Safety Agency.</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.48.1" id="mkin-09481-2019-03-04">mkin 0.9.48.1 (2019-03-04)<a class="anchor" aria-label="anchor" href="#mkin-09481-2019-03-04"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.48.1" id="mkin-09481-2019-03-04">mkin 0.9.48.1 (2019-03-04)<a class="anchor" aria-label="anchor" href="#mkin-09481-2019-03-04"></a></h2> <ul><li><p>Add the function ‘logLik.mkinfit’ which makes it possible to calculate an AIC for mkinfit objects</p></li> <li><p>Add the function ‘AIC.mmkin’ to make it easy to compare columns of mmkin objects</p></li> <li><p>‘add_err’: Respect the argument giving the number of replicates in the synthetic dataset</p></li> @@ -336,23 +301,23 @@ <li><p>‘nafta’: Add evaluations according to the NAFTA guidance</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.47.5" id="mkin-09475-2018-09-14">mkin 0.9.47.5 (2018-09-14)<a class="anchor" aria-label="anchor" href="#mkin-09475-2018-09-14"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.47.5" id="mkin-09475-2018-09-14">mkin 0.9.47.5 (2018-09-14)<a class="anchor" aria-label="anchor" href="#mkin-09475-2018-09-14"></a></h2> <ul><li><p>Make the two-component error model stop in cases where it is inadequate to avoid nls crashes on windows</p></li> <li><p>Move two vignettes to a location where they will not be built on CRAN (to avoid more NOTES from long execution times)</p></li> <li><p>Exclude more example code from testing on CRAN to avoid NOTES from long execution times</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.47.3" id="mkin-09473">mkin 0.9.47.3<a class="anchor" aria-label="anchor" href="#mkin-09473"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.47.3" id="mkin-09473">mkin 0.9.47.3<a class="anchor" aria-label="anchor" href="#mkin-09473"></a></h2> <ul><li><p>‘mkinfit’: Improve fitting the error model for reweight.method = ‘tc’. Add ‘manual’ to possible arguments for ‘weight’</p></li> <li><p>Test that FOCUS_2006_C can be evaluated with DFOP and reweight.method = ‘tc’</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.47.2" id="mkin-09472-2018-07-19">mkin 0.9.47.2 (2018-07-19)<a class="anchor" aria-label="anchor" href="#mkin-09472-2018-07-19"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.47.2" id="mkin-09472-2018-07-19">mkin 0.9.47.2 (2018-07-19)<a class="anchor" aria-label="anchor" href="#mkin-09472-2018-07-19"></a></h2> <ul><li><p>‘sigma_twocomp’: Rename ‘sigma_rl’ to ‘sigma_twocomp’ as the Rocke and Lorenzato model assumes lognormal distribution for large y. Correct references to the Rocke and Lorenzato model accordingly.</p></li> <li><p>‘mkinfit’: Use 1.1 as starting value for N parameter of IORE models to obtain convergence in more difficult cases. Show parameter names when ‘trace_parms’ is ‘TRUE’.</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.47.1" id="mkin-09471-2018-02-06">mkin 0.9.47.1 (2018-02-06)<a class="anchor" aria-label="anchor" href="#mkin-09471-2018-02-06"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.47.1" id="mkin-09471-2018-02-06">mkin 0.9.47.1 (2018-02-06)<a class="anchor" aria-label="anchor" href="#mkin-09471-2018-02-06"></a></h2> <ul><li><p>Skip some tests on CRAN and winbuilder to avoid timeouts</p></li> <li><p>‘test_data_from_UBA_2014’: Added this list of datasets containing experimental data used in the expertise from 2014</p></li> <li><p>‘mkinfit’: Added the iterative reweighting method ‘tc’ using the two-component error model from Rocke and Lorenzato. NA values in the data are not returned any more.</p></li> @@ -361,41 +326,41 @@ <li><p>‘summary.mkinfit’: Show versions of mkin and R used for fitting (not the ones used for the summary) if the fit was generated with mkin >= 0.9.47.1</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.46.3" id="mkin-09463-2017-11-16">mkin 0.9.46.3 (2017-11-16)<a class="anchor" aria-label="anchor" href="#mkin-09463-2017-11-16"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.46.3" id="mkin-09463-2017-11-16">mkin 0.9.46.3 (2017-11-16)<a class="anchor" aria-label="anchor" href="#mkin-09463-2017-11-16"></a></h2> <ul><li><p><code>README.md</code>, <code>vignettes/mkin.Rmd</code>: URLs were updated</p></li> <li><p><code>synthetic_data_for_UBA</code>: Add the code used to generate the data in the interest of reproducibility</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.46.2" id="mkin-09462-2017-10-10">mkin 0.9.46.2 (2017-10-10)<a class="anchor" aria-label="anchor" href="#mkin-09462-2017-10-10"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.46.2" id="mkin-09462-2017-10-10">mkin 0.9.46.2 (2017-10-10)<a class="anchor" aria-label="anchor" href="#mkin-09462-2017-10-10"></a></h2> <ul><li><p>Converted the vignette FOCUS_Z from tex/pdf to markdown/html</p></li> <li><p><code>DESCRIPTION</code>: Add ORCID</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.46.1" id="mkin-09461-2017-09-14">mkin 0.9.46.1 (2017-09-14)<a class="anchor" aria-label="anchor" href="#mkin-09461-2017-09-14"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.46.1" id="mkin-09461-2017-09-14">mkin 0.9.46.1 (2017-09-14)<a class="anchor" aria-label="anchor" href="#mkin-09461-2017-09-14"></a></h2> <ul><li><p><code>plot.mkinfit</code>: Fix scaling of residual plots for the case of separate plots for each observed variable</p></li> <li><p><code>plot.mkinfit</code>: Use all data points of the fitted curve for y axis scaling for the case of separate plots for each observed variable</p></li> <li><p>Documentation updates</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.46" id="mkin-0946-2017-07-24">mkin 0.9.46 (2017-07-24)<a class="anchor" aria-label="anchor" href="#mkin-0946-2017-07-24"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.46" id="mkin-0946-2017-07-24">mkin 0.9.46 (2017-07-24)<a class="anchor" aria-label="anchor" href="#mkin-0946-2017-07-24"></a></h2> <ul><li>Remove <code>test_FOMC_ill-defined.R</code> as it is too platform dependent</li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.45.2" id="mkin-09452-2017-07-24">mkin 0.9.45.2 (2017-07-24)<a class="anchor" aria-label="anchor" href="#mkin-09452-2017-07-24"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.45.2" id="mkin-09452-2017-07-24">mkin 0.9.45.2 (2017-07-24)<a class="anchor" aria-label="anchor" href="#mkin-09452-2017-07-24"></a></h2> <ul><li><p>Rename <code>twa</code> to <code>max_twa_parent</code> to avoid conflict with <code>twa</code> from my <code>pfm</code> package</p></li> <li><p>Update URLs in documentation</p></li> <li><p>Limit test code to one core to pass on windows</p></li> <li><p>Switch from <code>microbenchmark</code> to <code>rbenchmark</code> as the former is not supported on all platforms</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.45.1" id="mkin-09451-2016-12-20">mkin 0.9.45.1 (2016-12-20)<a class="anchor" aria-label="anchor" href="#mkin-09451-2016-12-20"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.45.1" id="mkin-09451-2016-12-20">mkin 0.9.45.1 (2016-12-20)<a class="anchor" aria-label="anchor" href="#mkin-09451-2016-12-20"></a></h2> <div class="section level3"> <h3 id="new-features-0-9-45-1">New features<a class="anchor" aria-label="anchor" href="#new-features-0-9-45-1"></a></h3> <ul><li>A <code>twa</code> function, calculating maximum time weighted average concentrations for the parent (SFO, FOMC and DFOP).</li> </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.45" id="mkin-0945-2016-12-08">mkin 0.9.45 (2016-12-08)<a class="anchor" aria-label="anchor" href="#mkin-0945-2016-12-08"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.45" id="mkin-0945-2016-12-08">mkin 0.9.45 (2016-12-08)<a class="anchor" aria-label="anchor" href="#mkin-0945-2016-12-08"></a></h2> <div class="section level3"> <h3 id="minor-changes-0-9-45">Minor changes<a class="anchor" aria-label="anchor" href="#minor-changes-0-9-45"></a></h3> <ul><li><p><code>plot.mkinfit</code> and <code>plot.mmkin</code>: If the plotting device is <code>tikz</code>, LaTeX markup is being used for the chi2 error in the graphs.</p></li> @@ -404,14 +369,14 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.44" id="mkin-0944-2016-06-29">mkin 0.9.44 (2016-06-29)<a class="anchor" aria-label="anchor" href="#mkin-0944-2016-06-29"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.44" id="mkin-0944-2016-06-29">mkin 0.9.44 (2016-06-29)<a class="anchor" aria-label="anchor" href="#mkin-0944-2016-06-29"></a></h2> <div class="section level3"> <h3 id="bug-fixes-0-9-44">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-44"></a></h3> <ul><li>The test <code>test_FOMC_ill-defined</code> failed on several architectures, so the test is now skipped</li> </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.43" id="mkin-0943-2016-06-28">mkin 0.9.43 (2016-06-28)<a class="anchor" aria-label="anchor" href="#mkin-0943-2016-06-28"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.43" id="mkin-0943-2016-06-28">mkin 0.9.43 (2016-06-28)<a class="anchor" aria-label="anchor" href="#mkin-0943-2016-06-28"></a></h2> <div class="section level3"> <h3 id="major-changes-0-9-43">Major changes<a class="anchor" aria-label="anchor" href="#major-changes-0-9-43"></a></h3> <ul><li><p>The title was changed to <code>Kinetic evaluations of chemical degradation data</code></p></li> @@ -439,7 +404,7 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9.42" id="mkin-0942-2016-03-25">mkin 0.9.42 (2016-03-25)<a class="anchor" aria-label="anchor" href="#mkin-0942-2016-03-25"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9.42" id="mkin-0942-2016-03-25">mkin 0.9.42 (2016-03-25)<a class="anchor" aria-label="anchor" href="#mkin-0942-2016-03-25"></a></h2> <div class="section level3"> <h3 id="major-changes-0-9-42">Major changes<a class="anchor" aria-label="anchor" href="#major-changes-0-9-42"></a></h3> <ul><li>Add the argument <code>from_max_mean</code> to <code>mkinfit</code>, for fitting only the decline from the maximum observed value for models with a single observed variable</li> @@ -452,7 +417,7 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-41" id="mkin-09-41-2015-11-09">mkin 0.9-41 (2015-11-09)<a class="anchor" aria-label="anchor" href="#mkin-09-41-2015-11-09"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-41" id="mkin-09-41-2015-11-09">mkin 0.9-41 (2015-11-09)<a class="anchor" aria-label="anchor" href="#mkin-09-41-2015-11-09"></a></h2> <div class="section level3"> <h3 id="minor-changes-0-9-41">Minor changes<a class="anchor" aria-label="anchor" href="#minor-changes-0-9-41"></a></h3> <ul><li><p>Add an R6 class <code>mkinds</code> representing datasets with a printing method</p></li> @@ -467,7 +432,7 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-40" id="mkin-09-40-2015-07-21">mkin 0.9-40 (2015-07-21)<a class="anchor" aria-label="anchor" href="#mkin-09-40-2015-07-21"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-40" id="mkin-09-40-2015-07-21">mkin 0.9-40 (2015-07-21)<a class="anchor" aria-label="anchor" href="#mkin-09-40-2015-07-21"></a></h2> <div class="section level3"> <h3 id="bug-fixes-0-9-40">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-40"></a></h3> <ul><li> @@ -480,7 +445,7 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-39" id="mkin-09-39-2015-06-26">mkin 0.9-39 (2015-06-26)<a class="anchor" aria-label="anchor" href="#mkin-09-39-2015-06-26"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-39" id="mkin-09-39-2015-06-26">mkin 0.9-39 (2015-06-26)<a class="anchor" aria-label="anchor" href="#mkin-09-39-2015-06-26"></a></h2> <div class="section level3"> <h3 id="major-changes-0-9-39">Major changes<a class="anchor" aria-label="anchor" href="#major-changes-0-9-39"></a></h3> <ul><li><p>New function <code><a href="../reference/mmkin.html">mmkin()</a></code>: This function takes a character vector of model shorthand names, or alternatively a list of mkinmod models, as well as a list of dataset as main arguments. It returns a matrix of mkinfit objects, with a row for each model and a column for each dataset. A subsetting method with single brackets is available. Fitting the models in parallel using the <code>parallel</code> package is supported.</p></li> @@ -493,7 +458,7 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-38" id="mkin-09-38-2015-06-24">mkin 0.9-38 (2015-06-24)<a class="anchor" aria-label="anchor" href="#mkin-09-38-2015-06-24"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-38" id="mkin-09-38-2015-06-24">mkin 0.9-38 (2015-06-24)<a class="anchor" aria-label="anchor" href="#mkin-09-38-2015-06-24"></a></h2> <div class="section level3"> <h3 id="minor-changes-0-9-38">Minor changes<a class="anchor" aria-label="anchor" href="#minor-changes-0-9-38"></a></h3> <ul><li><p><code>vignettes/compiled_models.html</code>: Show the performance improvement factor actually obtained when building the vignette, as well as mkin version, some system info and the CPU model used for building the vignette.</p></li> @@ -506,7 +471,7 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-36" id="mkin-09-36-2015-06-21">mkin 0.9-36 (2015-06-21)<a class="anchor" aria-label="anchor" href="#mkin-09-36-2015-06-21"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-36" id="mkin-09-36-2015-06-21">mkin 0.9-36 (2015-06-21)<a class="anchor" aria-label="anchor" href="#mkin-09-36-2015-06-21"></a></h2> <div class="section level3"> <h3 id="major-changes-0-9-36">Major changes<a class="anchor" aria-label="anchor" href="#major-changes-0-9-36"></a></h3> <ul><li><p><code><a href="../reference/summary.mkinfit.html">summary.mkinfit()</a></code>: A one-sided t-test for significant difference of untransformed parameters from zero is now always shown, based on the assumption of normal distribution for estimators of all untransformed parameters. Use with caution, as this assumption is unrealistic e.g. for rate constants in these nonlinear kinetic models.</p></li> @@ -520,7 +485,7 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-35" id="mkin-09-35-2015-05-15">mkin 0.9-35 (2015-05-15)<a class="anchor" aria-label="anchor" href="#mkin-09-35-2015-05-15"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-35" id="mkin-09-35-2015-05-15">mkin 0.9-35 (2015-05-15)<a class="anchor" aria-label="anchor" href="#mkin-09-35-2015-05-15"></a></h2> <div class="section level3"> <h3 id="major-changes-0-9-35">Major changes<a class="anchor" aria-label="anchor" href="#major-changes-0-9-35"></a></h3> <ul><li>Switch from RUnit to testthat for testing</li> @@ -541,7 +506,7 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-34" id="mkin-09-34-2014-11-22">mkin 0.9-34 (2014-11-22)<a class="anchor" aria-label="anchor" href="#mkin-09-34-2014-11-22"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-34" id="mkin-09-34-2014-11-22">mkin 0.9-34 (2014-11-22)<a class="anchor" aria-label="anchor" href="#mkin-09-34-2014-11-22"></a></h2> <div class="section level3"> <h3 id="new-features-0-9-34">New features<a class="anchor" aria-label="anchor" href="#new-features-0-9-34"></a></h3> <ul><li><p>Add the convenience function <code><a href="../reference/mkinmod.html">mkinsub()</a></code> for creating the lists used in <code><a href="../reference/mkinmod.html">mkinmod()</a></code></p></li> @@ -555,7 +520,7 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-33" id="mkin-09-33-2014-10-22">mkin 0.9-33 (2014-10-22)<a class="anchor" aria-label="anchor" href="#mkin-09-33-2014-10-22"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-33" id="mkin-09-33-2014-10-22">mkin 0.9-33 (2014-10-22)<a class="anchor" aria-label="anchor" href="#mkin-09-33-2014-10-22"></a></h2> <div class="section level3"> <h3 id="new-features-0-9-33">New features<a class="anchor" aria-label="anchor" href="#new-features-0-9-33"></a></h3> <ul><li><p>The initial value (state.ini) for the observed variable with the highest observed residue is set to 100 in case it has no time zero observation and <code>state.ini = "auto"</code></p></li> @@ -577,7 +542,7 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-32" id="mkin-09-32-2014-07-24">mkin 0.9-32 (2014-07-24)<a class="anchor" aria-label="anchor" href="#mkin-09-32-2014-07-24"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-32" id="mkin-09-32-2014-07-24">mkin 0.9-32 (2014-07-24)<a class="anchor" aria-label="anchor" href="#mkin-09-32-2014-07-24"></a></h2> <div class="section level3"> <h3 id="new-features-0-9-32">New features<a class="anchor" aria-label="anchor" href="#new-features-0-9-32"></a></h3> <ul><li><p>The number of degrees of freedom is difficult to define in the case of ilr transformation of formation fractions. Now for each source compartment the number of ilr parameters (=number of optimised parameters) is divided by the number of pathways to metabolites (=number of affected data series) which leads to fractional degrees of freedom in some cases.</p></li> @@ -603,14 +568,14 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-31" id="mkin-09-31-2014-07-14">mkin 0.9-31 (2014-07-14)<a class="anchor" aria-label="anchor" href="#mkin-09-31-2014-07-14"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-31" id="mkin-09-31-2014-07-14">mkin 0.9-31 (2014-07-14)<a class="anchor" aria-label="anchor" href="#mkin-09-31-2014-07-14"></a></h2> <div class="section level3"> <h3 id="bug-fixes-0-9-31">Bug fixes<a class="anchor" aria-label="anchor" href="#bug-fixes-0-9-31"></a></h3> <ul><li>The internal renaming of optimised parameters in Version 0.9-30 led to errors in the determination of the degrees of freedom for the chi2 error level calulations in <code><a href="../reference/mkinerrmin.html">mkinerrmin()</a></code> used by the summary function.</li> </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-30" id="mkin-09-30-2014-07-11">mkin 0.9-30 (2014-07-11)<a class="anchor" aria-label="anchor" href="#mkin-09-30-2014-07-11"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-30" id="mkin-09-30-2014-07-11">mkin 0.9-30 (2014-07-11)<a class="anchor" aria-label="anchor" href="#mkin-09-30-2014-07-11"></a></h2> <div class="section level3"> <h3 id="new-features-0-9-30">New features<a class="anchor" aria-label="anchor" href="#new-features-0-9-30"></a></h3> <ul><li>It is now possible to use formation fractions in combination with turning off the sink in <code><a href="../reference/mkinmod.html">mkinmod()</a></code>.</li> @@ -631,19 +596,19 @@ </ul></div> </div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-29" id="mkin-09-29-2014-06-27">mkin 0.9-29 (2014-06-27)<a class="anchor" aria-label="anchor" href="#mkin-09-29-2014-06-27"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-29" id="mkin-09-29-2014-06-27">mkin 0.9-29 (2014-06-27)<a class="anchor" aria-label="anchor" href="#mkin-09-29-2014-06-27"></a></h2> <ul><li><p>R/mkinresplot.R: Make it possible to specify <code>xlim</code></p></li> <li><p>R/geometric_mean.R, man/geometric_mean.Rd: Add geometric mean function</p></li> <li><p>R/endpoints.R, man/endpoints.Rd: Calculate additional (pseudo)-DT50 values for FOMC, DFOP, HS and SFORB. Avoid calculation of formation fractions from rate constants when they are directly fitted</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-28" id="mkin-09-28-2014-05-20">mkin 0.9-28 (2014-05-20)<a class="anchor" aria-label="anchor" href="#mkin-09-28-2014-05-20"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-28" id="mkin-09-28-2014-05-20">mkin 0.9-28 (2014-05-20)<a class="anchor" aria-label="anchor" href="#mkin-09-28-2014-05-20"></a></h2> <ul><li><p>Do not backtransform confidence intervals for formation fractions if more than one compound is formed, as such parameters only define the pathways as a set</p></li> <li><p>Add historical remarks and some background to the main package vignette</p></li> <li><p>Correct ‘isotropic’ into ‘isometric’ for the ilr transformation</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-27" id="mkin-09-27-2014-05-10">mkin 0.9-27 (2014-05-10)<a class="anchor" aria-label="anchor" href="#mkin-09-27-2014-05-10"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-27" id="mkin-09-27-2014-05-10">mkin 0.9-27 (2014-05-10)<a class="anchor" aria-label="anchor" href="#mkin-09-27-2014-05-10"></a></h2> <ul><li><p>Fork the GUI into a separate package <a href="https://github.com/jranke/gmkin" class="external-link">gmkin</a></p></li> <li><p>DESCRIPTION, NAMESPACE, TODO: Adapt and add copyright information</p></li> <li><p>Remove files belonging to the GUI</p></li> @@ -663,13 +628,13 @@ <li><p>Add gmkin workspace datasets FOCUS_2006_gmkin and FOCUS_2006_Z_gmkin</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-24" id="mkin-09-24-2013-11-06">mkin 0.9-24 (2013-11-06)<a class="anchor" aria-label="anchor" href="#mkin-09-24-2013-11-06"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-24" id="mkin-09-24-2013-11-06">mkin 0.9-24 (2013-11-06)<a class="anchor" aria-label="anchor" href="#mkin-09-24-2013-11-06"></a></h2> <ul><li><p>Bugfix re-enabling the fixing of any combination of initial values for state variables</p></li> <li><p>Default values for kinetic rate constants are not all 0.1 any more but are “salted” with a small increment to avoid numeric artefacts with the eigenvalue based solutions</p></li> <li><p>Backtransform fixed ODE parameters for the summary</p></li> </ul></div> <div class="section level2"> -<h2 class="page-header" data-toc-text="0.9-22" id="mkin-09-22-2013-10-26">mkin 0.9-22 (2013-10-26)<a class="anchor" aria-label="anchor" href="#mkin-09-22-2013-10-26"></a></h2> +<h2 class="pkg-version" data-toc-text="0.9-22" id="mkin-09-22-2013-10-26">mkin 0.9-22 (2013-10-26)<a class="anchor" aria-label="anchor" href="#mkin-09-22-2013-10-26"></a></h2> <ul><li><p>Get rid of the optimisation step in <code>mkinerrmin</code> - this was unnecessary. Thanks to KinGUII for the inspiration - actually this is equation 6-2 in FOCUS kinetics p. 91 that I had overlooked originally</p></li> <li><p>Fix <code>plot.mkinfit</code> as it passed graphical arguments like main to the solver</p></li> <li><p>Do not use <code>plot=TRUE</code> in <code><a href="../reference/mkinfit.html">mkinfit()</a></code> example</p></li> @@ -683,28 +648,22 @@ <li><p>Do not use 0 values at time zero for chi2 error level calculations. This is the way it is done in KinGUII and it makes sense. It does impact the chi2 error levels in the output. Generally they seem to be lower for metabolites now, presumably because the mean of the observed values is higher</p></li> </ul><p>For a detailed list of changes to the mkin source please consult the commit history on <a href="http://github.com/jranke/mkin" class="external-link uri">http://github.com/jranke/mkin</a></p> </div> - </div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> - - - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/pkgdown.js b/docs/pkgdown.js index 6f0eee40..5fccd9c0 100644 --- a/docs/pkgdown.js +++ b/docs/pkgdown.js @@ -2,70 +2,30 @@ (function($) { $(function() { - $('.navbar-fixed-top').headroom(); + $('nav.navbar').headroom(); - $('body').css('padding-top', $('.navbar').height() + 10); - $(window).resize(function(){ - $('body').css('padding-top', $('.navbar').height() + 10); + Toc.init({ + $nav: $("#toc"), + $scope: $("main h2, main h3, main h4, main h5, main h6") }); - $('[data-toggle="tooltip"]').tooltip(); - - var cur_path = paths(location.pathname); - var links = $("#navbar ul li a"); - var max_length = -1; - var pos = -1; - for (var i = 0; i < links.length; i++) { - if (links[i].getAttribute("href") === "#") - continue; - // Ignore external links - if (links[i].host !== location.host) - continue; - - var nav_path = paths(links[i].pathname); - - var length = prefix_length(nav_path, cur_path); - if (length > max_length) { - max_length = length; - pos = i; - } - } - - // Add class to parent <li>, and enclosing <li> if in dropdown - if (pos >= 0) { - var menu_anchor = $(links[pos]); - menu_anchor.parent().addClass("active"); - menu_anchor.closest("li.dropdown").addClass("active"); - } - }); - - function paths(pathname) { - var pieces = pathname.split("/"); - pieces.shift(); // always starts with / - - var end = pieces[pieces.length - 1]; - if (end === "index.html" || end === "") - pieces.pop(); - return(pieces); - } - - // Returns -1 if not found - function prefix_length(needle, haystack) { - if (needle.length > haystack.length) - return(-1); - - // Special case for length-0 haystack, since for loop won't run - if (haystack.length === 0) { - return(needle.length === 0 ? 0 : -1); + if ($('#toc').length) { + $('body').scrollspy({ + target: '#toc', + offset: $("nav.navbar").outerHeight() + 1 + }); } - for (var i = 0; i < haystack.length; i++) { - if (needle[i] != haystack[i]) - return(i); - } + // Activate popovers + $('[data-bs-toggle="popover"]').popover({ + container: 'body', + html: true, + trigger: 'focus', + placement: "top", + sanitize: false, + }); - return(haystack.length); - } + $('[data-bs-toggle="tooltip"]').tooltip(); /* Clipboard --------------------------*/ @@ -78,7 +38,7 @@ if(ClipboardJS.isSupported()) { $(document).ready(function() { - var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-label='Copy to clipboard' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy'></i></button>"; + var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' title='Copy to clipboard' aria-label='Copy to clipboard' data-toggle='tooltip' data-placement='left' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy'></i></button>"; $("div.sourceCode").addClass("hasCopyButton"); @@ -89,20 +49,108 @@ $('.btn-copy-ex').tooltip({container: 'body'}); // Initialize clipboard: - var clipboardBtnCopies = new 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<main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Calculate the AIC for a column of an mmkin object</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/AIC.mmkin.R" class="external-link"><code>R/AIC.mmkin.R</code></a></small> + <div class="d-none name"><code>AIC.mmkin.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Provides a convenient way to compare different kinetic models fitted to the same dataset.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mmkin</span></span> <span><span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span>, k <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span> <span></span> @@ -122,8 +89,8 @@ same dataset.</p> <span><span class="fu"><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">BIC</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>An object of class <code><a href="mmkin.html">mmkin</a></code>, containing only one column.</p></dd> @@ -137,20 +104,20 @@ column.</p></dd> <dd><p>As in the generic method</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>As in the generic method (a numeric value for single fits, or a dataframe if there are several fits in the column).</p> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span> <span class="co"># skip, as it takes > 10 s on winbuilder</span></span></span> <span class="r-in"><span> <span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>,</span></span> @@ -199,26 +166,22 @@ dataframe if there are several fits in the column).</p> <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/CAKE_export.html b/docs/reference/CAKE_export.html index 92cb2755..a9aac1ef 100644 --- a/docs/reference/CAKE_export.html +++ 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list of datasets format to a CAKE study file</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/CAKE_export.R" class="external-link"><code>R/CAKE_export.R</code></a></small> + <div class="d-none name"><code>CAKE_export.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>In addition to the datasets, the pathways in the degradation model can be specified as well.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">CAKE_export</span><span class="op">(</span></span> <span> <span class="va">ds</span>,</span> <span> map <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>parent <span class="op">=</span> <span class="st">"Parent"</span><span class="op">)</span>,</span> @@ -132,8 +99,8 @@ specified as well.</p> <span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>ds</dt> <dd><p>A named list of datasets in long format as compatible with <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd> @@ -191,37 +158,33 @@ compatible with CAKE.</p></dd> <dd><p>Can be OLS or IRLS.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>The function is called for its side effect.</p> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> </div> - </div> - <div 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http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 — D24_2014 • 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" 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href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 — D24_2014"><meta property="og:description" content="The five datasets were extracted from the active substance evaluation dossier +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="The five datasets were extracted from the active substance evaluation dossier +published by EFSA. Kinetic evaluations shown for these datasets are intended +to illustrate and advance kinetic modelling. 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<div class="hidden name"><code>D24_2014.Rd</code></div> + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Aerobic soil degradation data on 2,4-D from the EU assessment in 2014</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/D24_2014.R" class="external-link"><code>R/D24_2014.R</code></a></small> + <div class="d-none name"><code>D24_2014.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>The five datasets were extracted from the active substance evaluation dossier published by EFSA. Kinetic evaluations shown for these datasets are intended to illustrate and advance kinetic modelling. The fact that these data and @@ -119,23 +92,24 @@ context of pesticide registrations, as the use of the data may be constrained by data protection regulations.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">D24_2014</span></span></code></pre></div> </div> - <div id="format"> - <h2>Format</h2> + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>An <a href="mkindsg.html">mkindsg</a> object grouping five datasets</p> </div> - <div id="source"> - <h2>Source</h2> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <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 https://open.efsa.europa.eu/study-inventory/EFSA-Q-2013-00811</p> </div> - <div id="details"> - <h2>Details</h2> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <p>Data for the first dataset are from p. 685. Data for the other four datasets were used in the preprocessed versions given in the kinetics section (p. 761ff.), with the exception of residues smaller than 1 for DCP @@ -145,8 +119,8 @@ in the 'dataset_generation' directory. In the code, page numbers are given for specific pieces of information in the comments.</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">D24_2014</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> <mkindsg> holding 5 mkinds objects</span> <span class="r-out co"><span class="r-pr">#></span> Title $title: Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 </span> @@ -235,26 +209,22 @@ specific pieces of information in the comments.</p> <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/DFOP.solution-1.png b/docs/reference/DFOP.solution-1.png Binary files differindex 5ebba336..6b78836f 100644 --- a/docs/reference/DFOP.solution-1.png +++ b/docs/reference/DFOP.solution-1.png diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index b526ac9e..62b78f3e 100644 --- a/docs/reference/DFOP.solution.html +++ 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data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Double First-Order in Parallel kinetics</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/parent_solutions.R" class="external-link"><code>R/parent_solutions.R</code></a></small> - <div class="hidden name"><code>DFOP.solution.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Double First-Order in Parallel kinetics</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/parent_solutions.R" class="external-link"><code>R/parent_solutions.R</code></a></small> + <div class="d-none name"><code>DFOP.solution.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Function describing decline from a defined starting value using the sum of two exponential decline functions.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">DFOP.solution</span><span class="op">(</span><span class="va">t</span>, <span class="va">parent_0</span>, <span class="va">k1</span>, <span class="va">k2</span>, <span class="va">g</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>t</dt> <dd><p>Time.</p></dd> @@ -141,14 +108,14 @@ two exponential decline functions.</p> kinetic constant.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>The value of the response variable at time <code>t</code>.</p> </div> - <div id="references"> - <h2>References</h2> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, @@ -160,8 +127,8 @@ EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, Version 1.1, 18 December 2014 <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> </div> - <div id="see-also"> - <h2>See also</h2> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <div class="dont-index"><p>Other parent solutions: <code><a href="FOMC.solution.html">FOMC.solution</a>()</code>, <code><a href="HS.solution.html">HS.solution</a>()</code>, @@ -171,34 +138,30 @@ Version 1.1, 18 December 2014 <code><a href="logistic.solution.html">logistic.solution</a>()</code></p></div> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></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/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">DFOP.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">5</span>, <span class="fl">0.5</span>, <span class="fl">0.3</span><span class="op">)</span>, <span class="fl">0</span>, <span class="fl">4</span>, ylim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>,<span class="fl">100</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="DFOP.solution-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" 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evaluations with (generalised) nonlinear least squares</h6> + <a class="dropdown-item" href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + <a class="dropdown-item" href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + <a class="dropdown-item" href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Example evaluations with hierarchical models (nonlinear mixed-effects models)</h6> + <a class="dropdown-item" href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> + <a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> + <a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Performance</h6> + <a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a class="dropdown-item" href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + <a class="dropdown-item" href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6> + <a class="dropdown-item" href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a class="dropdown-item" href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </div> </li> - </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> +<li class="nav-item"> + <a class="nav-link" href="../news/index.html">News</a> +</li> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Subsetting method for mmkin objects</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mmkin.R" class="external-link"><code>R/mmkin.R</code></a></small> - <div class="hidden name"><code>Extract.mmkin.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Subsetting method for mmkin objects</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mmkin.R" class="external-link"><code>R/mmkin.R</code></a></small> + <div class="d-none name"><code>Extract.mmkin.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Subsetting method for mmkin objects</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre><code># S3 method for mmkin [(x, i, j, ..., drop = FALSE)</code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>x</dt> <dd><p>An <code><a href="mmkin.html">mmkin</a> object</code></p></dd> @@ -140,19 +106,19 @@ either a list of mkinfit objects or a single mkinfit object.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>An object of class <code><a href="mmkin.html">mmkin</a></code>.</p> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span> <span class="co"># Only use one core, to pass R CMD check --as-cran</span></span></span> <span class="r-in"><span> <span class="va">fits</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span><span class="op">)</span>, <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>B <span class="op">=</span> <span class="va">FOCUS_2006_B</span>, C <span class="op">=</span> <span class="va">FOCUS_2006_C</span><span class="op">)</span>,</span></span> @@ -212,26 +178,22 @@ either a list of mkinfit objects or a single mkinfit object.</p></dd> <span class="r-out co"><span class="r-pr">#></span> </span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html index 2483a632..62059414 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -1,118 +1,87 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" 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the resulting DT50 and DT90 values +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="A table with the fitted parameters and the resulting DT50 and DT90 values +generated with different software packages. 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The results from fitting the data with the Topfit software was removed, as the initial concentration of the parent compound was fixed to a value of 100 in this fit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--></head><body data-spy="scroll" data-target="#toc"> +<![endif]--></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - <div class="container template-reference-topic"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> - 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</ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - + </ul></div> - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)</h1> - <div class="hidden name"><code>FOCUS_2006_DFOP_ref_A_to_B.Rd</code></div> + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)</h1> + + <div class="d-none name"><code>FOCUS_2006_DFOP_ref_A_to_B.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). The results from fitting the data with the Topfit software was removed, as @@ -120,12 +89,13 @@ the initial concentration of the parent compound was fixed to a value of 100 in this fit.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">FOCUS_2006_DFOP_ref_A_to_B</span></span></code></pre></div> </div> - <div id="format"> - <h2>Format</h2> + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>A data frame containing the following variables.</p><dl><dt><code>package</code></dt> <dd><p>a factor giving the name of the software package</p></dd> @@ -152,8 +122,8 @@ in this fit.</p> </dl></div> - <div id="source"> - <h2>Source</h2> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, @@ -161,31 +131,27 @@ in this fit.</p> <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">FOCUS_2006_DFOP_ref_A_to_B</span><span class="op">)</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html index d3ee5aba..3aca90d2 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -1,118 +1,87 @@ <!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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</ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - + </ul></div> - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)</h1> - <div class="hidden name"><code>FOCUS_2006_FOMC_ref_A_to_F.Rd</code></div> + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)</h1> + + <div class="d-none name"><code>FOCUS_2006_FOMC_ref_A_to_F.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). The results from fitting the data with the Topfit software was removed, as @@ -120,12 +89,13 @@ the initial concentration of the parent compound was fixed to a value of 100 in this fit.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">FOCUS_2006_FOMC_ref_A_to_F</span></span></code></pre></div> </div> - <div id="format"> - <h2>Format</h2> + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>A data frame containing the following variables.</p><dl><dt><code>package</code></dt> <dd><p>a factor giving the name of the software package</p></dd> @@ -149,8 +119,8 @@ in this fit.</p> </dl></div> - <div id="source"> - <h2>Source</h2> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, @@ -158,31 +128,27 @@ in this fit.</p> <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">FOCUS_2006_FOMC_ref_A_to_F</span><span class="op">)</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html index cb563cdf..d7e0d269 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -1,118 +1,87 @@ <!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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<div class="ref-description"> + <div class="ref-description section level2"> <p>A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). The results from fitting the data with the Topfit software was removed, as @@ -120,12 +89,13 @@ the initial concentration of the parent compound was fixed to a value of 100 in this fit.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">FOCUS_2006_HS_ref_A_to_F</span></span></code></pre></div> </div> - <div id="format"> - <h2>Format</h2> + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>A data frame containing the following variables.</p><dl><dt><code>package</code></dt> <dd><p>a factor giving the name of the software package</p></dd> @@ -152,8 +122,8 @@ in this fit.</p> </dl></div> - <div id="source"> - <h2>Source</h2> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, @@ -161,31 +131,27 @@ in this fit.</p> <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">FOCUS_2006_HS_ref_A_to_F</span><span class="op">)</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html index 93fc9030..b92d94d4 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -1,118 +1,87 @@ <!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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<div class="ref-description"> + <div class="ref-description section level2"> <p>A table with the fitted parameters and the resulting DT50 and DT90 values generated with different software packages. Taken directly from FOCUS (2006). The results from fitting the data with the Topfit software was removed, as @@ -120,12 +89,13 @@ the initial concentration of the parent compound was fixed to a value of 100 in this fit.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">FOCUS_2006_SFO_ref_A_to_F</span></span></code></pre></div> </div> - <div id="format"> - <h2>Format</h2> + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>A data frame containing the following variables.</p><dl><dt><code>package</code></dt> <dd><p>a factor giving the name of the software package</p></dd> @@ -146,8 +116,8 @@ in this fit.</p> </dl></div> - <div id="source"> - <h2>Source</h2> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, @@ -155,31 +125,27 @@ in this fit.</p> <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">FOCUS_2006_SFO_ref_A_to_F</span><span class="op">)</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index f1343c5c..72d9c7db 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -1,118 +1,84 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta 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id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">FOCUS_2006_A</span></span> <span> <span class="va">FOCUS_2006_B</span></span> <span> <span class="va">FOCUS_2006_C</span></span> @@ -121,8 +87,8 @@ <span> <span class="va">FOCUS_2006_F</span></span></code></pre></div> </div> - <div id="format"> - <h2>Format</h2> + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>6 datasets with observations on the following variables.</p><dl><dt><code>name</code></dt> <dd><p>a factor containing the name of the observed variable</p></dd> @@ -134,8 +100,8 @@ </dl></div> - <div id="source"> - <h2>Source</h2> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, @@ -143,8 +109,8 @@ <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">FOCUS_2006_C</span></span></span> <span class="r-out co"><span class="r-pr">#></span> name time value</span> <span class="r-out co"><span class="r-pr">#></span> 1 parent 0 85.1</span> @@ -158,26 +124,22 @@ <span class="r-out co"><span class="r-pr">#></span> 9 parent 119 0.6</span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" 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href="https://github.com/jranke/mkin/blob/HEAD/R/parent_solutions.R" class="external-link"><code>R/parent_solutions.R</code></a></small> + <div class="d-none name"><code>FOMC.solution.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Function describing exponential decline from a defined starting value, with a decreasing rate constant.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">FOMC.solution</span><span class="op">(</span><span class="va">t</span>, <span class="va">parent_0</span>, <span class="va">alpha</span>, <span class="va">beta</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>t</dt> <dd><p>Time.</p></dd> @@ -137,26 +104,26 @@ constant values.</p></dd> <dd><p>Location parameter.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>The value of the response variable at time <code>t</code>.</p> </div> - <div id="details"> - <h2>Details</h2> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <p>The form given here differs slightly from the original reference by Gustafson and Holden (1990). The parameter <code>beta</code> corresponds to 1/beta in the original equation.</p> </div> - <div id="note"> - <h2>Note</h2> + <div class="section level2"> + <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2> <p>The solution of the FOMC kinetic model reduces to the <code><a href="SFO.solution.html">SFO.solution</a></code> for large values of <code>alpha</code> and <code>beta</code> with \(k = \frac{\beta}{\alpha}\).</p> </div> - <div id="references"> - <h2>References</h2> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, @@ -171,8 +138,8 @@ Version 1.1, 18 December 2014 A new model based on spatial variability. <em>Environmental Science and Technology</em> <b>24</b>, 1032-1038</p> </div> - <div id="see-also"> - <h2>See also</h2> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <div class="dont-index"><p>Other parent solutions: <code><a href="DFOP.solution.html">DFOP.solution</a>()</code>, <code><a href="HS.solution.html">HS.solution</a>()</code>, @@ -182,34 +149,30 @@ Technology</em> <b>24</b>, 1032-1038</p> <code><a href="logistic.solution.html">logistic.solution</a>()</code></p></div> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></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/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">FOMC.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">10</span>, <span class="fl">2</span><span class="op">)</span>, <span class="fl">0</span>, <span class="fl">2</span>, ylim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">100</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="FOMC.solution-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/HS.solution-1.png b/docs/reference/HS.solution-1.png Binary files differindex dd7a76c8..61d89dbc 100644 --- a/docs/reference/HS.solution-1.png +++ b/docs/reference/HS.solution-1.png diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index d24015a0..d7f339b7 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -1,125 +1,92 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta 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</ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> +<li class="nav-item"> + <a class="nav-link" href="../news/index.html">News</a> +</li> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Hockey-Stick kinetics</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/parent_solutions.R" class="external-link"><code>R/parent_solutions.R</code></a></small> - <div class="hidden name"><code>HS.solution.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Hockey-Stick kinetics</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/parent_solutions.R" class="external-link"><code>R/parent_solutions.R</code></a></small> + <div class="d-none name"><code>HS.solution.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Function describing two exponential decline functions with a break point between them.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">HS.solution</span><span class="op">(</span><span class="va">t</span>, <span class="va">parent_0</span>, <span class="va">k1</span>, <span class="va">k2</span>, <span class="va">tb</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>t</dt> <dd><p>Time.</p></dd> @@ -142,14 +109,14 @@ between them.</p> according to <code>k2</code>.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>The value of the response variable at time <code>t</code>.</p> </div> - <div id="references"> - <h2>References</h2> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, @@ -161,8 +128,8 @@ EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, Version 1.1, 18 December 2014 <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> </div> - <div id="see-also"> - <h2>See also</h2> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <div class="dont-index"><p>Other parent solutions: <code><a href="DFOP.solution.html">DFOP.solution</a>()</code>, <code><a href="FOMC.solution.html">FOMC.solution</a>()</code>, @@ -172,34 +139,30 @@ Version 1.1, 18 December 2014 <code><a href="logistic.solution.html">logistic.solution</a>()</code></p></div> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></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/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">HS.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">2</span>, <span class="fl">0.3</span>, <span class="fl">0.5</span><span class="op">)</span>, <span class="fl">0</span>, <span class="fl">2</span>, ylim<span class="op">=</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>,<span class="fl">100</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="HS.solution-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git 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href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> + <a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> + <a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Performance</h6> + <a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a class="dropdown-item" href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + <a class="dropdown-item" href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6> + <a class="dropdown-item" href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a class="dropdown-item" href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </div> </li> - </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> +<li class="nav-item"> + <a class="nav-link" href="../news/index.html">News</a> +</li> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Indeterminate order rate equation kinetics</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/parent_solutions.R" class="external-link"><code>R/parent_solutions.R</code></a></small> - <div class="hidden name"><code>IORE.solution.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Indeterminate order rate equation kinetics</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/parent_solutions.R" class="external-link"><code>R/parent_solutions.R</code></a></small> + <div class="d-none name"><code>IORE.solution.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Function describing exponential decline from a defined starting value, with a concentration dependent rate constant.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">IORE.solution</span><span class="op">(</span><span class="va">t</span>, <span class="va">parent_0</span>, <span class="va">k__iore</span>, <span class="va">N</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>t</dt> <dd><p>Time.</p></dd> @@ -137,26 +104,26 @@ units used.</p></dd> <dd><p>Exponent describing the nonlinearity of the rate equation</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>The value of the response variable at time <code>t</code>.</p> </div> - <div id="note"> - <h2>Note</h2> + <div class="section level2"> + <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2> <p>The solution of the IORE kinetic model reduces to the <code><a href="SFO.solution.html">SFO.solution</a></code> if N = 1. The parameters of the IORE model can be transformed to equivalent parameters of the FOMC mode - see the NAFTA guidance for details.</p> </div> - <div id="references"> - <h2>References</h2> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for Evaluating and Calculating Degradation Kinetics in Environmental Media</p> </div> - <div id="see-also"> - <h2>See also</h2> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <div class="dont-index"><p>Other parent solutions: <code><a href="DFOP.solution.html">DFOP.solution</a>()</code>, <code><a href="FOMC.solution.html">FOMC.solution</a>()</code>, @@ -166,8 +133,8 @@ for Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <code><a href="logistic.solution.html">logistic.solution</a>()</code></p></div> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></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/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">IORE.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">0.2</span>, <span class="fl">1.3</span><span class="op">)</span>, <span class="fl">0</span>, <span class="fl">2</span>, ylim <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">100</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="IORE.solution-1.png" alt="" width="700" height="433"></span> @@ -195,26 +162,22 @@ for Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git 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--> - </div><!--/.container --> -</div><!--/.navbar --> - - + </ul></div> - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Example datasets from the NAFTA SOP published 2015</h1> - <div class="hidden name"><code>NAFTA_SOP_2015.Rd</code></div> + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Example datasets from the NAFTA SOP published 2015</h1> + + <div class="d-none name"><code>NAFTA_SOP_2015.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Data taken from US EPA (2015), p. 19 and 23.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">NAFTA_SOP_Appendix_B</span></span> <span> <span class="va">NAFTA_SOP_Appendix_D</span></span></code></pre></div> </div> - <div id="format"> - <h2>Format</h2> + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>2 datasets with observations on the following variables.</p><dl><dt><code>name</code></dt> <dd><p>a factor containing the name of the observed variable</p></dd> @@ -130,8 +96,8 @@ </dl></div> - <div id="source"> - <h2>Source</h2> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <p>NAFTA (2011) Guidance for evaluating and calculating degradation kinetics in environmental media. NAFTA Technical Working Group on Pesticides <a href="https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation" class="external-link">https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation</a> @@ -142,8 +108,8 @@ <a href="https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance" class="external-link">https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="va">nafta_evaluation</span> <span class="op"><-</span> <span class="fu"><a href="nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Appendix_D</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span> <span class="r-msg co"><span class="r-pr">#></span> The representative half-life of the IORE model is longer than the one corresponding</span> @@ -192,26 +158,22 @@ <span class="r-plt img"><img src="NAFTA_SOP_2015-1.png" alt="" width="700" height="433"></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> 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pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> + <a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> + <a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Performance</h6> + <a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a class="dropdown-item" 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data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - + </ul></div> - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Example datasets from Attachment 1 to the NAFTA SOP published 2015</h1> - <div class="hidden name"><code>NAFTA_SOP_Attachment.Rd</code></div> + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Example datasets from Attachment 1 to the NAFTA SOP published 2015</h1> + + <div class="d-none name"><code>NAFTA_SOP_Attachment.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Data taken from from Attachment 1 of the SOP.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">NAFTA_SOP_Attachment</span></span></code></pre></div> </div> - <div id="format"> - <h2>Format</h2> + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>A list (NAFTA_SOP_Attachment) containing 16 datasets suitable for the evaluation with <code><a href="nafta.html">nafta</a></code></p> </div> - <div id="source"> - <h2>Source</h2> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <p>NAFTA (2011) Guidance for evaluating and calculating degradation kinetics in environmental media. NAFTA Technical Working Group on Pesticides <a href="https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation" class="external-link">https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation</a> @@ -133,8 +99,8 @@ <a href="https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance" class="external-link">https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="va">nafta_att_p5a</span> <span class="op"><-</span> <span class="fu"><a href="nafta.html">nafta</a></span><span class="op">(</span><span class="va">NAFTA_SOP_Attachment</span><span class="op">[[</span><span class="st">"p5a"</span><span class="op">]</span><span class="op">]</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span> <span class="r-msg co"><span class="r-pr">#></span> The half-life obtained from the IORE model may be used</span> @@ -181,26 +147,22 @@ <span class="r-plt img"><img src="NAFTA_SOP_Attachment-1.png" alt="" width="700" height="433"></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png Binary files differindex ca982688..5de2bdc7 100644 --- a/docs/reference/Rplot001.png +++ b/docs/reference/Rplot001.png diff --git a/docs/reference/Rplot002.png b/docs/reference/Rplot002.png Binary files differindex de2d61aa..556ca0a7 100644 --- a/docs/reference/Rplot002.png +++ b/docs/reference/Rplot002.png diff --git a/docs/reference/Rplot003.png b/docs/reference/Rplot003.png Binary files differindex 8fd02b8e..b50287c2 100644 --- a/docs/reference/Rplot003.png +++ b/docs/reference/Rplot003.png diff --git a/docs/reference/Rplot004.png b/docs/reference/Rplot004.png Binary files differindex 2c12ceb1..d5fef0f0 100644 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role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Single First-Order kinetics</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/parent_solutions.R" class="external-link"><code>R/parent_solutions.R</code></a></small> - <div class="hidden name"><code>SFO.solution.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Single First-Order kinetics</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/parent_solutions.R" class="external-link"><code>R/parent_solutions.R</code></a></small> + <div class="d-none name"><code>SFO.solution.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Function describing exponential decline from a defined starting value.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">SFO.solution</span><span class="op">(</span><span class="va">t</span>, <span class="va">parent_0</span>, <span class="va">k</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>t</dt> <dd><p>Time.</p></dd> @@ -130,14 +96,14 @@ <dd><p>Kinetic rate constant.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>The value of the response variable at time <code>t</code>.</p> </div> - <div id="references"> - <h2>References</h2> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, @@ -149,8 +115,8 @@ EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, Version 1.1, 18 December 2014 <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> </div> - <div id="see-also"> - <h2>See also</h2> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <div class="dont-index"><p>Other parent solutions: <code><a href="DFOP.solution.html">DFOP.solution</a>()</code>, <code><a href="FOMC.solution.html">FOMC.solution</a>()</code>, @@ -160,34 +126,30 @@ Version 1.1, 18 December 2014 <code><a href="logistic.solution.html">logistic.solution</a>()</code></p></div> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></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/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">SFO.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">3</span><span class="op">)</span>, <span class="fl">0</span>, <span class="fl">2</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="SFO.solution-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/SFORB.solution-1.png b/docs/reference/SFORB.solution-1.png Binary files differindex 7bea3b78..08d25616 100644 --- a/docs/reference/SFORB.solution-1.png +++ b/docs/reference/SFORB.solution-1.png diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index a99deac7..70ea8779 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -1,118 +1,87 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, 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</ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Single First-Order Reversible Binding kinetics</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/parent_solutions.R" class="external-link"><code>R/parent_solutions.R</code></a></small> - <div class="hidden name"><code>SFORB.solution.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Single First-Order Reversible Binding kinetics</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/parent_solutions.R" class="external-link"><code>R/parent_solutions.R</code></a></small> + <div class="d-none name"><code>SFORB.solution.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Function describing the solution of the differential equations describing the kinetic model with first-order terms for a two-way transfer from a free to a bound fraction, and a first-order degradation term for the free @@ -120,12 +89,13 @@ fraction. The initial condition is a defined amount in the free fraction and no substance in the bound fraction.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">SFORB.solution</span><span class="op">(</span><span class="va">t</span>, <span class="va">parent_0</span>, <span class="va">k_12</span>, <span class="va">k_21</span>, <span class="va">k_1output</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>t</dt> <dd><p>Time.</p></dd> @@ -147,15 +117,15 @@ and no substance in the bound fraction.</p> fraction.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>The value of the response variable, which is the sum of free and bound fractions at time <code>t</code>.</p> </div> - <div id="references"> - <h2>References</h2> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, @@ -167,8 +137,8 @@ EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, Version 1.1, 18 December 2014 <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> </div> - <div id="see-also"> - <h2>See also</h2> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <div class="dont-index"><p>Other parent solutions: <code><a href="DFOP.solution.html">DFOP.solution</a>()</code>, <code><a href="FOMC.solution.html">FOMC.solution</a>()</code>, @@ -178,34 +148,30 @@ Version 1.1, 18 December 2014 <code><a href="logistic.solution.html">logistic.solution</a>()</code></p></div> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></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/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">SFORB.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">0.5</span>, <span class="fl">2</span>, <span class="fl">3</span><span class="op">)</span>, <span class="fl">0</span>, <span class="fl">2</span><span class="op">)</span></span></span> <span class="r-plt img"><img src="SFORB.solution-1.png" alt="" width="700" height="433"></span> <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/add_err-1.png b/docs/reference/add_err-1.png Binary files differindex 4a3b4062..68cfb344 100644 --- a/docs/reference/add_err-1.png +++ b/docs/reference/add_err-1.png diff --git a/docs/reference/add_err-2.png b/docs/reference/add_err-2.png Binary files differindex 5aec1744..d2f0cf08 100644 --- a/docs/reference/add_err-2.png +++ b/docs/reference/add_err-2.png diff --git a/docs/reference/add_err-3.png b/docs/reference/add_err-3.png Binary files differindex 2e71f02f..17b5416a 100644 --- a/docs/reference/add_err-3.png +++ b/docs/reference/add_err-3.png diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 4db51d10..ea29115c 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -1,122 +1,90 @@ <!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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</ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> +<li class="nav-item"> + <a class="nav-link" href="../news/index.html">News</a> +</li> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Add normally distributed errors to simulated kinetic degradation data</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/add_err.R" class="external-link"><code>R/add_err.R</code></a></small> - <div class="hidden name"><code>add_err.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Add normally distributed errors to simulated kinetic degradation data</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/add_err.R" class="external-link"><code>R/add_err.R</code></a></small> + <div class="d-none name"><code>add_err.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Normally distributed errors are added to data predicted for a specific degradation model using <code><a href="mkinpredict.html">mkinpredict</a></code>. The variance of the error may depend on the predicted value and is specified as a standard deviation.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">add_err</span><span class="op">(</span></span> <span> <span class="va">prediction</span>,</span> <span> <span class="va">sdfunc</span>,</span> @@ -129,8 +97,8 @@ may depend on the predicted value and is specified as a standard deviation.</p> <span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>prediction</dt> <dd><p>A prediction from a kinetic model as produced by <code><a href="mkinpredict.html">mkinpredict</a></code>.</p></dd> @@ -169,27 +137,27 @@ adding the random error will be set to NA.</p></dd> seed is not set.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>A list of datasets compatible with <code><a href="mmkin.html">mmkin</a></code>, i.e. the components of the list are datasets compatible with <code><a href="mkinfit.html">mkinfit</a></code>.</p> </div> - <div id="references"> - <h2>References</h2> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>Ranke J and Lehmann R (2015) To t-test or not to t-test, that is the question. XV Symposium on Pesticide Chemistry 2-4 September 2015, Piacenza, Italy https://jrwb.de/posters/piacenza_2015.pdf</p> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># The kinetic model</span></span></span> <span class="r-in"><span><span class="va">m_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M1"</span><span class="op">)</span>,</span></span> @@ -239,26 +207,22 @@ https://jrwb.de/posters/piacenza_2015.pdf</p> <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/anova.saem.mmkin.html b/docs/reference/anova.saem.mmkin.html index 03ca588d..a514800a 100644 --- a/docs/reference/anova.saem.mmkin.html +++ b/docs/reference/anova.saem.mmkin.html @@ -1,124 +1,93 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Anova method for saem.mmkin objects — anova.saem.mmkin • 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="Anova method for saem.mmkin objects — anova.saem.mmkin"><meta property="og:description" content="Generate an anova object. 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</ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Anova method for saem.mmkin objects</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/anova.saem.mmkin.R" class="external-link"><code>R/anova.saem.mmkin.R</code></a></small> - <div class="hidden name"><code>anova.saem.mmkin.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Anova method for saem.mmkin objects</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/anova.saem.mmkin.R" class="external-link"><code>R/anova.saem.mmkin.R</code></a></small> + <div class="d-none name"><code>anova.saem.mmkin.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Generate an anova object. The method to calculate the BIC is that from the saemix package. As in other prominent anova methods, models are sorted by number of parameters, and the tests (if requested) are always relative to the model on the previous line.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for saem.mmkin</span></span> <span><span class="fu"><a href="https://rdrr.io/r/stats/anova.html" class="external-link">anova</a></span><span class="op">(</span></span> <span> <span class="va">object</span>,</span> @@ -129,8 +98,8 @@ the model on the previous line.</p> <span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>An <a href="saem.html">saem.mmkin</a> object</p></dd> @@ -155,33 +124,29 @@ only be done for nested models.</p></dd> <dd><p>Optional character vector of model names</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>an "anova" data frame; the traditional (S3) result of anova()</p> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git 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for model averaging</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/aw.R" class="external-link"><code>R/aw.R</code></a></small> + <div class="d-none name"><code>aw.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Akaike weights are calculated based on the relative expected Kullback-Leibler information as specified by Burnham and Anderson (2004).</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">aw</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> <span><span class="co"># S3 method for mkinfit</span></span> @@ -132,8 +100,8 @@ by Burnham and Anderson (2004).</p> <span><span class="fu">aw</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>An <a href="mmkin.html">mmkin</a> column object, containing two or more <a href="mkinfit.html">mkinfit</a> models that have been fitted to the same data, @@ -147,15 +115,15 @@ as dots arguments.</p></dd> further <a href="mkinfit.html">mkinfit</a> objects in the method for mkinfit objects.</p></dd> </dl></div> - <div id="references"> - <h2>References</h2> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>Burnham KP and Anderson DR (2004) Multimodel Inference: Understanding AIC and BIC in Model Selection. <em>Sociological Methods & Research</em> <strong>33</strong>(2) 261-304</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> <span class="r-in"><span><span class="va">f_sfo</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_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">f_dfop</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">FOCUS_2006_D</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> @@ -174,26 +142,22 @@ Inference: Understanding AIC and BIC in Model Selection. <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/confint.mkinfit.html b/docs/reference/confint.mkinfit.html index 48240abc..4d4fa012 100644 --- a/docs/reference/confint.mkinfit.html +++ b/docs/reference/confint.mkinfit.html @@ -1,5 +1,12 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Confidence intervals for parameters of mkinfit objects — confint.mkinfit • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" 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approximation of +the curvature of the likelihood function at the maximum likelihood parameter +estimates. +The alternative method 'profile' is based on the profile likelihood for each +parameter. 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The alternative method 'profile' is based on the profile likelihood for each @@ -9,113 +16,78 @@ platforms. The speed of the method could likely be improved by using the method of Venzon and Moolgavkar (1988)."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--></head><body data-spy="scroll" data-target="#toc"> +<![endif]--></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - <div class="container template-reference-topic"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - 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</ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> +<li class="nav-item"> + <a class="nav-link" href="../news/index.html">News</a> +</li> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Confidence intervals for parameters of mkinfit objects</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/confint.mkinfit.R" class="external-link"><code>R/confint.mkinfit.R</code></a></small> - <div class="hidden name"><code>confint.mkinfit.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Confidence intervals for parameters of mkinfit objects</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/confint.mkinfit.R" class="external-link"><code>R/confint.mkinfit.R</code></a></small> + <div class="d-none name"><code>confint.mkinfit.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>The default method 'quadratic' is based on the quadratic approximation of the curvature of the likelihood function at the maximum likelihood parameter estimates. @@ -126,7 +98,8 @@ platforms. The speed of the method could likely be improved by using the method of Venzon and Moolgavkar (1988).</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> <span><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span></span> <span> <span class="va">object</span>,</span> @@ -144,8 +117,8 @@ method of Venzon and Moolgavkar (1988).</p> <span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>An <code><a href="mkinfit.html">mkinfit</a></code> object</p></dd> @@ -207,15 +180,15 @@ the quadratic method?</p></dd> <dd><p>Not used</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>A matrix with columns giving lower and upper confidence limits for each parameter.</p> </div> - <div id="references"> - <h2>References</h2> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>Bates DM and Watts GW (1988) Nonlinear regression analysis & its applications</p> <p>Pawitan Y (2013) In all likelihood - Statistical modelling and inference using likelihood. Clarendon Press, Oxford.</p> @@ -224,8 +197,8 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, 87–94.</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/confint.html" class="external-link">confint</a></span><span class="op">(</span><span class="va">f</span>, method <span class="op">=</span> <span class="st">"quadratic"</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> 2.5% 97.5%</span> @@ -257,7 +230,7 @@ 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> 2.578 0.005 2.599 </span> +<span class="r-out co"><span class="r-pr">#></span> 1.203 0.000 1.203 </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> @@ -265,7 +238,7 @@ 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> 0.963 0.255 0.636 </span> +<span class="r-out co"><span class="r-pr">#></span> 0.438 0.097 0.301 </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> @@ -400,26 +373,22 @@ Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + 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class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/create_deg_func.R" class="external-link"><code>R/create_deg_func.R</code></a></small> - <div class="hidden name"><code>create_deg_func.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Create degradation functions for known analytical solutions</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/create_deg_func.R" class="external-link"><code>R/create_deg_func.R</code></a></small> + <div class="d-none name"><code>create_deg_func.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Create degradation functions for known analytical solutions</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">create_deg_func</span><span class="op">(</span><span class="va">spec</span>, use_of_ff <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">"min"</span>, <span class="st">"max"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>spec</dt> <dd><p>List of model specifications as contained in mkinmod objects</p></dd> @@ -126,15 +92,15 @@ <dd><p>Minimum or maximum use of formation fractions</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>Degradation function to be attached to mkinmod objects</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> <span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span></span> @@ -151,8 +117,8 @@ <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 0.421 1.000 0.412 0.000 0</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.601 1.428 0.566 0.024 0</span> +<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.233 1.000 0.232 0.001 0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.293 1.258 0.293 0.000 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> @@ -165,34 +131,30 @@ <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 0.762 1.000 0.758 0.004 0</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 1.194 1.567 1.140 0.052 0</span> +<span class="r-out co"><span class="r-pr">#></span> 1 analytical 2 0.375 1.000 0.375 0 0</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve 2 0.508 1.355 0.508 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> <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/dimethenamid_2018.html b/docs/reference/dimethenamid_2018.html index 961b28d2..71f1f5d1 100644 --- a/docs/reference/dimethenamid_2018.html +++ b/docs/reference/dimethenamid_2018.html @@ -1,5 +1,10 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do 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Kinetic evaluations shown for these datasets are intended to illustrate and advance kinetic modelling. The fact that these data and some results are shown here does not imply a license to use them in the @@ -7,110 +12,78 @@ context of pesticide registrations, as the use of the data may be constrained by data protection regulations."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--></head><body data-spy="scroll" data-target="#toc"> +<![endif]--></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - <div class="container template-reference-topic"> - 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<div class="hidden name"><code>dimethenamid_2018.Rd</code></div> + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/dimethenamid_2018.R" class="external-link"><code>R/dimethenamid_2018.R</code></a></small> + <div class="d-none name"><code>dimethenamid_2018.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>The datasets were extracted from the active substance evaluation dossier published by EFSA. Kinetic evaluations shown for these datasets are intended to illustrate and advance kinetic modelling. The fact that these data and @@ -119,30 +92,31 @@ context of pesticide registrations, as the use of the data may be constrained by data protection regulations.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">dimethenamid_2018</span></span></code></pre></div> </div> - <div id="format"> - <h2>Format</h2> + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>An <a href="mkindsg.html">mkindsg</a> object grouping seven datasets with some meta information</p> </div> - <div id="source"> - <h2>Source</h2> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <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 https://open.efsa.europa.eu/study-inventory/EFSA-Q-2014-00716</p> </div> - <div id="details"> - <h2>Details</h2> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <p>The R code used to create this data object is installed with this package in the 'dataset_generation' directory. In the code, page numbers are given for specific pieces of information in the comments.</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">dimethenamid_2018</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> <mkindsg> holding 7 mkinds objects</span> <span class="r-out co"><span class="r-pr">#></span> Title $title: Aerobic soil degradation data on dimethenamid-P from the EU assessment in 2018 </span> @@ -222,10 +196,10 @@ specific pieces of information in the comments.</p> <span class="r-in"><span><span class="co">#saemix::plot(f_dmta_saem_tc$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: 1.2.5 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Wed Aug 9 17:55:36 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Wed Aug 9 17:55:36 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.6 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 16 04:14:53 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 16 04:14:53 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 +212,7 @@ 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 796.123 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 302.335 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> @@ -364,26 +338,22 @@ specific pieces of information in the comments.</p> <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/ds_mixed-1.png b/docs/reference/ds_mixed-1.png Binary 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name"><code>ds_mixed.Rd</code></div> + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Synthetic data for hierarchical kinetic degradation models</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/ds_mixed.R" class="external-link"><code>R/ds_mixed.R</code></a></small> + <div class="d-none name"><code>ds_mixed.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>The R code used to create this data object is installed with this package in the 'dataset_generation' directory.</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> <span class="r-in"><span> <span class="va">sfo_mmkin</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">ds_sfo</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, error_model <span class="op">=</span> <span class="st">"tc"</span>, cores <span class="op">=</span> <span class="fl">15</span><span class="op">)</span></span></span> <span class="r-in"><span> <span class="va">sfo_saem</span> <span class="op"><-</span> <span class="fu"><a href="saem.html">saem</a></span><span class="op">(</span><span class="va">sfo_mmkin</span>, no_random_effect <span class="op">=</span> <span class="st">"parent_0"</span><span class="op">)</span></span></span> @@ -234,26 +200,21 @@ the 'dataset_generation' directory.</p> <span class="r-out co"><span class="r-pr">#></span> #save(ds_sfo, ds_fomc, ds_dfop, ds_hs, ds_dfop_sfo, file = "data/ds_mixed.rda", version = 2)</span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index 4ce6a8ca..c6e216d9 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -1,6 +1,10 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Function to calculate endpoints for further use from kinetic models fitted -with mkinfit — endpoints • 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 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If the SFORB model was specified +for one of the parents or metabolites, the Eigenvalues are returned. These +are equivalent to the rate constants of the DFOP model, but with the +advantage that the SFORB model can also be used for metabolites."><title>Function to calculate endpoints for further use from kinetic models fitted +with mkinfit — endpoints • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- 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><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Function to calculate endpoints for further use from kinetic models fitted with mkinfit — endpoints"><meta property="og:description" content="This function calculates DT50 and DT90 values as well as formation fractions from kinetic models fitted with mkinfit. If the SFORB model was specified for one of the parents or metabolites, the Eigenvalues are returned. These @@ -8,114 +12,79 @@ are equivalent to the rate constants of the DFOP model, but with the advantage that the SFORB model can also be used for metabolites."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--></head><body data-spy="scroll" data-target="#toc"> +<![endif]--></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - <div class="container template-reference-topic"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> - 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<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/endpoints.R" class="external-link"><code>R/endpoints.R</code></a></small> - <div class="hidden name"><code>endpoints.Rd</code></div> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/endpoints.R" class="external-link"><code>R/endpoints.R</code></a></small> + <div class="d-none name"><code>endpoints.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>This function calculates DT50 and DT90 values as well as formation fractions from kinetic models fitted with mkinfit. If the SFORB model was specified for one of the parents or metabolites, the Eigenvalues are returned. These @@ -123,12 +92,13 @@ are equivalent to the rate constants of the DFOP model, but with the advantage that the SFORB model can also be used for metabolites.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">endpoints</span><span class="op">(</span><span class="va">fit</span>, covariates <span class="op">=</span> <span class="cn">NULL</span>, covariate_quantile <span class="op">=</span> <span class="fl">0.5</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>fit</dt> <dd><p>An object of class <a href="mkinfit.html">mkinfit</a>, <a href="nlme.mmkin.html">nlme.mmkin</a> or <a href="saem.html">saem.mmkin</a>, or another object that has list components mkinmod containing an <a href="mkinmod.html">mkinmod</a> @@ -147,8 +117,8 @@ object has covariate models. If so, the default is to show endpoints for the median of the covariate values (50th percentile).</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>A list with a matrix of dissipation times named distimes, and, if @@ -156,23 +126,23 @@ applicable, a vector of formation fractions named ff and, if the SFORB model was in use, a vector of eigenvalues of these SFORB models, equivalent to DFOP rate constants</p> </div> - <div id="details"> - <h2>Details</h2> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <p>Additional DT50 values are calculated from the FOMC DT90 and k1 and k2 from HS and DFOP, as well as from Eigenvalues b1 and b2 of any SFORB models</p> </div> - <div id="note"> - <h2>Note</h2> + <div class="section level2"> + <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2> <p>The function is used internally by <a href="summary.mkinfit.html">summary.mkinfit</a>, <a href="summary.nlme.mmkin.html">summary.nlme.mmkin</a> and <a href="summary.saem.mmkin.html">summary.saem.mmkin</a>.</p> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span> <span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span> <span class="fu">endpoints</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> @@ -205,26 +175,22 @@ HS and DFOP, as well as from Eigenvalues b1 and b2 of any SFORB models</p> <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/experimental_data_for_UBA-1.png b/docs/reference/experimental_data_for_UBA-1.png Binary files differindex 4de80e3a..f0dfab85 100644 --- a/docs/reference/experimental_data_for_UBA-1.png +++ b/docs/reference/experimental_data_for_UBA-1.png diff --git a/docs/reference/experimental_data_for_UBA.html b/docs/reference/experimental_data_for_UBA.html index 6a02f430..8940bbc2 100644 --- a/docs/reference/experimental_data_for_UBA.html +++ b/docs/reference/experimental_data_for_UBA.html @@ -1,5 +1,33 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Experimental datasets used for development and testing of error models — experimental_data_for_UBA_2019 • 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="Experimental datasets used for development and testing of error models — experimental_data_for_UBA_2019"><meta property="og:description" content="The 12 datasets were extracted from active substance evaluation dossiers published +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="The 12 datasets were extracted from active substance evaluation dossiers published + by EFSA. Kinetic evaluations shown for these datasets are intended to illustrate + and advance error model specifications. The fact that these data and some + results are shown here do not imply a license to use them in the context of + pesticide registrations, as the use of the data may be constrained by + data protection regulations. +Preprocessing of data was performed based on the recommendations of the FOCUS + kinetics workgroup (FOCUS, 2014) as described below. +Datasets 1 and 2 are from the Renewal Assessment Report (RAR) for imazamox + (France, 2015, p. 15). For setting values reported as zero, an LOQ of 0.1 + was assumed. Metabolite residues reported for day zero were added to the + parent compound residues. +Datasets 3 and 4 are from the Renewal Assessment Report (RAR) for isofetamid + (Belgium, 2014, p. 8) and show the data for two different radiolabels. For + dataset 4, the value given for the metabolite in the day zero sampling + in replicate B was added to the parent compound, following the respective + FOCUS recommendation. +Dataset 5 is from the Renewal Assessment Report (RAR) for ethofumesate + (Austria, 2015, p. 16). +Datasets 6 to 10 are from the Renewal Assessment Report (RAR) for glyphosate + (Germany, 2013, pages 8, 28, 50, 51). For the initial sampling, + the residues given for the metabolite were added to the parent + value, following the recommendation of the FOCUS kinetics workgroup. +Dataset 11 is from the Renewal Assessment Report (RAR) for 2,4-D + (Hellas, 2013, p. 644). Values reported as zero were set to NA, with + the exception of the day three sampling of metabolite A2, which was set + to one half of the LOD reported to be 1% AR. +Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl + (United Kingdom, 2014, p. 81)."><title>Experimental datasets used for development and testing of error models — experimental_data_for_UBA_2019 • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- 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><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Experimental datasets used for development and testing of error models — experimental_data_for_UBA_2019"><meta property="og:description" content="The 12 datasets were extracted from active substance evaluation dossiers published by EFSA. Kinetic evaluations shown for these datasets are intended to illustrate and advance error model specifications. The fact that these data and some results are shown here do not imply a license to use them in the context of @@ -30,113 +58,78 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl (United Kingdom, 2014, p. 81)."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--></head><body data-spy="scroll" data-target="#toc"> +<![endif]--></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - <div class="container template-reference-topic"> - 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<div class="ref-description"> + <div class="ref-description section level2"> <p>The 12 datasets were extracted from active substance evaluation dossiers published by EFSA. Kinetic evaluations shown for these datasets are intended to illustrate and advance error model specifications. The fact that these data and some @@ -168,12 +161,13 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl (United Kingdom, 2014, p. 81).</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">experimental_data_for_UBA_2019</span></span></code></pre></div> </div> - <div id="format"> - <h2>Format</h2> + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>A list containing twelve datasets as an R6 class defined by <code><a href="mkinds.html">mkinds</a></code>, each containing, among others, the following components</p><dl><dt><code>title</code></dt> <dd><p>The name of the dataset, e.g. <code>Soil 1</code></p></dd> @@ -183,8 +177,8 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl </dl></div> - <div id="source"> - <h2>Source</h2> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <p>Austria (2015). Ethofumesate Renewal Assessment Report Volume 3 Annex B.8 (AS)</p> @@ -206,8 +200,8 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl 1141/2010 for renewal of an active substance</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> <span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># Model definitions</span></span></span> @@ -252,26 +246,22 @@ Dataset 12 is from the Renewal Assessment Report (RAR) for thifensulfuron-methyl <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 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guidance</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/f_time_norm_focus.R" class="external-link"><code>R/f_time_norm_focus.R</code></a></small> + <div class="d-none name"><code>f_time_norm_focus.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Time step normalisation factors for aerobic soil degradation as described in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369).</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">f_time_norm_focus</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> <span><span class="co"># S3 method for numeric</span></span> @@ -140,8 +107,8 @@ in Appendix 8 to the FOCUS kinetics guidance (FOCUS 2014, p. 369).</p> <span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>An object containing information used for the calculations</p></dd> @@ -183,8 +150,8 @@ to a reference moisture given in the meta information, otherwise the focus soil moisture for the soil class is used</p></dd> </dl></div> - <div id="references"> - <h2>References</h2> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, @@ -196,13 +163,13 @@ EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, Version 1.1, 18 December 2014 <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> </div> - <div id="see-also"> - <h2>See also</h2> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <div class="dont-index"><p><a href="focus_soil_moisture.html">focus_soil_moisture</a></p></div> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">f_time_norm_focus</span><span class="op">(</span><span class="fl">25</span>, <span class="fl">20</span>, <span class="fl">25</span><span class="op">)</span> <span class="co"># 1.37, compare FOCUS 2014 p. 184</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] 1.373956</span> <span class="r-in"><span></span></span> @@ -225,26 +192,22 @@ Version 1.1, 18 December 2014 <span class="r-msg co"><span class="r-pr">#></span> $f_time_norm was (re)set to normalised values</span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/focus_soil_moisture.html 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<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/focus_soil_moisture.R" class="external-link"><code>R/focus_soil_moisture.R</code></a></small> - <div class="hidden name"><code>focus_soil_moisture.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/focus_soil_moisture.R" class="external-link"><code>R/focus_soil_moisture.R</code></a></small> + <div class="d-none name"><code>focus_soil_moisture.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>The value were transcribed from p. 36. The table assumes field capacity corresponds to pF2, MWHC to pF 1 and 1/3 bar to pF 2.5.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">focus_soil_moisture</span></span></code></pre></div> </div> - <div id="format"> - <h2>Format</h2> + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>A matrix with upper case USDA soil classes as row names, and water tension ('pF1', 'pF2', 'pF 2.5') as column names</p> </div> - <div id="source"> - <h2>Source</h2> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <p>Anonymous (2014) Generic Guidance for Tier 1 FOCUS Ground Water Assessment Version 2.2, May 2014 <a href="https://esdac.jrc.ec.europa.eu/projects/ground-water" class="external-link">https://esdac.jrc.ec.europa.eu/projects/ground-water</a></p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">focus_soil_moisture</span></span></span> <span class="r-out co"><span class="r-pr">#></span> pF1 pF2 pF2.5</span> <span class="r-out co"><span class="r-pr">#></span> Sand 24 12 7</span> @@ -147,26 +114,22 @@ Version 2.2, May 2014 <a href="https://esdac.jrc.ec.europa.eu/projects/ground-wa <span class="r-out co"><span class="r-pr">#></span> Clay 53 48 43</span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this 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href="https://github.com/jranke/mkin/blob/HEAD/R/nlme.mmkin.R" class="external-link"><code>R/nlme.mmkin.R</code></a></small> + <div class="d-none name"><code>get_deg_func.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Retrieve a degradation function from the mmkin namespace</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">get_deg_func</span><span class="op">(</span><span class="op">)</span></span></code></pre></div> </div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>A function that was likely previously assigned from within nlme.mmkin</p> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/hierarchical_kinetics.html b/docs/reference/hierarchical_kinetics.html index ab0b3d04..5cc24e79 100644 --- a/docs/reference/hierarchical_kinetics.html +++ b/docs/reference/hierarchical_kinetics.html @@ -1,5 +1,12 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" 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</li> - <li class="divider"> - <li class="dropdown-header">Performance</li> - <li> - <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> - </li> - <li> - <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> - </li> - <li> - <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> - </li> - <li class="divider"> - <li class="dropdown-header">Miscellaneous</li> - <li> - <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> - </li> - <li> - <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> - </li> - </ul></li> -<li> - <a href="../news/index.html">News</a> +<li class="nav-item dropdown"> + <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a> + <div class="dropdown-menu" aria-labelledby="dropdown-articles"> + <a class="dropdown-item" href="../articles/mkin.html">Introduction to mkin</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Example evaluations with (generalised) nonlinear least squares</h6> + <a class="dropdown-item" href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> + <a class="dropdown-item" href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + <a class="dropdown-item" href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Example evaluations with hierarchical models (nonlinear mixed-effects models)</h6> + <a class="dropdown-item" href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> + <a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> + <a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Performance</h6> + <a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a class="dropdown-item" href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + <a class="dropdown-item" href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6> + <a class="dropdown-item" href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a class="dropdown-item" href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </div> </li> - </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> +<li class="nav-item"> + <a class="nav-link" href="../news/index.html">News</a> +</li> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Hierarchical kinetics template</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/hierarchical_kinetics.R" class="external-link"><code>R/hierarchical_kinetics.R</code></a></small> - <div class="hidden name"><code>hierarchical_kinetics.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Hierarchical kinetics template</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/hierarchical_kinetics.R" class="external-link"><code>R/hierarchical_kinetics.R</code></a></small> + <div class="d-none name"><code>hierarchical_kinetics.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>R markdown format for setting up hierarchical kinetics based on a template provided with the mkin package. This format is based on <a href="https://pkgs.rstudio.com/rmarkdown/reference/pdf_document.html" class="external-link">rmarkdown::pdf_document</a>. Chunk options are adapted. Echoing R code from code chunks and caching are @@ -126,12 +98,13 @@ figures will not move around in the document, but stay where the user includes them.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">hierarchical_kinetics</span><span class="op">(</span><span class="va">...</span>, keep_tex <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>...</dt> <dd><p>Arguments to <code><a href="https://pkgs.rstudio.com/rmarkdown/reference/pdf_document.html" class="external-link">rmarkdown::pdf_document</a></code></p></dd> @@ -140,8 +113,8 @@ includes them.</p> <dd><p>Keep the intermediate tex file used in the conversion to PDF</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>R Markdown output format to pass to @@ -149,8 +122,8 @@ includes them.</p> </div> - <div id="details"> - <h2>Details</h2> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <p>The latter feature (positioning the figures with "H") depends on the LaTeX package 'float'. In addition, the LaTeX package 'listing' is used in the template for showing model fit summaries in the Appendix. This means that @@ -162,8 +135,8 @@ is present before) is to install the 'tinytex' R package, to run and then to run 'tinytex::tlmgr_install(c("float", "listing"))'.</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># \dontrun{</span></span></span> <span class="r-in"><span><span class="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://github.com/rstudio/rmarkdown" class="external-link">rmarkdown</a></span><span class="op">)</span></span></span> @@ -174,26 +147,22 @@ and then to run 'tinytex::tlmgr_install(c("float", "listing"))'.</p> <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/illparms.html b/docs/reference/illparms.html index bd90c0ed..75c540cc 100644 --- a/docs/reference/illparms.html +++ b/docs/reference/illparms.html @@ -1,118 +1,87 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Method to get the names of ill-defined parameters — illparms • 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="Method to get the names of ill-defined parameters — illparms"><meta property="og:description" content="The method for generalised nonlinear regression fits as obtained +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="The method for generalised nonlinear regression fits as obtained +with mkinfit and mmkin checks if the degradation parameters +pass the Wald test (in degradation kinetics often simply called t-test) for +significant difference from zero. 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</ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Method to get the names of ill-defined parameters</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/illparms.R" class="external-link"><code>R/illparms.R</code></a></small> - <div class="hidden name"><code>illparms.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Method to get the names of ill-defined parameters</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/illparms.R" class="external-link"><code>R/illparms.R</code></a></small> + <div class="d-none name"><code>illparms.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>The method for generalised nonlinear regression fits as obtained with <a href="mkinfit.html">mkinfit</a> and <a href="mmkin.html">mmkin</a> checks if the degradation parameters pass the Wald test (in degradation kinetics often simply called t-test) for @@ -120,7 +89,8 @@ significant difference from zero. For this test, the parameterisation without parameter transformations is used.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">illparms</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> <span><span class="co"># S3 method for mkinfit</span></span> @@ -155,8 +125,8 @@ without parameter transformations is used.</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="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>The object to investigate</p></dd> @@ -188,16 +158,16 @@ should slope parameters in the covariate model(starting with 'beta_') be tested?</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>For <a href="mkinfit.html">mkinfit</a> or <a href="saem.html">saem</a> objects, a character vector of parameter names. For <a href="mmkin.html">mmkin</a> or <a href="mhmkin.html">mhmkin</a> objects, a matrix like object of class 'illparms.mmkin' or 'illparms.mhmkin'.</p> </div> - <div id="details"> - <h2>Details</h2> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <p>The method for hierarchical model fits, also known as nonlinear mixed-effects model fits as obtained with <a href="saem.html">saem</a> and <a href="mhmkin.html">mhmkin</a> checks if any of the confidence intervals for the random @@ -205,14 +175,14 @@ effects expressed as standard deviations include zero, and if the confidence intervals for the error model parameters include zero.</p> </div> - <div id="note"> - <h2>Note</h2> + <div class="section level2"> + <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2> <p>All return objects have printing methods. For the single fits, printing does not output anything in the case no ill-defined parameters are found.</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_A</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>Optimisation did not converge:</span> <span class="r-wrn co"><span class="r-pr">#></span> false convergence (8)</span> @@ -232,26 +202,22 @@ does not output anything in the case no ill-defined parameters are found.</p> <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 7937d770..04a8ab76 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -1,157 +1,124 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta 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href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a class="dropdown-item" href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </div> </li> - </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> +<li class="nav-item"> + <a class="nav-link" href="../news/index.html">News</a> +</li> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Function to perform isometric log-ratio transformation</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/ilr.R" class="external-link"><code>R/ilr.R</code></a></small> - <div class="hidden name"><code>ilr.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Function to perform isometric log-ratio transformation</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/ilr.R" class="external-link"><code>R/ilr.R</code></a></small> + <div class="d-none name"><code>ilr.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>This implementation is a special case of the class of isometric log-ratio transformations.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">ilr</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span> <span></span> <span><span class="fu">invilr</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>x</dt> <dd><p>A numeric vector. Naturally, the forward transformation is only sensible for vectors with all elements being greater than zero.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>The result of the forward or backward transformation. The returned components always sum to 1 for the case of the inverse log-ratio transformation.</p> </div> - <div id="references"> - <h2>References</h2> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>Peter Filzmoser, Karel Hron (2008) Outlier Detection for Compositional Data Using Robust Methods. Math Geosci 40 233-248</p> </div> - <div id="see-also"> - <h2>See also</h2> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <div class="dont-index"><p>Another implementation can be found in R package <code>robCompositions</code>.</p></div> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>René Lehmann and Johannes Ranke</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># Order matters</span></span></span> <span class="r-in"><span><span class="fu">ilr</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0.1</span>, <span class="fl">1</span>, <span class="fl">10</span><span class="op">)</span><span class="op">)</span></span></span> @@ -187,26 +154,22 @@ Compositional Data Using Robust Methods. Math Geosci 40 233-248</p> <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/index.html b/docs/reference/index.html index a7f02199..d4a1b253 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -1,530 +1,661 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html 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--> - </div><!--/.container --> -</div><!--/.navbar --> + </ul></div> + + + </div> +</nav><div class="container template-reference-index"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Function reference</h1> + </div> + <div class="section level2"> + <h2 id="main-functions">Main functions<a class="anchor" aria-label="anchor" href="#main-functions"></a></h2> + <p class="section-desc"></p><p>Essential functionality</p> - </header><div class="row"> - <div class="contents col-md-9"> - <div class="page-header"> - <h1>Reference</h1> - </div> + + </div><div id="" class="section level2"> + + + - <table class="ref-index"><colgroup><col class="alias"><col class="title"></colgroup><tbody><tr><th colspan="2"> - <h2 id="main-functions">Main functions <a href="#main-functions" class="anchor" aria-hidden="true"></a></h2> - <p class="section-desc"></p><p>Essential functionality</p> - </th> - </tr></tbody><tbody><tr><td> - <p><code><a href="mkinmod.html">mkinmod()</a></code> <code><a href="mkinmod.html">print(<i><mkinmod></i>)</a></code> <code><a href="mkinmod.html">mkinsub()</a></code> </p> - </td> - <td><p>Function to set up a kinetic model with one or more state variables</p></td> - </tr><tr><td> - <p><code><a href="mkinfit.html">mkinfit()</a></code> </p> - </td> - <td><p>Fit a kinetic model to data with one or more state variables</p></td> - </tr><tr><td> - <p><code><a href="mmkin.html">mmkin()</a></code> <code><a href="mmkin.html">print(<i><mmkin></i>)</a></code> </p> - </td> - <td><p>Fit one or more kinetic models with one or more state variables to one or -more datasets</p></td> - </tr><tr><td> - <p><code><a href="mhmkin.html">mhmkin()</a></code> <code><a href="mhmkin.html">`[`(<i><mhmkin></i>)</a></code> <code><a href="mhmkin.html">print(<i><mhmkin></i>)</a></code> </p> - </td> - <td><p>Fit nonlinear mixed-effects models built from one or more kinetic -degradation models and one or more error models</p></td> - </tr></tbody><tbody><tr><th colspan="2"> - <h2 id="generics">Generics <a href="#generics" class="anchor" aria-hidden="true"></a></h2> - <p class="section-desc"></p><p>Generic functions introduced by the package</p> - </th> - </tr></tbody><tbody><tr><td> - <p><code><a href="parms.html">parms()</a></code> </p> - </td> - <td><p>Extract model parameters</p></td> - </tr><tr><td> - <p><code><a href="status.html">status()</a></code> <code><a href="status.html">print(<i><status.mmkin></i>)</a></code> <code><a href="status.html">print(<i><status.mhmkin></i>)</a></code> </p> - </td> - <td><p>Method to get status information for fit array objects</p></td> - </tr><tr><td> - <p><code><a href="illparms.html">illparms()</a></code> <code><a href="illparms.html">print(<i><illparms.mkinfit></i>)</a></code> <code><a href="illparms.html">print(<i><illparms.mmkin></i>)</a></code> <code><a href="illparms.html">print(<i><illparms.saem.mmkin></i>)</a></code> <code><a href="illparms.html">print(<i><illparms.mhmkin></i>)</a></code> </p> - </td> - <td><p>Method to get the names of ill-defined parameters</p></td> - </tr><tr><td> - <p><code><a href="endpoints.html">endpoints()</a></code> </p> - </td> - <td><p>Function to calculate endpoints for further use from kinetic models fitted -with mkinfit</p></td> - </tr><tr><td> - <p><code><a href="aw.html">aw()</a></code> </p> - </td> - <td><p>Calculate Akaike weights for model averaging</p></td> - </tr></tbody><tbody><tr><th colspan="2"> - <h2 id="show-results">Show results <a href="#show-results" class="anchor" aria-hidden="true"></a></h2> - <p class="section-desc"></p><p>Functions working with mkinfit objects</p> - </th> - </tr></tbody><tbody><tr><td> - <p><code><a href="plot.mkinfit.html">plot(<i><mkinfit></i>)</a></code> <code><a href="plot.mkinfit.html">plot_sep()</a></code> <code><a href="plot.mkinfit.html">plot_res()</a></code> <code><a href="plot.mkinfit.html">plot_err()</a></code> </p> - </td> - <td><p>Plot the observed data and the fitted model of an mkinfit object</p></td> - </tr><tr><td> - <p><code><a href="summary.mkinfit.html">summary(<i><mkinfit></i>)</a></code> <code><a href="summary.mkinfit.html">print(<i><summary.mkinfit></i>)</a></code> </p> - </td> - <td><p>Summary method for class "mkinfit"</p></td> - </tr><tr><td> - <p><code><a href="confint.mkinfit.html">confint(<i><mkinfit></i>)</a></code> </p> - </td> - <td><p>Confidence intervals for parameters of mkinfit objects</p></td> - </tr><tr><td> - <p><code><a href="update.mkinfit.html">update(<i><mkinfit></i>)</a></code> </p> - </td> - <td><p>Update an mkinfit model with different arguments</p></td> - </tr><tr><td> - <p><code><a href="lrtest.mkinfit.html">lrtest(<i><mkinfit></i>)</a></code> <code><a href="lrtest.mkinfit.html">lrtest(<i><mmkin></i>)</a></code> </p> - </td> - <td><p>Likelihood ratio test for mkinfit models</p></td> - </tr><tr><td> - <p><code><a href="loftest.html">loftest()</a></code> </p> - </td> - <td><p>Lack-of-fit test for models fitted to data with replicates</p></td> - </tr><tr><td> - <p><code><a href="mkinerrmin.html">mkinerrmin()</a></code> </p> - </td> - <td><p>Calculate the minimum error to assume in order to pass the variance test</p></td> - </tr><tr><td> - <p><code><a href="CAKE_export.html">CAKE_export()</a></code> </p> - </td> - <td><p>Export a list of datasets format to a CAKE study file</p></td> - </tr></tbody><tbody><tr><th colspan="2"> - <h2 id="work-with-mmkin-objects">Work with mmkin objects <a href="#work-with-mmkin-objects" class="anchor" aria-hidden="true"></a></h2> - <p class="section-desc"></p><p>Functions working with aggregated results</p> - </th> - </tr></tbody><tbody><tr><td> - <p><code><a href="Extract.mmkin.html">`[`(<i><mmkin></i>)</a></code> </p> - </td> - <td><p>Subsetting method for mmkin objects</p></td> - </tr><tr><td> - <p><code><a href="plot.mmkin.html">plot(<i><mmkin></i>)</a></code> </p> - </td> - <td><p>Plot model fits (observed and fitted) and the residuals for a row or column -of an mmkin object</p></td> - </tr><tr><td> - <p><code><a href="AIC.mmkin.html">AIC(<i><mmkin></i>)</a></code> <code><a href="AIC.mmkin.html">BIC(<i><mmkin></i>)</a></code> </p> - </td> - <td><p>Calculate the AIC for a column of an mmkin object</p></td> - </tr><tr><td> - <p><code><a href="summary.mmkin.html">summary(<i><mmkin></i>)</a></code> <code><a href="summary.mmkin.html">print(<i><summary.mmkin></i>)</a></code> </p> - </td> - <td><p>Summary method for class "mmkin"</p></td> - </tr></tbody><tbody><tr><th colspan="2"> - <h2 id="mixed-models">Mixed models <a href="#mixed-models" class="anchor" aria-hidden="true"></a></h2> - <p class="section-desc"></p><p>Create and work with nonlinear hierarchical models</p> - </th> - </tr></tbody><tbody><tr><td> - <p><code><a href="hierarchical_kinetics.html">hierarchical_kinetics()</a></code> </p> - </td> - <td><p>Hierarchical kinetics template</p></td> - </tr><tr><td> - <p><code><a href="read_spreadsheet.html">read_spreadsheet()</a></code> </p> - </td> - <td><p>Read datasets and relevant meta information from a spreadsheet file</p></td> - </tr><tr><td> - <p><code><a href="nlme.mmkin.html">nlme(<i><mmkin></i>)</a></code> <code><a href="nlme.mmkin.html">print(<i><nlme.mmkin></i>)</a></code> <code><a href="nlme.mmkin.html">update(<i><nlme.mmkin></i>)</a></code> </p> - </td> - <td><p>Create an nlme model for an mmkin row object</p></td> - </tr><tr><td> - <p><code><a href="saem.html">saem()</a></code> <code><a href="saem.html">print(<i><saem.mmkin></i>)</a></code> <code><a href="saem.html">saemix_model()</a></code> <code><a href="saem.html">saemix_data()</a></code> </p> - </td> - <td><p>Fit nonlinear mixed models with SAEM</p></td> - </tr><tr><td> - <p><code><a href="mhmkin.html">mhmkin()</a></code> <code><a href="mhmkin.html">`[`(<i><mhmkin></i>)</a></code> <code><a href="mhmkin.html">print(<i><mhmkin></i>)</a></code> </p> - </td> - <td><p>Fit nonlinear mixed-effects models built from one or more kinetic -degradation models and one or more error models</p></td> - </tr><tr><td> - <p><code><a href="plot.mixed.mmkin.html">plot(<i><mixed.mmkin></i>)</a></code> </p> - </td> - <td><p>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</p></td> - </tr><tr><td> - <p><code><a href="summary.nlme.mmkin.html">summary(<i><nlme.mmkin></i>)</a></code> <code><a href="summary.nlme.mmkin.html">print(<i><summary.nlme.mmkin></i>)</a></code> </p> - </td> - <td><p>Summary method for class "nlme.mmkin"</p></td> - </tr><tr><td> - <p><code><a href="summary.saem.mmkin.html">summary(<i><saem.mmkin></i>)</a></code> <code><a href="summary.saem.mmkin.html">print(<i><summary.saem.mmkin></i>)</a></code> </p> - </td> - <td><p>Summary method for class "saem.mmkin"</p></td> - </tr><tr><td> - <p><code><a href="anova.saem.mmkin.html">anova(<i><saem.mmkin></i>)</a></code> </p> - </td> - <td><p>Anova method for saem.mmkin objects</p></td> - </tr><tr><td> - <p><code><a href="logLik.saem.mmkin.html">logLik(<i><saem.mmkin></i>)</a></code> </p> - </td> - <td><p>logLik method for saem.mmkin objects</p></td> - </tr><tr><td> - <p><code><a href="nlme.html">nlme_function()</a></code> <code><a href="nlme.html">nlme_data()</a></code> </p> - </td> - <td><p>Helper functions to create nlme models from mmkin row objects</p></td> - </tr><tr><td> - <p><code><a href="get_deg_func.html">get_deg_func()</a></code> </p> - </td> - <td><p>Retrieve a degradation function from the mmkin namespace</p></td> - </tr><tr><td> - <p><code><a href="mixed.html">mixed()</a></code> <code><a href="mixed.html">print(<i><mixed.mmkin></i>)</a></code> </p> - </td> - <td><p>Create a mixed effects model from an mmkin row object</p></td> - </tr><tr><td> - <p><code><a href="reexports.html">reexports</a></code> <code><a href="reexports.html">intervals</a></code> <code><a href="reexports.html">lrtest</a></code> <code><a href="reexports.html">nlme</a></code> </p> - </td> - <td><p>Objects exported from other packages</p></td> - </tr><tr><td> - <p><code><a href="intervals.saem.mmkin.html">intervals(<i><saem.mmkin></i>)</a></code> </p> - </td> - <td><p>Confidence intervals for parameters in saem.mmkin objects</p></td> - </tr><tr><td> - <p><code><a href="multistart.html">multistart()</a></code> <code><a href="multistart.html">print(<i><multistart></i>)</a></code> <code><a href="multistart.html">best()</a></code> <code><a href="multistart.html">which.best()</a></code> </p> - </td> - <td><p>Perform a hierarchical model fit with multiple starting values</p></td> - </tr><tr><td> - <p><code><a href="llhist.html">llhist()</a></code> </p> - </td> - <td><p>Plot the distribution of log likelihoods from multistart objects</p></td> - </tr><tr><td> - <p><code><a href="parplot.html">parplot()</a></code> </p> - </td> - <td><p>Plot parameter variability of multistart objects</p></td> - </tr></tbody><tbody><tr><th colspan="2"> - <h2 id="datasets-and-known-results">Datasets and known results <a href="#datasets-and-known-results" class="anchor" aria-hidden="true"></a></h2> - <p class="section-desc"></p> - </th> - </tr></tbody><tbody><tr><td> - <p><code><a href="ds_mixed.html">ds_mixed</a></code> <code><a href="ds_mixed.html">ds_sfo</a></code> <code><a href="ds_mixed.html">ds_fomc</a></code> <code><a href="ds_mixed.html">ds_dfop</a></code> <code><a href="ds_mixed.html">ds_hs</a></code> <code><a href="ds_mixed.html">ds_dfop_sfo</a></code> </p> - </td> - <td><p>Synthetic data for hierarchical kinetic degradation models</p></td> - </tr><tr><td> - <p><code><a href="D24_2014.html">D24_2014</a></code> </p> - </td> - <td><p>Aerobic soil degradation data on 2,4-D from the EU assessment in 2014</p></td> - </tr><tr><td> - <p><code><a href="dimethenamid_2018.html">dimethenamid_2018</a></code> </p> - </td> - <td><p>Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018</p></td> - </tr><tr><td> - <p><code><a href="FOCUS_2006_datasets.html">FOCUS_2006_A</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_B</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_C</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_D</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_E</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_F</a></code> </p> - </td> - <td><p>Datasets A to F from the FOCUS Kinetics report from 2006</p></td> - </tr><tr><td> - <p><code><a href="FOCUS_2006_SFO_ref_A_to_F.html">FOCUS_2006_SFO_ref_A_to_F</a></code> </p> - </td> - <td><p>Results of fitting the SFO model to Datasets A to F of FOCUS (2006)</p></td> - </tr><tr><td> - <p><code><a href="FOCUS_2006_FOMC_ref_A_to_F.html">FOCUS_2006_FOMC_ref_A_to_F</a></code> </p> - </td> - <td><p>Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)</p></td> - </tr><tr><td> - <p><code><a href="FOCUS_2006_HS_ref_A_to_F.html">FOCUS_2006_HS_ref_A_to_F</a></code> </p> - </td> - <td><p>Results of fitting the HS model to Datasets A to F of FOCUS (2006)</p></td> - </tr><tr><td> - <p><code><a href="FOCUS_2006_DFOP_ref_A_to_B.html">FOCUS_2006_DFOP_ref_A_to_B</a></code> </p> - </td> - <td><p>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)</p></td> - </tr><tr><td> - <p><code><a href="NAFTA_SOP_2015.html">NAFTA_SOP_Appendix_B</a></code> <code><a href="NAFTA_SOP_2015.html">NAFTA_SOP_Appendix_D</a></code> </p> - </td> - <td><p>Example datasets from the NAFTA SOP published 2015</p></td> - </tr><tr><td> - <p><code><a href="NAFTA_SOP_Attachment.html">NAFTA_SOP_Attachment</a></code> </p> - </td> - <td><p>Example datasets from Attachment 1 to the NAFTA SOP published 2015</p></td> - </tr><tr><td> - <p><code><a href="mccall81_245T.html">mccall81_245T</a></code> </p> - </td> - <td><p>Datasets on aerobic soil metabolism of 2,4,5-T in six soils</p></td> - </tr><tr><td> - <p><code><a href="schaefer07_complex_case.html">schaefer07_complex_case</a></code> </p> - </td> - <td><p>Metabolism data set used for checking the software quality of KinGUI</p></td> - </tr><tr><td> - <p><code><a href="synthetic_data_for_UBA_2014.html">synthetic_data_for_UBA_2014</a></code> </p> - </td> - <td><p>Synthetic datasets for one parent compound with two metabolites</p></td> - </tr><tr><td> - <p><code><a href="experimental_data_for_UBA.html">experimental_data_for_UBA_2019</a></code> </p> - </td> - <td><p>Experimental datasets used for development and testing of error models</p></td> - </tr><tr><td> - <p><code><a href="test_data_from_UBA_2014.html">test_data_from_UBA_2014</a></code> </p> - </td> - <td><p>Three experimental datasets from two water sediment systems and one soil</p></td> - </tr><tr><td> - <p><code><a href="focus_soil_moisture.html">focus_soil_moisture</a></code> </p> - </td> - <td><p>FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar</p></td> - </tr><tr><td> - <p><code><a href="mkinds.html">print(<i><mkinds></i>)</a></code> </p> - </td> - <td><p>A dataset class for mkin</p></td> - </tr><tr><td> - <p><code><a href="mkindsg.html">print(<i><mkindsg></i>)</a></code> </p> - </td> - <td><p>A class for dataset groups for mkin</p></td> - </tr></tbody><tbody><tr><th colspan="2"> - <h2 id="nafta-guidance">NAFTA guidance <a href="#nafta-guidance" class="anchor" aria-hidden="true"></a></h2> - <p class="section-desc"></p> - </th> - </tr></tbody><tbody><tr><td> - <p><code><a href="nafta.html">nafta()</a></code> <code><a href="nafta.html">print(<i><nafta></i>)</a></code> </p> - </td> - <td><p>Evaluate parent kinetics using the NAFTA guidance</p></td> - </tr><tr><td> - <p><code><a href="plot.nafta.html">plot(<i><nafta></i>)</a></code> </p> - </td> - <td><p>Plot the results of the three models used in the NAFTA scheme.</p></td> - </tr></tbody><tbody><tr><th colspan="2"> - <h2 id="utility-functions">Utility functions <a href="#utility-functions" class="anchor" aria-hidden="true"></a></h2> - <p class="section-desc"></p> - </th> - </tr></tbody><tbody><tr><td> - <p><code><a href="summary_listing.html">summary_listing()</a></code> <code><a href="summary_listing.html">tex_listing()</a></code> <code><a href="summary_listing.html">html_listing()</a></code> </p> - </td> - <td><p>Display the output of a summary function according to the output format</p></td> - </tr><tr><td> - <p><code><a href="f_time_norm_focus.html">f_time_norm_focus()</a></code> </p> - </td> - <td><p>Normalisation factors for aerobic soil degradation according to FOCUS guidance</p></td> - </tr><tr><td> - <p><code><a href="set_nd_nq.html">set_nd_nq()</a></code> <code><a href="set_nd_nq.html">set_nd_nq_focus()</a></code> </p> - </td> - <td><p>Set non-detects and unquantified values in residue series without replicates</p></td> - </tr><tr><td> - <p><code><a href="max_twa_parent.html">max_twa_parent()</a></code> <code><a href="max_twa_parent.html">max_twa_sfo()</a></code> <code><a href="max_twa_parent.html">max_twa_fomc()</a></code> <code><a href="max_twa_parent.html">max_twa_dfop()</a></code> <code><a href="max_twa_parent.html">max_twa_hs()</a></code> </p> - </td> - <td><p>Function to calculate maximum time weighted average concentrations from -kinetic models fitted with mkinfit</p></td> - </tr><tr><td> - <p><code><a href="mkin_wide_to_long.html">mkin_wide_to_long()</a></code> </p> - </td> - <td><p>Convert a dataframe with observations over time into long format</p></td> - </tr><tr><td> - <p><code><a href="mkin_long_to_wide.html">mkin_long_to_wide()</a></code> </p> - </td> - <td><p>Convert a dataframe from long to wide format</p></td> - </tr></tbody><tbody><tr><th colspan="2"> - <h2 id="helper-functions-mainly-used-internally">Helper functions mainly used internally <a href="#helper-functions-mainly-used-internally" class="anchor" aria-hidden="true"></a></h2> - <p class="section-desc"></p> - </th> - </tr></tbody><tbody><tr><td> - <p><code><a href="mkinpredict.html">mkinpredict()</a></code> </p> - </td> - <td><p>Produce predictions from a kinetic model using specific parameters</p></td> - </tr><tr><td> - <p><code><a href="transform_odeparms.html">transform_odeparms()</a></code> <code><a href="transform_odeparms.html">backtransform_odeparms()</a></code> </p> - </td> - <td><p>Functions to transform and backtransform kinetic parameters for fitting</p></td> - </tr><tr><td> - <p><code><a href="ilr.html">ilr()</a></code> <code><a href="ilr.html">invilr()</a></code> </p> - </td> - <td><p>Function to perform isometric log-ratio transformation</p></td> - </tr><tr><td> - <p><code><a href="logLik.mkinfit.html">logLik(<i><mkinfit></i>)</a></code> </p> - </td> - <td><p>Calculated the log-likelihood of a fitted mkinfit object</p></td> - </tr><tr><td> - <p><code><a href="residuals.mkinfit.html">residuals(<i><mkinfit></i>)</a></code> </p> - </td> - <td><p>Extract residuals from an mkinfit model</p></td> - </tr><tr><td> - <p><code><a href="nobs.mkinfit.html">nobs(<i><mkinfit></i>)</a></code> </p> - </td> - <td><p>Number of observations on which an mkinfit object was fitted</p></td> - </tr><tr><td> - <p><code><a href="mkinresplot.html">mkinresplot()</a></code> </p> - </td> - <td><p>Function to plot residuals stored in an mkin object</p></td> - </tr><tr><td> - <p><code><a href="mkinparplot.html">mkinparplot()</a></code> </p> - </td> - <td><p>Function to plot the confidence intervals obtained using mkinfit</p></td> - </tr><tr><td> - <p><code><a href="mkinerrplot.html">mkinerrplot()</a></code> </p> - </td> - <td><p>Function to plot squared residuals and the error model for an mkin object</p></td> - </tr><tr><td> - <p><code><a href="mean_degparms.html">mean_degparms()</a></code> </p> - </td> - <td><p>Calculate mean degradation parameters for an mmkin row object</p></td> - </tr><tr><td> - <p><code><a href="create_deg_func.html">create_deg_func()</a></code> </p> - </td> - <td><p>Create degradation functions for known analytical solutions</p></td> - </tr></tbody><tbody><tr><th colspan="2"> - <h2 id="analytical-solutions">Analytical solutions <a href="#analytical-solutions" class="anchor" aria-hidden="true"></a></h2> - <p class="section-desc"></p><p>Parent only model solutions</p> - </th> - </tr></tbody><tbody><tr><td> - <p><code><a href="SFO.solution.html">SFO.solution()</a></code> </p> - </td> - <td><p>Single First-Order kinetics</p></td> - </tr><tr><td> - <p><code><a href="FOMC.solution.html">FOMC.solution()</a></code> </p> - </td> - <td><p>First-Order Multi-Compartment kinetics</p></td> - </tr><tr><td> - <p><code><a href="DFOP.solution.html">DFOP.solution()</a></code> </p> - </td> - <td><p>Double First-Order in Parallel kinetics</p></td> - </tr><tr><td> - <p><code><a href="SFORB.solution.html">SFORB.solution()</a></code> </p> - </td> - <td><p>Single First-Order Reversible Binding kinetics</p></td> - </tr><tr><td> - <p><code><a href="HS.solution.html">HS.solution()</a></code> </p> - </td> - <td><p>Hockey-Stick kinetics</p></td> - </tr><tr><td> - <p><code><a href="IORE.solution.html">IORE.solution()</a></code> </p> - </td> - <td><p>Indeterminate order rate equation kinetics</p></td> - </tr><tr><td> - <p><code><a href="logistic.solution.html">logistic.solution()</a></code> </p> - </td> - <td><p>Logistic kinetics</p></td> - </tr></tbody><tbody><tr><th colspan="2"> - <h2 id="generate-synthetic-datasets">Generate synthetic datasets <a href="#generate-synthetic-datasets" class="anchor" aria-hidden="true"></a></h2> - <p class="section-desc"></p> - </th> - </tr></tbody><tbody><tr><td> - <p><code><a href="add_err.html">add_err()</a></code> </p> - </td> - <td><p>Add normally distributed errors to simulated kinetic degradation data</p></td> - </tr><tr><td> - <p><code><a href="sigma_twocomp.html">sigma_twocomp()</a></code> </p> - </td> - <td><p>Two-component error model</p></td> - </tr></tbody><tbody><tr><th colspan="2"> - <h2 id="deprecated-functions">Deprecated functions <a href="#deprecated-functions" class="anchor" aria-hidden="true"></a></h2> - <p class="section-desc"></p><p>Functions that have been superseded</p> - </th> - </tr></tbody><tbody><tr><td> - <p><code><a href="mkinplot.html">mkinplot()</a></code> </p> - </td> - <td><p>Plot the observed data and the fitted model of an mkinfit object</p></td> - </tr></tbody></table></div> - - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + <dl><dt> + + <code><a href="mkinmod.html">mkinmod()</a></code> <code><a href="mkinmod.html">print(<i><mkinmod></i>)</a></code> <code><a href="mkinmod.html">mkinsub()</a></code> + </dt> + <dd>Function to set up a kinetic model with one or more state variables</dd> + </dl><dl><dt> + + <code><a href="mkinfit.html">mkinfit()</a></code> + </dt> + <dd>Fit a kinetic model to data with one or more state variables</dd> + </dl><dl><dt> + + <code><a href="mmkin.html">mmkin()</a></code> <code><a href="mmkin.html">print(<i><mmkin></i>)</a></code> + </dt> + <dd>Fit one or more kinetic models with one or more state variables to one or +more datasets</dd> + </dl><dl><dt> + + <code><a href="mhmkin.html">mhmkin()</a></code> <code><a href="mhmkin.html">`[`(<i><mhmkin></i>)</a></code> <code><a href="mhmkin.html">print(<i><mhmkin></i>)</a></code> + </dt> + <dd>Fit nonlinear mixed-effects models built from one or more kinetic +degradation models and one or more error models</dd> + </dl></div><div class="section level2"> + <h2 id="generics">Generics<a class="anchor" aria-label="anchor" href="#generics"></a></h2> + + <p class="section-desc"></p><p>Generic functions introduced by the package</p> + + </div><div id="" class="section level2"> + + + - <footer><div class="copyright"> + <dl><dt> + + <code><a href="parms.html">parms()</a></code> + </dt> + <dd>Extract model parameters</dd> + </dl><dl><dt> + + <code><a href="status.html">status()</a></code> <code><a href="status.html">print(<i><status.mmkin></i>)</a></code> <code><a href="status.html">print(<i><status.mhmkin></i>)</a></code> + </dt> + <dd>Method to get status information for fit array objects</dd> + </dl><dl><dt> + + <code><a href="illparms.html">illparms()</a></code> <code><a href="illparms.html">print(<i><illparms.mkinfit></i>)</a></code> <code><a href="illparms.html">print(<i><illparms.mmkin></i>)</a></code> <code><a href="illparms.html">print(<i><illparms.saem.mmkin></i>)</a></code> <code><a href="illparms.html">print(<i><illparms.mhmkin></i>)</a></code> + </dt> + <dd>Method to get the names of ill-defined parameters</dd> + </dl><dl><dt> + + <code><a href="endpoints.html">endpoints()</a></code> + </dt> + <dd>Function to calculate endpoints for further use from kinetic models fitted +with mkinfit</dd> + </dl><dl><dt> + + <code><a href="aw.html">aw()</a></code> + </dt> + <dd>Calculate Akaike weights for model averaging</dd> + </dl></div><div class="section level2"> + <h2 id="show-results">Show results<a class="anchor" aria-label="anchor" href="#show-results"></a></h2> + + <p class="section-desc"></p><p>Functions working with mkinfit objects</p> + + + </div><div id="" class="section level2"> + + + + + <dl><dt> + + <code><a href="plot.mkinfit.html">plot(<i><mkinfit></i>)</a></code> <code><a href="plot.mkinfit.html">plot_sep()</a></code> <code><a href="plot.mkinfit.html">plot_res()</a></code> <code><a href="plot.mkinfit.html">plot_err()</a></code> + </dt> + <dd>Plot the observed data and the fitted model of an mkinfit object</dd> + </dl><dl><dt> + + <code><a href="summary.mkinfit.html">summary(<i><mkinfit></i>)</a></code> <code><a href="summary.mkinfit.html">print(<i><summary.mkinfit></i>)</a></code> + </dt> + <dd>Summary method for class "mkinfit"</dd> + </dl><dl><dt> + + <code><a href="confint.mkinfit.html">confint(<i><mkinfit></i>)</a></code> + </dt> + <dd>Confidence intervals for parameters of mkinfit objects</dd> + </dl><dl><dt> + + <code><a href="update.mkinfit.html">update(<i><mkinfit></i>)</a></code> + </dt> + <dd>Update an mkinfit model with different arguments</dd> + </dl><dl><dt> + + <code><a href="lrtest.mkinfit.html">lrtest(<i><mkinfit></i>)</a></code> <code><a href="lrtest.mkinfit.html">lrtest(<i><mmkin></i>)</a></code> + </dt> + <dd>Likelihood ratio test for mkinfit models</dd> + </dl><dl><dt> + + <code><a href="loftest.html">loftest()</a></code> + </dt> + <dd>Lack-of-fit test for models fitted to data with replicates</dd> + </dl><dl><dt> + + <code><a href="mkinerrmin.html">mkinerrmin()</a></code> + </dt> + <dd>Calculate the minimum error to assume in order to pass the variance test</dd> + </dl><dl><dt> + + <code><a href="CAKE_export.html">CAKE_export()</a></code> + </dt> + <dd>Export a list of datasets format to a CAKE study file</dd> + </dl></div><div class="section level2"> + <h2 id="work-with-mmkin-objects">Work with mmkin objects<a class="anchor" aria-label="anchor" href="#work-with-mmkin-objects"></a></h2> + + <p class="section-desc"></p><p>Functions working with aggregated results</p> + + + </div><div id="" class="section level2"> + + + + + <dl><dt> + + <code><a href="Extract.mmkin.html">`[`(<i><mmkin></i>)</a></code> + </dt> + <dd>Subsetting method for mmkin objects</dd> + </dl><dl><dt> + + <code><a href="plot.mmkin.html">plot(<i><mmkin></i>)</a></code> + </dt> + <dd>Plot model fits (observed and fitted) and the residuals for a row or column +of an mmkin object</dd> + </dl><dl><dt> + + <code><a href="AIC.mmkin.html">AIC(<i><mmkin></i>)</a></code> <code><a href="AIC.mmkin.html">BIC(<i><mmkin></i>)</a></code> + </dt> + <dd>Calculate the AIC for a column of an mmkin object</dd> + </dl><dl><dt> + + <code><a href="summary.mmkin.html">summary(<i><mmkin></i>)</a></code> <code><a href="summary.mmkin.html">print(<i><summary.mmkin></i>)</a></code> + </dt> + <dd>Summary method for class "mmkin"</dd> + </dl></div><div class="section level2"> + <h2 id="mixed-models">Mixed models<a class="anchor" aria-label="anchor" href="#mixed-models"></a></h2> + + <p class="section-desc"></p><p>Create and work with nonlinear hierarchical models</p> + + + </div><div id="" class="section level2"> + + + + + <dl><dt> + + <code><a href="hierarchical_kinetics.html">hierarchical_kinetics()</a></code> + </dt> + <dd>Hierarchical kinetics template</dd> + </dl><dl><dt> + + <code><a href="read_spreadsheet.html">read_spreadsheet()</a></code> + </dt> + <dd>Read datasets and relevant meta information from a spreadsheet file</dd> + </dl><dl><dt> + + <code><a href="nlme.mmkin.html">nlme(<i><mmkin></i>)</a></code> <code><a href="nlme.mmkin.html">print(<i><nlme.mmkin></i>)</a></code> <code><a href="nlme.mmkin.html">update(<i><nlme.mmkin></i>)</a></code> + </dt> + <dd>Create an nlme model for an mmkin row object</dd> + </dl><dl><dt> + + <code><a href="saem.html">saem()</a></code> <code><a href="saem.html">print(<i><saem.mmkin></i>)</a></code> <code><a href="saem.html">saemix_model()</a></code> <code><a href="saem.html">saemix_data()</a></code> + </dt> + <dd>Fit nonlinear mixed models with SAEM</dd> + </dl><dl><dt> + + <code><a href="mhmkin.html">mhmkin()</a></code> <code><a href="mhmkin.html">`[`(<i><mhmkin></i>)</a></code> <code><a href="mhmkin.html">print(<i><mhmkin></i>)</a></code> + </dt> + <dd>Fit nonlinear mixed-effects models built from one or more kinetic +degradation models and one or more error models</dd> + </dl><dl><dt> + + <code><a href="plot.mixed.mmkin.html">plot(<i><mixed.mmkin></i>)</a></code> + </dt> + <dd>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</dd> + </dl><dl><dt> + + <code><a href="summary.nlme.mmkin.html">summary(<i><nlme.mmkin></i>)</a></code> <code><a href="summary.nlme.mmkin.html">print(<i><summary.nlme.mmkin></i>)</a></code> + </dt> + <dd>Summary method for class "nlme.mmkin"</dd> + </dl><dl><dt> + + <code><a href="summary.saem.mmkin.html">summary(<i><saem.mmkin></i>)</a></code> <code><a href="summary.saem.mmkin.html">print(<i><summary.saem.mmkin></i>)</a></code> + </dt> + <dd>Summary method for class "saem.mmkin"</dd> + </dl><dl><dt> + + <code><a href="anova.saem.mmkin.html">anova(<i><saem.mmkin></i>)</a></code> + </dt> + <dd>Anova method for saem.mmkin objects</dd> + </dl><dl><dt> + + <code><a href="logLik.saem.mmkin.html">logLik(<i><saem.mmkin></i>)</a></code> + </dt> + <dd>logLik method for saem.mmkin objects</dd> + </dl><dl><dt> + + <code><a href="nlme.html">nlme_function()</a></code> <code><a href="nlme.html">nlme_data()</a></code> + </dt> + <dd>Helper functions to create nlme models from mmkin row objects</dd> + </dl><dl><dt> + + <code><a href="get_deg_func.html">get_deg_func()</a></code> + </dt> + <dd>Retrieve a degradation function from the mmkin namespace</dd> + </dl><dl><dt> + + <code><a href="mixed.html">mixed()</a></code> <code><a href="mixed.html">print(<i><mixed.mmkin></i>)</a></code> + </dt> + <dd>Create a mixed effects model from an mmkin row object</dd> + </dl><dl><dt> + + <code><a href="reexports.html">reexports</a></code> <code><a href="reexports.html">intervals</a></code> <code><a href="reexports.html">lrtest</a></code> <code><a href="reexports.html">nlme</a></code> + </dt> + <dd>Objects exported from other packages</dd> + </dl><dl><dt> + + <code><a href="intervals.saem.mmkin.html">intervals(<i><saem.mmkin></i>)</a></code> + </dt> + <dd>Confidence intervals for parameters in saem.mmkin objects</dd> + </dl><dl><dt> + + <code><a href="multistart.html">multistart()</a></code> <code><a href="multistart.html">print(<i><multistart></i>)</a></code> <code><a href="multistart.html">best()</a></code> <code><a href="multistart.html">which.best()</a></code> + </dt> + <dd>Perform a hierarchical model fit with multiple starting values</dd> + </dl><dl><dt> + + <code><a href="llhist.html">llhist()</a></code> + </dt> + <dd>Plot the distribution of log likelihoods from multistart objects</dd> + </dl><dl><dt> + + <code><a href="parplot.html">parplot()</a></code> + </dt> + <dd>Plot parameter variability of multistart objects</dd> + </dl></div><div class="section level2"> + <h2 id="datasets-and-known-results">Datasets and known results<a class="anchor" aria-label="anchor" href="#datasets-and-known-results"></a></h2> + + + + + </div><div id="" class="section level2"> + + + + + <dl><dt> + + <code><a href="ds_mixed.html">ds_mixed</a></code> <code><a href="ds_mixed.html">ds_sfo</a></code> <code><a href="ds_mixed.html">ds_fomc</a></code> <code><a href="ds_mixed.html">ds_dfop</a></code> <code><a href="ds_mixed.html">ds_hs</a></code> <code><a href="ds_mixed.html">ds_dfop_sfo</a></code> + </dt> + <dd>Synthetic data for hierarchical kinetic degradation models</dd> + </dl><dl><dt> + + <code><a href="D24_2014.html">D24_2014</a></code> + </dt> + <dd>Aerobic soil degradation data on 2,4-D from the EU assessment in 2014</dd> + </dl><dl><dt> + + <code><a href="dimethenamid_2018.html">dimethenamid_2018</a></code> + </dt> + <dd>Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018</dd> + </dl><dl><dt> + + <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_A</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_B</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_C</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_D</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_E</a></code> <code><a href="FOCUS_2006_datasets.html">FOCUS_2006_F</a></code> + </dt> + <dd>Datasets A to F from the FOCUS Kinetics report from 2006</dd> + </dl><dl><dt> + + <code><a href="FOCUS_2006_SFO_ref_A_to_F.html">FOCUS_2006_SFO_ref_A_to_F</a></code> + </dt> + <dd>Results of fitting the SFO model to Datasets A to F of FOCUS (2006)</dd> + </dl><dl><dt> + + <code><a href="FOCUS_2006_FOMC_ref_A_to_F.html">FOCUS_2006_FOMC_ref_A_to_F</a></code> + </dt> + <dd>Results of fitting the FOMC model to Datasets A to F of FOCUS (2006)</dd> + </dl><dl><dt> + + <code><a href="FOCUS_2006_HS_ref_A_to_F.html">FOCUS_2006_HS_ref_A_to_F</a></code> + </dt> + <dd>Results of fitting the HS model to Datasets A to F of FOCUS (2006)</dd> + </dl><dl><dt> + + <code><a href="FOCUS_2006_DFOP_ref_A_to_B.html">FOCUS_2006_DFOP_ref_A_to_B</a></code> + </dt> + <dd>Results of fitting the DFOP model to Datasets A to B of FOCUS (2006)</dd> + </dl><dl><dt> + + <code><a href="NAFTA_SOP_2015.html">NAFTA_SOP_Appendix_B</a></code> <code><a href="NAFTA_SOP_2015.html">NAFTA_SOP_Appendix_D</a></code> + </dt> + <dd>Example datasets from the NAFTA SOP published 2015</dd> + </dl><dl><dt> + + <code><a href="NAFTA_SOP_Attachment.html">NAFTA_SOP_Attachment</a></code> + </dt> + <dd>Example datasets from Attachment 1 to the NAFTA SOP published 2015</dd> + </dl><dl><dt> + + <code><a href="mccall81_245T.html">mccall81_245T</a></code> + </dt> + <dd>Datasets on aerobic soil metabolism of 2,4,5-T in six soils</dd> + </dl><dl><dt> + + <code><a href="schaefer07_complex_case.html">schaefer07_complex_case</a></code> + </dt> + <dd>Metabolism data set used for checking the software quality of KinGUI</dd> + </dl><dl><dt> + + <code><a href="synthetic_data_for_UBA_2014.html">synthetic_data_for_UBA_2014</a></code> + </dt> + <dd>Synthetic datasets for one parent compound with two metabolites</dd> + </dl><dl><dt> + + <code><a href="experimental_data_for_UBA.html">experimental_data_for_UBA_2019</a></code> + </dt> + <dd>Experimental datasets used for development and testing of error models</dd> + </dl><dl><dt> + + <code><a href="test_data_from_UBA_2014.html">test_data_from_UBA_2014</a></code> + </dt> + <dd>Three experimental datasets from two water sediment systems and one soil</dd> + </dl><dl><dt> + + <code><a href="focus_soil_moisture.html">focus_soil_moisture</a></code> + </dt> + <dd>FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar</dd> + </dl><dl><dt> + + <code><a href="mkinds.html">print(<i><mkinds></i>)</a></code> + </dt> + <dd>A dataset class for mkin</dd> + </dl><dl><dt> + + <code><a href="mkindsg.html">print(<i><mkindsg></i>)</a></code> + </dt> + <dd>A class for dataset groups for mkin</dd> + </dl></div><div class="section level2"> + <h2 id="nafta-guidance">NAFTA guidance<a class="anchor" aria-label="anchor" href="#nafta-guidance"></a></h2> + + + + + </div><div id="" class="section level2"> + + + + + <dl><dt> + + <code><a href="nafta.html">nafta()</a></code> <code><a href="nafta.html">print(<i><nafta></i>)</a></code> + </dt> + <dd>Evaluate parent kinetics using the NAFTA guidance</dd> + </dl><dl><dt> + + <code><a href="plot.nafta.html">plot(<i><nafta></i>)</a></code> + </dt> + <dd>Plot the results of the three models used in the NAFTA scheme.</dd> + </dl></div><div class="section level2"> + <h2 id="utility-functions">Utility functions<a class="anchor" aria-label="anchor" href="#utility-functions"></a></h2> + + + + + </div><div id="" class="section level2"> + + + + + <dl><dt> + + <code><a href="summary_listing.html">summary_listing()</a></code> <code><a href="summary_listing.html">tex_listing()</a></code> <code><a href="summary_listing.html">html_listing()</a></code> + </dt> + <dd>Display the output of a summary function according to the output format</dd> + </dl><dl><dt> + + <code><a href="f_time_norm_focus.html">f_time_norm_focus()</a></code> + </dt> + <dd>Normalisation factors for aerobic soil degradation according to FOCUS guidance</dd> + </dl><dl><dt> + + <code><a href="set_nd_nq.html">set_nd_nq()</a></code> <code><a href="set_nd_nq.html">set_nd_nq_focus()</a></code> + </dt> + <dd>Set non-detects and unquantified values in residue series without replicates</dd> + </dl><dl><dt> + + <code><a href="max_twa_parent.html">max_twa_parent()</a></code> <code><a href="max_twa_parent.html">max_twa_sfo()</a></code> <code><a href="max_twa_parent.html">max_twa_fomc()</a></code> <code><a href="max_twa_parent.html">max_twa_dfop()</a></code> <code><a href="max_twa_parent.html">max_twa_hs()</a></code> + </dt> + <dd>Function to calculate maximum time weighted average concentrations from +kinetic models fitted with mkinfit</dd> + </dl><dl><dt> + + <code><a href="mkin_wide_to_long.html">mkin_wide_to_long()</a></code> + </dt> + <dd>Convert a dataframe with observations over time into long format</dd> + </dl><dl><dt> + + <code><a href="mkin_long_to_wide.html">mkin_long_to_wide()</a></code> + </dt> + <dd>Convert a dataframe from long to wide format</dd> + </dl></div><div class="section level2"> + <h2 id="helper-functions-mainly-used-internally">Helper functions mainly used internally<a class="anchor" aria-label="anchor" href="#helper-functions-mainly-used-internally"></a></h2> + + + + + </div><div id="" class="section level2"> + + + + + <dl><dt> + + <code><a href="mkinpredict.html">mkinpredict()</a></code> + </dt> + <dd>Produce predictions from a kinetic model using specific parameters</dd> + </dl><dl><dt> + + <code><a href="transform_odeparms.html">transform_odeparms()</a></code> <code><a href="transform_odeparms.html">backtransform_odeparms()</a></code> + </dt> + <dd>Functions to transform and backtransform kinetic parameters for fitting</dd> + </dl><dl><dt> + + <code><a href="ilr.html">ilr()</a></code> <code><a href="ilr.html">invilr()</a></code> + </dt> + <dd>Function to perform isometric log-ratio transformation</dd> + </dl><dl><dt> + + <code><a href="logLik.mkinfit.html">logLik(<i><mkinfit></i>)</a></code> + </dt> + <dd>Calculated the log-likelihood of a fitted mkinfit object</dd> + </dl><dl><dt> + + <code><a href="residuals.mkinfit.html">residuals(<i><mkinfit></i>)</a></code> + </dt> + <dd>Extract residuals from an mkinfit model</dd> + </dl><dl><dt> + + <code><a href="nobs.mkinfit.html">nobs(<i><mkinfit></i>)</a></code> + </dt> + <dd>Number of observations on which an mkinfit object was fitted</dd> + </dl><dl><dt> + + <code><a href="mkinresplot.html">mkinresplot()</a></code> + </dt> + <dd>Function to plot residuals stored in an mkin object</dd> + </dl><dl><dt> + + <code><a href="mkinparplot.html">mkinparplot()</a></code> + </dt> + <dd>Function to plot the confidence intervals obtained using mkinfit</dd> + </dl><dl><dt> + + <code><a href="mkinerrplot.html">mkinerrplot()</a></code> + </dt> + <dd>Function to plot squared residuals and the error model for an mkin object</dd> + </dl><dl><dt> + + <code><a href="mean_degparms.html">mean_degparms()</a></code> + </dt> + <dd>Calculate mean degradation parameters for an mmkin row object</dd> + </dl><dl><dt> + + <code><a href="create_deg_func.html">create_deg_func()</a></code> + </dt> + <dd>Create degradation functions for known analytical solutions</dd> + </dl></div><div class="section level2"> + <h2 id="analytical-solutions">Analytical solutions<a class="anchor" aria-label="anchor" href="#analytical-solutions"></a></h2> + + <p class="section-desc"></p><p>Parent only model solutions</p> + + + </div><div id="" class="section level2"> + + + + + <dl><dt> + + <code><a href="SFO.solution.html">SFO.solution()</a></code> + </dt> + <dd>Single First-Order kinetics</dd> + </dl><dl><dt> + + <code><a href="FOMC.solution.html">FOMC.solution()</a></code> + </dt> + <dd>First-Order Multi-Compartment kinetics</dd> + </dl><dl><dt> + + <code><a href="DFOP.solution.html">DFOP.solution()</a></code> + </dt> + <dd>Double First-Order in Parallel kinetics</dd> + </dl><dl><dt> + + <code><a href="SFORB.solution.html">SFORB.solution()</a></code> + </dt> + <dd>Single First-Order Reversible Binding kinetics</dd> + </dl><dl><dt> + + <code><a href="HS.solution.html">HS.solution()</a></code> + </dt> + <dd>Hockey-Stick kinetics</dd> + </dl><dl><dt> + + <code><a href="IORE.solution.html">IORE.solution()</a></code> + </dt> + <dd>Indeterminate order rate equation kinetics</dd> + </dl><dl><dt> + + <code><a href="logistic.solution.html">logistic.solution()</a></code> + </dt> + <dd>Logistic kinetics</dd> + </dl></div><div class="section level2"> + <h2 id="generate-synthetic-datasets">Generate synthetic datasets<a class="anchor" aria-label="anchor" href="#generate-synthetic-datasets"></a></h2> + + + + + </div><div id="" class="section level2"> + + + + + <dl><dt> + + <code><a href="add_err.html">add_err()</a></code> + </dt> + <dd>Add normally distributed errors to simulated kinetic degradation data</dd> + </dl><dl><dt> + + <code><a href="sigma_twocomp.html">sigma_twocomp()</a></code> + </dt> + <dd>Two-component error model</dd> + </dl></div><div class="section level2"> + <h2 id="deprecated-functions">Deprecated functions<a class="anchor" aria-label="anchor" href="#deprecated-functions"></a></h2> + + <p class="section-desc"></p><p>Functions that have been superseded</p> + + + </div><div id="" class="section level2"> + + + + + <dl><dt> + + <code><a href="mkinplot.html">mkinplot()</a></code> + </dt> + <dd>Plot the observed data and the fitted model of an mkinfit object</dd> + </dl></div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> + + + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/intervals.saem.mmkin.html b/docs/reference/intervals.saem.mmkin.html index d52d8501..36341eba 100644 --- a/docs/reference/intervals.saem.mmkin.html +++ b/docs/reference/intervals.saem.mmkin.html @@ -1,124 +1,90 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta 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alt=""><h1>Confidence intervals for parameters in saem.mmkin objects</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/intervals.R" class="external-link"><code>R/intervals.R</code></a></small> + <div class="d-none name"><code>intervals.saem.mmkin.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Confidence intervals for parameters in saem.mmkin objects</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for saem.mmkin</span></span> <span><span class="fu"><a href="https://rdrr.io/pkg/nlme/man/intervals.html" class="external-link">intervals</a></span><span class="op">(</span><span class="va">object</span>, level <span class="op">=</span> <span class="fl">0.95</span>, backtransform <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>The fitted saem.mmkin object</p></dd> @@ -138,34 +104,30 @@ between transformed and backtransformed parameters exists?</p></dd> <dd><p>For compatibility with the generic method</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>An object with 'intervals.saem.mmkin' and 'intervals.lme' in the class attribute</p> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav 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<div class="hidden name"><code>llhist.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Plot the distribution of log likelihoods from multistart objects</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/llhist.R" class="external-link"><code>R/llhist.R</code></a></small> + <div class="d-none name"><code>llhist.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Produces a histogram of log-likelihoods. In addition, the likelihood of the original fit is shown as a red vertical line.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">llhist</span><span class="op">(</span><span class="va">object</span>, breaks <span class="op">=</span> <span class="st">"Sturges"</span>, lpos <span class="op">=</span> <span class="st">"topleft"</span>, main <span class="op">=</span> <span class="st">""</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>The <a href="multistart.html">multistart</a> object</p></dd> @@ -140,31 +107,27 @@ original fit is shown as a red vertical line.</p> <dd><p>Passed to <a href="https://rdrr.io/r/graphics/hist.html" class="external-link">hist</a></p></dd> </dl></div> - <div id="see-also"> - <h2>See also</h2> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <div class="dont-index"><p><a href="multistart.html">multistart</a></p></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/loftest-1.png b/docs/reference/loftest-1.png Binary files differindex f1dc5fa7..750a2acf 100644 --- a/docs/reference/loftest-1.png +++ b/docs/reference/loftest-1.png diff --git a/docs/reference/loftest-2.png b/docs/reference/loftest-2.png Binary files differindex 3f1015a9..d12c26e7 100644 --- a/docs/reference/loftest-2.png +++ b/docs/reference/loftest-2.png diff --git a/docs/reference/loftest-3.png b/docs/reference/loftest-3.png Binary files differindex e876cbab..1b2fd838 100644 --- a/docs/reference/loftest-3.png +++ b/docs/reference/loftest-3.png diff --git a/docs/reference/loftest-4.png b/docs/reference/loftest-4.png Binary files differindex ac44c162..3beb9d1a 100644 --- a/docs/reference/loftest-4.png +++ b/docs/reference/loftest-4.png diff --git a/docs/reference/loftest-5.png b/docs/reference/loftest-5.png Binary files differindex 14537feb..f60f5ff7 100644 --- a/docs/reference/loftest-5.png +++ b/docs/reference/loftest-5.png diff --git a/docs/reference/loftest.html b/docs/reference/loftest.html index b474ad20..ed4141a8 100644 --- a/docs/reference/loftest.html +++ b/docs/reference/loftest.html @@ -1,132 +1,101 @@ <!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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<div class="hidden name"><code>loftest.Rd</code></div> + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Lack-of-fit test for models fitted to data with replicates</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/loftest.R" class="external-link"><code>R/loftest.R</code></a></small> + <div class="d-none name"><code>loftest.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>This is a generic function with a method currently only defined for mkinfit objects. It fits an anova model to the data contained in the object and compares the likelihoods using the likelihood ratio test <code><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest.default</a></code> from the lmtest package.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">loftest</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> <span><span class="co"># S3 method for mkinfit</span></span> <span><span class="fu">loftest</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>A model object with a defined loftest method</p></dd> @@ -135,20 +104,20 @@ compares the likelihoods using the likelihood ratio test <dd><p>Not used</p></dd> </dl></div> - <div id="details"> - <h2>Details</h2> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <p>The anova model is interpreted as the simplest form of an mkinfit model, assuming only a constant variance about the means, but not enforcing any structure of the means, so we have one model parameter for every mean of replicate samples.</p> </div> - <div id="see-also"> - <h2>See also</h2> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <div class="dont-index"><p>lrtest</p></div> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> <span class="r-in"><span><span class="va">test_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, <span class="va">name</span> <span class="op">==</span> <span class="st">"parent"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">sfo_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">test_data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> @@ -319,26 +288,22 @@ of replicate samples.</p> <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/logLik.mkinfit.html b/docs/reference/logLik.mkinfit.html index 07884f26..7b7b15b6 100644 --- 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href="https://github.com/jranke/mkin/blob/HEAD/R/logLik.mkinfit.R" class="external-link"><code>R/logLik.mkinfit.R</code></a></small> - <div class="hidden name"><code>logLik.mkinfit.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Calculated the log-likelihood of a fitted mkinfit object</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/logLik.mkinfit.R" class="external-link"><code>R/logLik.mkinfit.R</code></a></small> + <div class="d-none name"><code>logLik.mkinfit.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>This function returns the product of the likelihood densities of each observed value, as calculated as part of the fitting procedure using <code><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">dnorm</a></code>, i.e. assuming normal distribution, and with the means @@ -120,13 +89,14 @@ predicted by the degradation model, and the standard deviations predicted by the error model.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> <span><span class="fu"><a href="https://rdrr.io/r/stats/logLik.html" class="external-link">logLik</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>An object of class <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd> @@ -135,32 +105,32 @@ the error model.</p> <dd><p>For compatibility with the generic method</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>An object of class <code><a href="https://rdrr.io/r/stats/logLik.html" class="external-link">logLik</a></code> with the number of estimated parameters (degradation model parameters plus variance model parameters) as attribute.</p> </div> - <div id="details"> - <h2>Details</h2> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <p>The total number of estimated parameters returned with the value of the likelihood is calculated as the sum of fitted degradation model parameters and the fitted error model parameters.</p> </div> - <div id="see-also"> - <h2>See also</h2> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <div class="dont-index"><p>Compare the AIC of columns of <code><a href="mmkin.html">mmkin</a></code> objects using <code><a href="AIC.mmkin.html">AIC.mmkin</a></code>.</p></div> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span> <span class="co"># \dontrun{</span></span></span> <span class="r-in"><span> <span class="va">sfo_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> @@ -181,26 +151,22 @@ and the fitted error model parameters.</p> <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/logLik.saem.mmkin.html b/docs/reference/logLik.saem.mmkin.html index 92d14aed..912abece 100644 --- a/docs/reference/logLik.saem.mmkin.html +++ b/docs/reference/logLik.saem.mmkin.html @@ -1,124 +1,90 @@ <!DOCTYPE html> 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mkin</a> + <a class="dropdown-item" href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + <a class="dropdown-item" href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6> + <a class="dropdown-item" href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a class="dropdown-item" href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </div> </li> - </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> +<li class="nav-item"> + <a class="nav-link" href="../news/index.html">News</a> +</li> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" 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for saem.mmkin objects</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/saem.R" class="external-link"><code>R/saem.R</code></a></small> + <div class="d-none name"><code>logLik.saem.mmkin.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>logLik method for saem.mmkin objects</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for saem.mmkin</span></span> <span><span class="fu"><a href="https://rdrr.io/r/stats/logLik.html" class="external-link">logLik</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span>, method <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"is"</span>, <span class="st">"lin"</span>, <span class="st">"gq"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>The fitted <a href="saem.html">saem.mmkin</a> object</p></dd> @@ -132,26 +98,22 @@ </dl></div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" 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--> - </div><!--/.container --> -</div><!--/.navbar --> + </ul></div> - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Logistic kinetics</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/parent_solutions.R" class="external-link"><code>R/parent_solutions.R</code></a></small> - <div class="hidden name"><code>logistic.solution.Rd</code></div> + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Logistic kinetics</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/parent_solutions.R" class="external-link"><code>R/parent_solutions.R</code></a></small> + <div class="d-none name"><code>logistic.solution.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Function describing exponential decline from a defined starting value, with an increasing rate constant, supposedly caused by microbial growth</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">logistic.solution</span><span class="op">(</span><span class="va">t</span>, <span class="va">parent_0</span>, <span class="va">kmax</span>, <span class="va">k0</span>, <span class="va">r</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>t</dt> <dd><p>Time.</p></dd> @@ -140,19 +107,19 @@ an increasing rate constant, supposedly caused by microbial growth</p> <dd><p>Growth rate of the increase in the rate constant.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>The value of the response variable at time <code>t</code>.</p> </div> - <div id="note"> - <h2>Note</h2> + <div class="section level2"> + <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2> <p>The solution of the logistic model reduces to the <code><a href="SFO.solution.html">SFO.solution</a></code> if <code>k0</code> is equal to <code>kmax</code>.</p> </div> - <div id="references"> - <h2>References</h2> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, @@ -164,8 +131,8 @@ EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, Version 1.1, 18 December 2014 <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> </div> - <div id="see-also"> - <h2>See also</h2> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <div class="dont-index"><p>Other parent solutions: <code><a href="DFOP.solution.html">DFOP.solution</a>()</code>, <code><a href="FOMC.solution.html">FOMC.solution</a>()</code>, @@ -175,8 +142,8 @@ Version 1.1, 18 December 2014 <code><a href="SFORB.solution.html">SFORB.solution</a>()</code></p></div> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span> <span class="co"># Reproduce the plot on page 57 of FOCUS (2014)</span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu">logistic.solution</span><span class="op">(</span><span class="va">x</span>, <span class="fl">100</span>, <span class="fl">0.08</span>, <span class="fl">0.0001</span>, <span class="fl">0.2</span><span class="op">)</span>,</span></span> @@ -230,26 +197,22 @@ Version 1.1, 18 December 2014 <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - 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It is the responsibility of the user to make sure +that the models are nested, i.e. one of them has less degrees of freedom +and can be expressed by fixing the parameters of the other."><title>Likelihood ratio test for mkinfit models — lrtest.mkinfit • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- 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><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Likelihood ratio test for mkinfit models — lrtest.mkinfit"><meta property="og:description" content="Compare two mkinfit models based on their likelihood. 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It is the responsibility of the user to make sure that the models are nested, i.e. one of them has less degrees of freedom and can be expressed by fixing the parameters of the other."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--></head><body data-spy="scroll" data-target="#toc"> +<![endif]--></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - <div class="container template-reference-topic"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> - 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<div class="hidden name"><code>lrtest.mkinfit.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Likelihood ratio test for mkinfit models</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/lrtest.mkinfit.R" class="external-link"><code>R/lrtest.mkinfit.R</code></a></small> + <div class="d-none name"><code>lrtest.mkinfit.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Compare two mkinfit models based on their likelihood. If two fitted mkinfit objects are given as arguments, it is checked if they have been fitted to the same data. It is the responsibility of the user to make sure @@ -120,7 +89,8 @@ that the models are nested, i.e. one of them has less degrees of freedom and can be expressed by fixing the parameters of the other.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> <span><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">object</span>, object_2 <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> @@ -128,8 +98,8 @@ and can be expressed by fixing the parameters of the other.</p> <span><span class="fu"><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>An <code><a href="mkinfit.html">mkinfit</a></code> object, or an <code><a href="mmkin.html">mmkin</a></code> column object containing two fits to the same data.</p></dd> @@ -144,8 +114,8 @@ object containing two fits to the same data.</p></dd> <code><a href="update.mkinfit.html">update.mkinfit</a></code> for creating the alternative fitted object.</p></dd> </dl></div> - <div id="details"> - <h2>Details</h2> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <p>Alternatively, an argument to mkinfit can be given which is then passed to <code><a href="update.mkinfit.html">update.mkinfit</a></code> to obtain the alternative model.</p> <p>The comparison is then made by the <code><a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest.default</a></code> @@ -154,8 +124,8 @@ parameters (alternative hypothesis) is listed first, then the model with the lower number of fitted parameters (null hypothesis).</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> <span class="r-in"><span><span class="va">test_data</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">synthetic_data_for_UBA_2014</span><span class="op">[[</span><span class="fl">12</span><span class="op">]</span><span class="op">]</span><span class="op">$</span><span class="va">data</span>, <span class="va">name</span> <span class="op">==</span> <span class="st">"parent"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">sfo_fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="va">test_data</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> @@ -210,26 +180,22 @@ lower number of fitted parameters (null hypothesis).</p> <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/max_twa_parent.html b/docs/reference/max_twa_parent.html index 892aa4e1..c560a763 100644 --- a/docs/reference/max_twa_parent.html +++ b/docs/reference/max_twa_parent.html @@ -1,6 +1,10 @@ <!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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<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/max_twa_parent.R" class="external-link"><code>R/max_twa_parent.R</code></a></small> - <div class="hidden name"><code>max_twa_parent.Rd</code></div> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/max_twa_parent.R" class="external-link"><code>R/max_twa_parent.R</code></a></small> + <div class="d-none name"><code>max_twa_parent.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>This function calculates maximum moving window time weighted average concentrations (TWAs) for kinetic models fitted with <code><a href="mkinfit.html">mkinfit</a></code>. Currently, only calculations for the parent are implemented for the SFO, @@ -123,7 +92,8 @@ FOMC, DFOP and HS models, using the analytical formulas given in the PEC soil section of the FOCUS guidance.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">max_twa_parent</span><span class="op">(</span><span class="va">fit</span>, <span class="va">windows</span><span class="op">)</span></span> <span></span> <span><span class="fu">max_twa_sfo</span><span class="op">(</span>M0 <span class="op">=</span> <span class="fl">1</span>, <span class="va">k</span>, <span class="va">t</span><span class="op">)</span></span> @@ -135,8 +105,8 @@ soil section of the FOCUS guidance.</p> <span><span class="fu">max_twa_hs</span><span class="op">(</span>M0 <span class="op">=</span> <span class="fl">1</span>, <span class="va">k1</span>, <span class="va">k2</span>, <span class="va">tb</span>, <span class="va">t</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>fit</dt> <dd><p>An object of class <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd> @@ -185,29 +155,29 @@ factor (f_twa) is calculated.</p></dd> <dd><p>Parameter of the HS model.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>For <code>max_twa_parent</code>, a numeric vector, named using the <code>windows</code> argument. For the other functions, a numeric vector of length one (also known as 'a number').</p> </div> - <div id="references"> - <h2>References</h2> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span> <span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"FOMC"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span> <span class="fu">max_twa_parent</span><span class="op">(</span><span class="va">fit</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">7</span>, <span class="fl">21</span><span class="op">)</span><span class="op">)</span></span></span> @@ -216,26 +186,22 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/mccall81_245T-1.png b/docs/reference/mccall81_245T-1.png Binary files differindex 79c45fe6..5e4ea6ef 100644 --- a/docs/reference/mccall81_245T-1.png +++ b/docs/reference/mccall81_245T-1.png diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 6b057c9d..6de846be 100644 --- 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soils</h1> + + <div class="d-none name"><code>mccall81_245T.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Time course of 2,4,5-trichlorophenoxyacetic acid, and the corresponding 2,4,5-trichlorophenol and 2,4,5-trichloroanisole as recovered in diethylether extracts.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">mccall81_245T</span></span></code></pre></div> </div> - <div id="format"> - <h2>Format</h2> + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>A dataframe containing the following variables.</p><dl><dt><code>name</code></dt> <dd><p>the name of the compound observed. Note that T245 is used as an acronym for 2,4,5-T. T245 is a legitimate object name @@ -140,14 +108,14 @@ </dl></div> - <div id="source"> - <h2>Source</h2> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <p>McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labelled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107 <a href="https://doi.org/10.1021/jf00103a026" class="external-link">doi:10.1021/jf00103a026</a></p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="va">SFO_SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>T245 <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"phenol"</span><span class="op">)</span>,</span></span> <span class="r-in"><span> phenol <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"anisole"</span><span class="op">)</span>,</span></span> <span class="r-in"><span> anisole <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> @@ -224,26 +192,22 @@ <span class="r-in"><span> <span class="co"># }</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div 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href="https://github.com/jranke/mkin/blob/HEAD/R/mean_degparms.R" class="external-link"><code>R/mean_degparms.R</code></a></small> + <div class="d-none name"><code>mean_degparms.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Calculate mean degradation parameters for an mmkin row object</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mean_degparms</span><span class="op">(</span></span> <span> <span class="va">object</span>,</span> <span> random <span class="op">=</span> <span class="cn">FALSE</span>,</span> @@ -122,8 +88,8 @@ <span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>An mmkin row object containing several fits of the same model to different datasets</p></dd> @@ -149,8 +115,8 @@ as a default value for the tested log parameters that failed the t-test.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>If random is FALSE (default), a named vector containing mean values @@ -159,26 +125,22 @@ fixed and random effects, in the format required by the start argument of nlme for the case of a single grouping variable ds.</p> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/mhmkin-1.png b/docs/reference/mhmkin-1.png Binary files differindex 2ecb6759..1c99aead 100644 --- a/docs/reference/mhmkin-1.png +++ b/docs/reference/mhmkin-1.png diff --git a/docs/reference/mhmkin-2.png b/docs/reference/mhmkin-2.png Binary files differindex 70cd7723..3051bddc 100644 --- a/docs/reference/mhmkin-2.png +++ b/docs/reference/mhmkin-2.png diff --git a/docs/reference/mhmkin.html b/docs/reference/mhmkin.html index 7fcb98fb..36003f7c 100644 --- a/docs/reference/mhmkin.html +++ b/docs/reference/mhmkin.html @@ -1,127 +1,96 @@ <!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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</ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> + </ul></div> - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Fit nonlinear mixed-effects models built from one or more kinetic + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Fit nonlinear mixed-effects models built from one or more kinetic degradation models and one or more error models</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mhmkin.R" class="external-link"><code>R/mhmkin.R</code></a></small> - <div class="hidden name"><code>mhmkin.Rd</code></div> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mhmkin.R" class="external-link"><code>R/mhmkin.R</code></a></small> + <div class="d-none name"><code>mhmkin.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>The name of the methods expresses that (<strong>m</strong>ultiple) <strong>h</strong>ierarchichal (also known as multilevel) <strong>m</strong>ulticompartment <strong>kin</strong>etic models are fitted. Our kinetic models are nonlinear, so we can use various nonlinear mixed-effects model fitting functions.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre><code>mhmkin(objects, ...) # S3 method for mmkin @@ -145,8 +114,8 @@ mhmkin( print(x, ...)</code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>objects</dt> <dd><p>A list of <a href="mmkin.html">mmkin</a> objects containing fits of the same degradation models to the same data, but using different error models. @@ -210,8 +179,8 @@ parallel execution.</p></dd> either a list of fit objects or a single fit object.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>A two-dimensional <a href="https://rdrr.io/r/base/array.html" class="external-link">array</a> of fit objects and/or try-errors that can @@ -222,17 +191,17 @@ attribute 'mhmkin'.</p> <p>An object inheriting from <code>mhmkin</code>.</p> </div> - <div id="see-also"> - <h2>See also</h2> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <div class="dont-index"><p><code>[.mhmkin</code> for subsetting mhmkin objects</p></div> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> <span class="r-in"><span><span class="co"># We start with separate evaluations of all the first six datasets with two</span></span></span> <span class="r-in"><span><span class="co"># degradation models and two error models</span></span></span> @@ -313,26 +282,22 @@ attribute 'mhmkin'.</p> <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/mixed-1.png b/docs/reference/mixed-1.png Binary files differindex 3992b681..846ca6a1 100644 --- a/docs/reference/mixed-1.png +++ b/docs/reference/mixed-1.png diff --git a/docs/reference/mixed.html b/docs/reference/mixed.html index b0cce30b..1da5e4e0 100644 --- a/docs/reference/mixed.html +++ b/docs/reference/mixed.html @@ -1,118 +1,84 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Create a mixed effects model from an mmkin row object — mixed • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" 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</li> - <li class="divider"> - <li class="dropdown-header">Example evaluations with (generalised) nonlinear least squares</li> - <li> - <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a> - </li> - <li> - <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> - </li> - <li> - <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> - </li> - <li class="divider"> - <li class="dropdown-header">Example evaluations with hierarchical models (nonlinear mixed-effects models)</li> - <li> - <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> - </li> - <li> - <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> - <a href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> - </li> - <li> - <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> - </li> - <li class="divider"> - <li class="dropdown-header">Performance</li> - <li> - <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> - </li> - <li> - <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> - </li> - <li> - <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> - </li> - <li 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href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a> + <a class="dropdown-item" href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Example evaluations with hierarchical models (nonlinear mixed-effects models)</h6> + <a class="dropdown-item" href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> + <a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> + <a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Performance</h6> + <a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a class="dropdown-item" href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + <a class="dropdown-item" href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6> + <a class="dropdown-item" href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a class="dropdown-item" href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </div> </li> - </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> +<li class="nav-item"> + <a class="nav-link" href="../news/index.html">News</a> +</li> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Create a mixed effects model from an mmkin row object</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mixed.mmkin.R" class="external-link"><code>R/mixed.mmkin.R</code></a></small> - <div class="hidden name"><code>mixed.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Create a mixed effects model from an mmkin row object</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mixed.mmkin.R" class="external-link"><code>R/mixed.mmkin.R</code></a></small> + <div class="d-none name"><code>mixed.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Create a mixed effects model from an mmkin row object</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mixed</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> <span><span class="co"># S3 method for mmkin</span></span> @@ -122,8 +88,8 @@ <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>An <a href="mmkin.html">mmkin</a> row object</p></dd> @@ -144,16 +110,16 @@ <dd><p>Number of digits to use for printing.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>An object of class 'mixed.mmkin' which has the observed data in a single dataframe which is convenient for plotting</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">n_biphasic</span> <span class="op"><-</span> <span class="fl">8</span></span></span> <span class="r-in"><span><span class="va">err_1</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>const <span class="op">=</span> <span class="fl">1</span>, prop <span class="op">=</span> <span class="fl">0.07</span><span class="op">)</span></span></span> @@ -224,26 +190,22 @@ single dataframe which is convenient for plotting</p> <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index 9e1487bd..5c1f9c09 100644 --- 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of the multistart method</a> - </li> - <li class="divider"> - <li class="dropdown-header">Performance</li> - <li> - <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> - </li> - <li> - <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> - </li> - <li> - <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> - </li> - <li class="divider"> - <li class="dropdown-header">Miscellaneous</li> - <li> - <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> - </li> - <li> - <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> - </li> - </ul></li> -<li> - <a href="../news/index.html">News</a> +<li class="nav-item dropdown"> + <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" 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dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> + <a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> + <a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Performance</h6> + <a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a class="dropdown-item" href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + <a class="dropdown-item" href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6> + <a class="dropdown-item" href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a class="dropdown-item" href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </div> </li> - </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> +<li class="nav-item"> + <a class="nav-link" href="../news/index.html">News</a> +</li> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Convert a dataframe from long to wide format</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkin_long_to_wide.R" class="external-link"><code>R/mkin_long_to_wide.R</code></a></small> - <div class="hidden name"><code>mkin_long_to_wide.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Convert a dataframe from long to wide format</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkin_long_to_wide.R" class="external-link"><code>R/mkin_long_to_wide.R</code></a></small> + <div class="d-none name"><code>mkin_long_to_wide.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>This function takes a dataframe in the long form, i.e. with a row for each observed value, and converts it into a dataframe with one independent variable and several dependent variables as columns.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkin_long_to_wide</span><span class="op">(</span><span class="va">long_data</span>, time <span class="op">=</span> <span class="st">"time"</span>, outtime <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>long_data</dt> <dd><p>The dataframe must contain one variable called "time" with the time values specified by the <code>time</code> argument, one column called @@ -137,19 +105,19 @@ observed values called "value".</p></dd> <dd><p>The name of the time variable in the wide output data.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>Dataframe in wide format.</p> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span><span class="fu">mkin_long_to_wide</span><span class="op">(</span><span class="va">FOCUS_2006_D</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> time parent m1</span> @@ -178,26 +146,22 @@ observed values called "value".</p></dd> <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index 8bf04bdf..3d8a2950 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -1,127 +1,95 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Convert a dataframe with observations over time into long format — mkin_wide_to_long • 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--> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Convert a dataframe with observations over time into long format</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkin_wide_to_long.R" class="external-link"><code>R/mkin_wide_to_long.R</code></a></small> - <div class="hidden name"><code>mkin_wide_to_long.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Convert a dataframe with observations over time into long format</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkin_wide_to_long.R" class="external-link"><code>R/mkin_wide_to_long.R</code></a></small> + <div class="d-none name"><code>mkin_wide_to_long.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>This function simply takes a dataframe with one independent variable and several dependent variable and converts it into the long form as required by <code><a href="mkinfit.html">mkinfit</a></code>.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkin_wide_to_long</span><span class="op">(</span><span class="va">wide_data</span>, time <span class="op">=</span> <span class="st">"t"</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>wide_data</dt> <dd><p>The dataframe must contain one variable with the time values specified by the <code>time</code> argument and usually more than one @@ -132,19 +100,19 @@ column of observed values.</p></dd> <dd><p>The name of the time variable.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>Dataframe in long format as needed for <code><a href="mkinfit.html">mkinfit</a></code>.</p> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span><span class="va">wide</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>t <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>,<span class="fl">2</span>,<span class="fl">3</span><span class="op">)</span>, x <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">1</span>,<span class="fl">4</span>,<span class="fl">7</span><span class="op">)</span>, y <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">3</span>,<span class="fl">4</span>,<span class="fl">5</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">mkin_wide_to_long</span><span class="op">(</span><span class="va">wide</span><span class="op">)</span></span></span> @@ -158,26 +126,22 @@ column of observed values.</p></dd> <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index dda44620..4d4ac772 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -1,130 +1,99 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>A dataset class for mkin — mkinds • 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 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For example, +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="At the moment this dataset class is hardly used in mkin. For example, +mkinfit does not take mkinds datasets as argument, but works with dataframes +such as the on contained in the data field of mkinds objects. 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For example, mkinfit does not take mkinds datasets as argument, but works with dataframes such as the on contained in the data field of mkinds objects. Some datasets provided by this package come as mkinds objects nevertheless."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--></head><body data-spy="scroll" data-target="#toc"> +<![endif]--></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - <div class="container template-reference-topic"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> - 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</ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> +<li class="nav-item"> + <a class="nav-link" href="../news/index.html">News</a> +</li> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>A dataset class for mkin</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinds.R" class="external-link"><code>R/mkinds.R</code></a></small> - <div class="hidden name"><code>mkinds.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>A dataset class for mkin</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinds.R" class="external-link"><code>R/mkinds.R</code></a></small> + <div class="d-none name"><code>mkinds.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>At the moment this dataset class is hardly used in mkin. For example, mkinfit does not take mkinds datasets as argument, but works with dataframes such as the on contained in the data field of mkinds objects. Some datasets provided by this package come as mkinds objects nevertheless.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinds</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, data <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>x</dt> <dd><p>An mkinds object.</p></dd> @@ -137,8 +106,8 @@ provided by this package come as mkinds objects nevertheless.</p> <dd><p>Not used.</p></dd> </dl></div> - <div id="public-fields"> - <h2>Public fields</h2> + <div class="section level2"> + <h2 id="public-fields">Public fields<a class="anchor" aria-label="anchor" href="#public-fields"></a></h2> <p></p><div class="r6-fields"><dl><dt><code>title</code></dt> <dd><p>A full title for the dataset</p></dd> @@ -170,8 +139,8 @@ and value in order to be compatible with mkinfit</p></dd> </dl><p></p></div> </div> - <div id="methods"> - <h2>Methods</h2> + <div class="section level2"> + <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2> <div class="section"> <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3> @@ -186,7 +155,7 @@ and value in order to be compatible with mkinfit</p></dd> </div> <div class="section"> -<h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4> +<h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#arguments-1"></a></h4> <p></p><div class="arguments"><dl><dt><code>title</code></dt> <dd><p>The dataset title</p></dd> @@ -214,7 +183,7 @@ and value in order to be compatible with mkinfit</p></dd> </div> <div class="section"> -<h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#arguments-1"></a></h4> +<h4 id="arguments-2">Arguments<a class="anchor" aria-label="anchor" href="#arguments-2"></a></h4> <p></p><div class="arguments"><dl><dt><code>deep</code></dt> <dd><p>Whether to make a deep clone.</p></dd> @@ -226,8 +195,8 @@ and value in order to be compatible with mkinfit</p></dd> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span><span class="va">mds</span> <span class="op"><-</span> <span class="va">mkinds</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"FOCUS A"</span>, <span class="va">FOCUS_2006_A</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">mds</span><span class="op">)</span></span></span> @@ -239,26 +208,22 @@ and value in order to be compatible with mkinfit</p></dd> <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/mkindsg.html b/docs/reference/mkindsg.html index ac6a2471..c8d73c1a 100644 --- a/docs/reference/mkindsg.html +++ b/docs/reference/mkindsg.html @@ -1,130 +1,99 @@ <!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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Time normalisation factors are initialised with a value of 1 for each dataset if no data are supplied."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--></head><body data-spy="scroll" data-target="#toc"> +<![endif]--></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - <div class="container template-reference-topic"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div 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models (nonlinear mixed-effects models)</h6> + <a class="dropdown-item" href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> + <a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> + <a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Performance</h6> + <a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a class="dropdown-item" href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + <a class="dropdown-item" href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6> + <a class="dropdown-item" href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a class="dropdown-item" href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </div> </li> - </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> +<li class="nav-item"> + <a class="nav-link" href="../news/index.html">News</a> +</li> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>A class for dataset groups for mkin</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinds.R" class="external-link"><code>R/mkinds.R</code></a></small> - <div class="hidden name"><code>mkindsg.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>A class for dataset groups for mkin</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinds.R" class="external-link"><code>R/mkinds.R</code></a></small> + <div class="d-none name"><code>mkindsg.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>A container for working with datasets that share at least one compound, so that combined evaluations are desirable.</p> <p>Time normalisation factors are initialised with a value of 1 for each dataset if no data are supplied.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkindsg</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, data <span class="op">=</span> <span class="cn">FALSE</span>, verbose <span class="op">=</span> <span class="va">data</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>x</dt> <dd><p>An mkindsg object.</p></dd> @@ -141,8 +110,8 @@ dataset if no data are supplied.</p> <dd><p>Not used.</p></dd> </dl></div> - <div id="public-fields"> - <h2>Public fields</h2> + <div class="section level2"> + <h2 id="public-fields">Public fields<a class="anchor" aria-label="anchor" href="#public-fields"></a></h2> <p></p><div class="r6-fields"><dl><dt><code>title</code></dt> <dd><p>A title for the dataset group</p></dd> @@ -169,8 +138,8 @@ or covariates like soil pH).</p></dd> </dl><p></p></div> </div> - <div id="methods"> - <h2>Methods</h2> + <div class="section level2"> + <h2 id="methods">Methods<a class="anchor" aria-label="anchor" href="#methods"></a></h2> <div class="section"> <h3 id="public-methods">Public methods<a class="anchor" aria-label="anchor" href="#public-methods"></a></h3> @@ -185,7 +154,7 @@ or covariates like soil pH).</p></dd> </div> <div class="section"> -<h4 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h4> +<h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#arguments-1"></a></h4> <p></p><div class="arguments"><dl><dt><code>title</code></dt> <dd><p>The title</p></dd> @@ -213,7 +182,7 @@ or covariates like soil pH).</p></dd> </div> <div class="section"> -<h4 id="arguments-1">Arguments<a class="anchor" aria-label="anchor" href="#arguments-1"></a></h4> +<h4 id="arguments-2">Arguments<a class="anchor" aria-label="anchor" href="#arguments-2"></a></h4> <p></p><div class="arguments"><dl><dt><code>deep</code></dt> <dd><p>Whether to make a deep clone.</p></dd> @@ -225,8 +194,8 @@ or covariates like soil pH).</p></dd> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span><span class="va">mdsg</span> <span class="op"><-</span> <span class="va">mkindsg</span><span class="op">$</span><span class="fu">new</span><span class="op">(</span><span class="st">"Experimental X"</span>, <span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">mdsg</span><span class="op">)</span></span></span> @@ -427,26 +396,22 @@ or covariates like soil pH).</p></dd> <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - 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template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Calculate the minimum error to assume in order to pass the variance test</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinerrmin.R" class="external-link"><code>R/mkinerrmin.R</code></a></small> + <div class="d-none name"><code>mkinerrmin.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>This function finds the smallest relative error still resulting in passing the chi-squared test as defined in the FOCUS kinetics report from 2006.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinerrmin</span><span class="op">(</span><span class="va">fit</span>, alpha <span class="op">=</span> <span class="fl">0.05</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>fit</dt> <dd><p>an object of class <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd> @@ -128,8 +95,8 @@ the chi-squared test as defined in the FOCUS kinetics report from 2006.</p> <dd><p>The confidence level chosen for the chi-squared test.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>A dataframe with the following components:</p> @@ -148,12 +115,12 @@ point with observed values in the series only counts one time.</p></dd> dataframe has one row for the total dataset and one further row for each observed state variable in the model.</p> </div> - <div id="details"> - <h2>Details</h2> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <p>This function is used internally by <code><a href="summary.mkinfit.html">summary.mkinfit</a></code>.</p> </div> - <div id="references"> - <h2>References</h2> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC @@ -161,8 +128,8 @@ Document Reference Sanco/10058/2005 version 2.0, 434 pp, <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span><span class="op">)</span>,</span></span> <span class="r-in"><span> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>,</span></span> @@ -187,26 +154,22 @@ Document Reference Sanco/10058/2005 version 2.0, 434 pp, <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/mkinerrplot-1.png b/docs/reference/mkinerrplot-1.png Binary files differindex 49bb1c0e..078614fc 100644 --- a/docs/reference/mkinerrplot-1.png +++ b/docs/reference/mkinerrplot-1.png diff --git a/docs/reference/mkinerrplot.html b/docs/reference/mkinerrplot.html index 6996eb86..cd1d93f1 100644 --- a/docs/reference/mkinerrplot.html +++ b/docs/reference/mkinerrplot.html @@ -1,118 +1,87 @@ 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<div class="hidden name"><code>mkinerrplot.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Function to plot squared residuals and the error model for an mkin object</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinerrplot.R" class="external-link"><code>R/mkinerrplot.R</code></a></small> + <div class="d-none name"><code>mkinerrplot.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>This function plots the squared residuals for the specified subset of the observed variables from an mkinfit object. In addition, one or more dashed line(s) show the fitted error model. A combined plot of the fitted model @@ -120,7 +89,8 @@ and this error model plot can be obtained with <code><a href="plot.mkinfit.html" using the argument <code>show_errplot = TRUE</code>.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinerrplot</span><span class="op">(</span></span> <span> <span class="va">object</span>,</span> <span> obs_vars <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">object</span><span class="op">$</span><span class="va">mkinmod</span><span class="op">$</span><span class="va">map</span><span class="op">)</span>,</span> @@ -137,8 +107,8 @@ using the argument <code>show_errplot = TRUE</code>.</p> <span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>A fit represented in an <code><a href="mkinfit.html">mkinfit</a></code> object.</p></dd> @@ -191,25 +161,25 @@ be passed on to <code><a href="https://rdrr.io/r/graphics/legend.html" class="ex <dd><p>further arguments passed to <code><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></code>.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.</p> </div> - <div id="see-also"> - <h2>See also</h2> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <div class="dont-index"><p><code><a href="mkinplot.html">mkinplot</a></code>, for a way to plot the data and the fitted lines of the mkinfit object.</p></div> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># \dontrun{</span></span></span> <span class="r-in"><span><span class="va">model</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> @@ -222,26 +192,22 @@ lines of the mkinfit object.</p></div> <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/mkinfit-1.png b/docs/reference/mkinfit-1.png Binary files differindex 7c51deb6..578f64a5 100644 --- a/docs/reference/mkinfit-1.png +++ b/docs/reference/mkinfit-1.png diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 865bdc28..7cd4eaa3 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -1,5 +1,13 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Fit a kinetic model to data with one or more state variables — mkinfit • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Fit a kinetic model to data with one or more state variables — mkinfit"><meta property="og:description" content="This function maximises the likelihood of the observed data using the Port +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; 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In each step of the optimisation, the +kinetic model is solved using the function mkinpredict(), except +if an analytical solution is implemented, in which case the model is solved +using the degradation function in the mkinmod object. 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In each step of the optimisation, the kinetic model is solved using the function mkinpredict(), except @@ -10,113 +18,78 @@ degradation model parameters, as both of them are arguments of the likelihood function."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--></head><body data-spy="scroll" data-target="#toc"> +<![endif]--></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - <div class="container template-reference-topic"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> - 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<div class="hidden name"><code>mkinfit.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Fit a kinetic model to data with one or more state variables</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinfit.R" class="external-link"><code>R/mkinfit.R</code></a></small> + <div class="d-none name"><code>mkinfit.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>This function maximises the likelihood of the observed data using the Port algorithm <code><a href="https://rdrr.io/r/stats/nlminb.html" class="external-link">stats::nlminb()</a></code>, and the specified initial or fixed parameters and starting values. In each step of the optimisation, the @@ -128,7 +101,8 @@ degradation model parameters, as both of them are arguments of the likelihood function.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinfit</span><span class="op">(</span></span> <span> <span class="va">mkinmod</span>,</span> <span> <span class="va">observed</span>,</span> @@ -158,8 +132,8 @@ likelihood function.</p> <span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>mkinmod</dt> <dd><p>A list of class <a href="mkinmod.html">mkinmod</a>, containing the kinetic model to be fitted to the data, or one of the shorthand names ("SFO", @@ -357,27 +331,27 @@ the error model parameters in IRLS fits.</p></dd> <code><a href="https://rdrr.io/pkg/deSolve/man/ode.html" class="external-link">deSolve::ode()</a></code>.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>A list with "mkinfit" in the class attribute.</p> </div> - <div id="details"> - <h2>Details</h2> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <p>Per default, parameters in the kinetic models are internally transformed in order to better satisfy the assumption of a normal distribution of their estimators.</p> </div> - <div id="note"> - <h2>Note</h2> + <div class="section level2"> + <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2> <p>When using the "IORE" submodel for metabolites, fitting with "transform_rates = TRUE" (the default) often leads to failures of the numerical ODE solver. In this situation it may help to switch off the internal rate transformation.</p> </div> - <div id="references"> - <h2>References</h2> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>Rocke DM and Lorenzato S (1995) A two-component model for measurement error in analytical chemistry. <em>Technometrics</em> 37(2), 176-184.</p> <p>Ranke J and Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical @@ -385,36 +359,36 @@ Degradation Data. <em>Environments</em> 6(12) 124 <a href="https://doi.org/10.3390/environments6120124" class="external-link">doi:10.3390/environments6120124</a> .</p> </div> - <div id="see-also"> - <h2>See also</h2> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <div class="dont-index"><p><a href="summary.mkinfit.html">summary.mkinfit</a>, <a href="plot.mkinfit.html">plot.mkinfit</a>, <a href="parms.html">parms</a> and <a href="https://rdrr.io/pkg/lmtest/man/lrtest.html" class="external-link">lrtest</a>.</p> <p>Comparisons of models fitted to the same data can be made using <code><a href="https://rdrr.io/r/stats/AIC.html" class="external-link">AIC</a></code> by virtue of the method <code><a href="logLik.mkinfit.html">logLik.mkinfit</a></code>.</p> <p>Fitting of several models to several datasets in a single call to <code><a href="mmkin.html">mmkin</a></code>.</p></div> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <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: 1.2.6 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Oct 30 09:30:09 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Oct 30 09:30:09 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 16 04:15:31 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 16 04:15:31 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> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 222 model solutions performed in 0.031 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 222 model solutions performed in 0.014 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> @@ -555,9 +529,9 @@ 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 0.465</span> -<span class="r-out co"><span class="r-pr">#></span> 2 eigen 2.260 1.051</span> -<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 2.282 1.061</span> +<span class="r-out co"><span class="r-pr">#></span> 3 analytical 1.000 0.223</span> +<span class="r-out co"><span class="r-pr">#></span> 2 eigen 1.973 0.440</span> +<span class="r-out co"><span class="r-pr">#></span> 1 deSolve_compiled 2.072 0.462</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> @@ -585,9 +559,9 @@ 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>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: 1.2.6 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Oct 30 09:30:19 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Oct 30 09:30:19 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 16 04:15:35 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 16 04:15:35 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> @@ -596,7 +570,7 @@ 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 4062 model solutions performed in 1.981 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 4062 model solutions performed in 0.768 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> @@ -696,26 +670,22 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div 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</ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Function to set up a kinetic model with one or more state variables</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinmod.R" class="external-link"><code>R/mkinmod.R</code></a>, <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinsub.R" class="external-link"><code>R/mkinsub.R</code></a></small> - <div class="hidden name"><code>mkinmod.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Function to set up a kinetic model with one or more state variables</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinmod.R" class="external-link"><code>R/mkinmod.R</code></a>, <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinsub.R" class="external-link"><code>R/mkinsub.R</code></a></small> + <div class="d-none name"><code>mkinmod.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>This function is usually called using a call to <code>mkinsub()</code> for each observed variable, specifying the corresponding submodel as well as outgoing pathways (see examples).</p> @@ -120,7 +89,8 @@ variable, specifying the corresponding submodel as well as outgoing pathways components.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinmod</span><span class="op">(</span></span> <span> <span class="va">...</span>,</span> <span> use_of_ff <span class="op">=</span> <span class="st">"max"</span>,</span> @@ -139,8 +109,8 @@ components.</p> <span><span class="fu">mkinsub</span><span class="op">(</span><span class="va">submodel</span>, to <span class="op">=</span> <span class="cn">NULL</span>, sink <span class="op">=</span> <span class="cn">TRUE</span>, full_name <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>...</dt> <dd><p>For each observed variable, a list as obtained by <code>mkinsub()</code> has to be specified as an argument (see examples). Currently, single @@ -230,8 +200,8 @@ your R code will not be portable, <em>i.e.</em> may produce unintended plot results on other operating systems or system configurations.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>A list of class <code>mkinmod</code> for use with <code><a href="mkinfit.html">mkinfit()</a></code>, @@ -262,8 +232,8 @@ returned by cfunction.</p></dd> </dl><p>A list for use with <code>mkinmod</code>.</p> </div> - <div id="details"> - <h2>Details</h2> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <p>For the definition of model types and their parameters, the equations given in the FOCUS and NAFTA guidance documents are used.</p> <p>For kinetic models with more than one observed variable, a symbolic solution @@ -274,14 +244,14 @@ is more than one observed variable in the specification, C code is generated for evaluating the differential equations, compiled using <code><a href="https://rdrr.io/pkg/inline/man/cfunction.html" class="external-link">inline::cfunction()</a></code> and added to the resulting mkinmod object.</p> </div> - <div id="note"> - <h2>Note</h2> + <div class="section level2"> + <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2> <p>The IORE submodel is not well tested for metabolites. When using this model for metabolites, you may want to read the note in the help page to <a href="mkinfit.html">mkinfit</a>.</p> </div> - <div id="references"> - <h2>References</h2> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, @@ -290,13 +260,13 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for Evaluating and Calculating Degradation Kinetics in Environmental Media</p> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</span></span></span> <span class="r-in"><span><span class="va">SFO</span> <span class="op"><-</span> <span class="fu">mkinmod</span><span class="op">(</span>parent <span class="op">=</span> <span class="fu">mkinsub</span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> @@ -333,7 +303,7 @@ 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/RtmpkUSV6I/file244bcd2ba24b1a.so to /home/agsad.admin.ch/f80868656/.local/share/mkin/SFO_SFO.so</span> +<span class="r-msg co"><span class="r-pr">#></span> Copied DLL from /tmp/Rtmpjn19MY/filee5f2f55ca8372.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> @@ -386,7 +356,7 @@ 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: 0x560630960080></span> +<span class="r-out co"><span class="r-pr">#></span> <environment: 0x555555f44b28></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> @@ -403,26 +373,22 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p> <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/mkinparplot-1.png 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degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> + <a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> + <a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Performance</h6> + <a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a class="dropdown-item" href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + <a class="dropdown-item" href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6> + <a class="dropdown-item" href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a class="dropdown-item" href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </div> </li> - </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> +<li class="nav-item"> + <a class="nav-link" href="../news/index.html">News</a> +</li> + </ul><form class="form-inline my-2 my-lg-0" 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+<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Function to plot the confidence intervals obtained using mkinfit</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinparplot.R" class="external-link"><code>R/mkinparplot.R</code></a></small> + <div class="d-none name"><code>mkinparplot.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>This function plots the confidence intervals for the parameters fitted using <code><a href="mkinfit.html">mkinfit</a></code>.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinparplot</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>A fit represented in an <code><a href="mkinfit.html">mkinfit</a></code> object.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.</p> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># \dontrun{</span></span></span> <span class="r-in"><span><span class="va">model</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> @@ -152,26 +119,22 @@ effect, namely to produce a plot.</p> <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index da047bf7..01e08e16 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -1,125 +1,92 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Plot the observed data and the fitted model of an mkinfit object — mkinplot • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" 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</ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> +<li class="nav-item"> + <a class="nav-link" href="../news/index.html">News</a> +</li> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Plot the observed data and the fitted model of an mkinfit object</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/plot.mkinfit.R" class="external-link"><code>R/plot.mkinfit.R</code></a></small> - <div class="hidden name"><code>mkinplot.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Plot the observed data and the fitted model of an mkinfit object</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/plot.mkinfit.R" class="external-link"><code>R/plot.mkinfit.R</code></a></small> + <div class="d-none name"><code>mkinplot.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Deprecated function. It now only calls the plot method <code><a href="plot.mkinfit.html">plot.mkinfit</a></code>.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinplot</span><span class="op">(</span><span class="va">fit</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>fit</dt> <dd><p>an object of class <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd> @@ -128,37 +95,33 @@ plot.mkinfit."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/li <dd><p>further arguments passed to <code><a href="plot.mkinfit.html">plot.mkinfit</a></code>.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>The function is called for its side effect.</p> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - 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href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> - </li> - <li> - <a href="../articles/web_only/multistart.html">Short demo of the multistart method</a> - </li> - <li class="divider"> - <li class="dropdown-header">Performance</li> - <li> - <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> - </li> - <li> - <a href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> - </li> - <li> - <a href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> - </li> - <li class="divider"> - <li class="dropdown-header">Miscellaneous</li> - <li> - <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> - </li> - <li> - <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> - </li> - </ul></li> -<li> - <a 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multistart method</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Performance</h6> + <a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a class="dropdown-item" href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + <a class="dropdown-item" href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6> + <a class="dropdown-item" href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a class="dropdown-item" href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </div> </li> - </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> +<li class="nav-item"> + <a class="nav-link" href="../news/index.html">News</a> +</li> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Produce predictions from a kinetic model using specific parameters</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinpredict.R" class="external-link"><code>R/mkinpredict.R</code></a></small> - <div class="hidden name"><code>mkinpredict.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Produce predictions from a kinetic model using specific parameters</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinpredict.R" class="external-link"><code>R/mkinpredict.R</code></a></small> + <div class="d-none name"><code>mkinpredict.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>This function produces a time series for all the observed variables in a kinetic model as specified by <a href="mkinmod.html">mkinmod</a>, using a specific set of kinetic parameters and initial values for the state variables.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinpredict</span><span class="op">(</span><span class="va">x</span>, <span class="va">odeparms</span>, <span class="va">odeini</span>, <span class="va">outtimes</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> <span><span class="co"># S3 method for mkinmod</span></span> @@ -153,8 +121,8 @@ kinetic parameters and initial values for the state variables.</p> <span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>x</dt> <dd><p>A kinetic model as produced by <a href="mkinmod.html">mkinmod</a>, or a kinetic fit as fitted by <a href="mkinfit.html">mkinfit</a>. In the latter case, the fitted parameters are used for @@ -231,19 +199,19 @@ as these always return mapped output.</p></dd> <dd><p>Should it be an error if ode returns NaN values</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>A matrix with the numeric solution in wide format</p> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span><span class="va">SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>degradinol <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="co"># Compare solution types</span></span></span> @@ -398,10 +366,10 @@ as these always return mapped output.</p></dd> <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-out co"><span class="r-pr">#></span> test relative elapsed</span> -<span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 1.0 0.005</span> -<span class="r-out co"><span class="r-pr">#></span> 4 analytical 1.0 0.005</span> -<span class="r-out co"><span class="r-pr">#></span> 1 eigen 3.2 0.016</span> -<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 24.4 0.122</span> +<span class="r-out co"><span class="r-pr">#></span> 4 analytical 1 0.001</span> +<span class="r-out co"><span class="r-pr">#></span> 2 deSolve_compiled 2 0.002</span> +<span class="r-out co"><span class="r-pr">#></span> 1 eigen 8 0.008</span> +<span class="r-out co"><span class="r-pr">#></span> 3 deSolve 64 0.064</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> @@ -413,26 +381,22 @@ as these always return mapped output.</p></dd> <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/mkinresplot-1.png b/docs/reference/mkinresplot-1.png Binary files differindex 97ccd762..7c64d0f0 100644 --- a/docs/reference/mkinresplot-1.png +++ b/docs/reference/mkinresplot-1.png diff --git a/docs/reference/mkinresplot.html b/docs/reference/mkinresplot.html index 4bfd033e..420c3190 100644 --- a/docs/reference/mkinresplot.html +++ b/docs/reference/mkinresplot.html @@ -1,124 +1,93 @@ <!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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A combined plot of the fitted model and the residuals can be obtained using plot.mkinfit using the argument show_residuals = TRUE."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--></head><body data-spy="scroll" data-target="#toc"> +<![endif]--></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - <div class="container template-reference-topic"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - 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</ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Function to plot residuals stored in an mkin object</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinresplot.R" class="external-link"><code>R/mkinresplot.R</code></a></small> - <div class="hidden name"><code>mkinresplot.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Function to plot residuals stored in an mkin object</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mkinresplot.R" class="external-link"><code>R/mkinresplot.R</code></a></small> + <div class="d-none name"><code>mkinresplot.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>This function plots the residuals for the specified subset of the observed variables from an mkinfit object. A combined plot of the fitted model and the residuals can be obtained using <code><a href="plot.mkinfit.html">plot.mkinfit</a></code> using the argument <code>show_residuals = TRUE</code>.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mkinresplot</span><span class="op">(</span></span> <span> <span class="va">object</span>,</span> <span> obs_vars <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">object</span><span class="op">$</span><span class="va">mkinmod</span><span class="op">$</span><span class="va">map</span><span class="op">)</span>,</span> @@ -136,8 +105,8 @@ argument <code>show_residuals = TRUE</code>.</p> <span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>A fit represented in an <code><a href="mkinfit.html">mkinfit</a></code> object.</p></dd> @@ -195,26 +164,26 @@ be passed on to <code><a href="https://rdrr.io/r/graphics/legend.html" class="ex <dd><p>further arguments passed to <code><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></code>.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>Nothing is returned by this function, as it is called for its side effect, namely to produce a plot.</p> </div> - <div id="see-also"> - <h2>See also</h2> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <div class="dont-index"><p><code><a href="mkinplot.html">mkinplot</a></code>, for a way to plot the data and the fitted lines of the mkinfit object, and <code><a href="plot.mkinfit.html">plot_res</a></code> for a function combining the plot of the fit and the residual plot.</p></div> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke and Katrin Lindenberger</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span><span class="va">model</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"m1"</span><span class="op">)</span>, m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> Temporary DLL for differentials generated and loaded</span> @@ -225,26 +194,22 @@ combining the plot of the fit and the residual plot.</p></div> <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/mmkin-1.png b/docs/reference/mmkin-1.png Binary files differindex 2361d3dc..9642db70 100644 --- a/docs/reference/mmkin-1.png +++ b/docs/reference/mmkin-1.png diff --git a/docs/reference/mmkin-2.png b/docs/reference/mmkin-2.png Binary files differindex 6ce2010f..d9aa755d 100644 --- a/docs/reference/mmkin-2.png +++ b/docs/reference/mmkin-2.png diff --git a/docs/reference/mmkin-3.png b/docs/reference/mmkin-3.png Binary files differindex 5d56da86..ed8e87e6 100644 --- a/docs/reference/mmkin-3.png +++ b/docs/reference/mmkin-3.png diff --git a/docs/reference/mmkin-4.png b/docs/reference/mmkin-4.png Binary files differindex 132380a8..11eae1f9 100644 --- a/docs/reference/mmkin-4.png +++ b/docs/reference/mmkin-4.png 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degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> + <a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> + <a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Performance</h6> + <a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a class="dropdown-item" href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + <a class="dropdown-item" href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6> + <a class="dropdown-item" href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a class="dropdown-item" href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </div> </li> - </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> +<li class="nav-item"> + <a class="nav-link" href="../news/index.html">News</a> +</li> + </ul><form class="form-inline my-2 my-lg-0" 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class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mmkin.R" class="external-link"><code>R/mmkin.R</code></a></small> - <div class="hidden name"><code>mmkin.Rd</code></div> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/mmkin.R" class="external-link"><code>R/mmkin.R</code></a></small> + <div class="d-none name"><code>mmkin.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>This function calls <code><a href="mkinfit.html">mkinfit</a></code> on all combinations of models and datasets specified in its first two arguments.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">mmkin</span><span class="op">(</span></span> <span> models <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span>, <span class="st">"DFOP"</span><span class="op">)</span>,</span> <span> <span class="va">datasets</span>,</span> @@ -130,8 +97,8 @@ datasets specified in its first two arguments.</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="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>models</dt> <dd><p>Either a character vector of shorthand names like <code>c("SFO", "FOMC", "DFOP", "HS", "SFORB")</code>, or an optionally named @@ -165,8 +132,8 @@ for parallel execution.</p></dd> <dd><p>An mmkin object.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>A two-dimensional <code><a href="https://rdrr.io/r/base/array.html" class="external-link">array</a></code> of <code><a href="mkinfit.html">mkinfit</a></code></p> @@ -176,18 +143,18 @@ for parallel execution.</p></dd> first index (row index) and the dataset names for the second index (column index).</p> </div> - <div id="see-also"> - <h2>See also</h2> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <div class="dont-index"><p><code><a href="Extract.mmkin.html">[.mmkin</a></code> for subsetting, <code><a href="plot.mmkin.html">plot.mmkin</a></code> for plotting.</p></div> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># \dontrun{</span></span></span> <span class="r-in"><span><span class="va">m_synth_SFO_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"M1"</span><span class="op">)</span>,</span></span> @@ -209,10 +176,10 @@ 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> 3.540 1.287 1.429 </span> +<span class="r-out co"><span class="r-pr">#></span> 1.653 0.553 0.654 </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> 4.074 0.037 4.142 </span> +<span class="r-out co"><span class="r-pr">#></span> 2.013 0.008 2.021 </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> @@ -268,26 +235,22 @@ plotting.</p></div> <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/multistart-1.png b/docs/reference/multistart-1.png Binary files differindex cf3cdca3..8133170b 100644 --- a/docs/reference/multistart-1.png +++ b/docs/reference/multistart-1.png diff --git a/docs/reference/multistart-2.png b/docs/reference/multistart-2.png Binary files differindex 05a160d0..5cfdbd63 100644 --- 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It is @@ -7,113 +12,78 @@ inspired by the article on practical identifiabiliy in the frame of nonlinear mixed-effects models by Duchesne et al (2021)."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--></head><body data-spy="scroll" data-target="#toc"> +<![endif]--></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - <div class="container template-reference-topic"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> - 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<div class="hidden name"><code>multistart.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Perform a hierarchical model fit with multiple starting values</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/multistart.R" class="external-link"><code>R/multistart.R</code></a></small> + <div class="d-none name"><code>multistart.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>The purpose of this method is to check if a certain algorithm for fitting nonlinear hierarchical models (also known as nonlinear mixed-effects models) will reliably yield results that are sufficiently similar to each other, if @@ -122,7 +92,8 @@ inspired by the article on practical identifiabiliy in the frame of nonlinear mixed-effects models by Duchesne et al (2021).</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">multistart</span><span class="op">(</span></span> <span> <span class="va">object</span>,</span> <span> n <span class="op">=</span> <span class="fl">50</span>,</span> @@ -148,8 +119,8 @@ mixed-effects models by Duchesne et al (2021).</p> <span><span class="fu">which.best</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>The fit object to work with</p></dd> @@ -176,8 +147,8 @@ for parallel execution.</p></dd> <dd><p>The multistart object to print</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>A list of <a href="saem.html">saem.mmkin</a> objects, with class attributes @@ -189,20 +160,20 @@ for parallel execution.</p></dd> <p>The index of the object with the highest likelihood</p> </div> - <div id="references"> - <h2>References</h2> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>Duchesne R, Guillemin A, Gandrillon O, Crauste F. Practical identifiability in the frame of nonlinear mixed effects models: the example of the in vitro erythropoiesis. BMC Bioinformatics. 2021 Oct 4;22(1):478. doi: 10.1186/s12859-021-04373-4.</p> </div> - <div id="see-also"> - <h2>See also</h2> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <div class="dont-index"><p><a href="parplot.html">parplot</a>, <a href="llhist.html">llhist</a></p></div> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> <span class="r-in"><span><span class="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="r-in"><span><span class="va">dmta_ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="fl">1</span><span class="op">:</span><span class="fl">7</span>, <span class="kw">function</span><span class="op">(</span><span class="va">i</span><span class="op">)</span> <span class="op">{</span></span></span> @@ -236,26 +207,22 @@ doi: 10.1186/s12859-021-04373-4.</p> <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/nafta-1.png b/docs/reference/nafta-1.png Binary files differindex 5d2d434b..98d4246c 100644 --- a/docs/reference/nafta-1.png +++ b/docs/reference/nafta-1.png diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html index 011b766a..af4d778a 100644 --- a/docs/reference/nafta.html +++ b/docs/reference/nafta.html @@ -1,118 +1,87 @@ <!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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Print nafta objects. The results for the three models are printed in the order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--></head><body data-spy="scroll" data-target="#toc"> +<![endif]--></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - <div class="container template-reference-topic"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - 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</ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> + </ul></div> - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Evaluate parent kinetics using the NAFTA guidance</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/nafta.R" class="external-link"><code>R/nafta.R</code></a></small> - <div class="hidden name"><code>nafta.Rd</code></div> + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Evaluate parent kinetics using the NAFTA guidance</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/nafta.R" class="external-link"><code>R/nafta.R</code></a></small> + <div class="d-none name"><code>nafta.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>The function fits the SFO, IORE and DFOP models using <code><a href="mmkin.html">mmkin</a></code> and returns an object of class <code>nafta</code> that has methods for printing and plotting.</p> @@ -120,15 +89,16 @@ and plotting.</p> order of increasing model complexity, i.e. SFO, then IORE, and finally DFOP.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">nafta</span><span class="op">(</span><span class="va">ds</span>, title <span class="op">=</span> <span class="cn">NA</span>, quiet <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> <span><span class="co"># S3 method for nafta</span></span> <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span>, digits <span class="op">=</span> <span class="fl">3</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="source"> - <h2>Source</h2> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <p>NAFTA (2011) Guidance for evaluating and calculating degradation kinetics in environmental media. NAFTA Technical Working Group on Pesticides @@ -139,8 +109,8 @@ Calculate Representative Half-life Values and Characterizing Pesticide Degradation <a href="https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance" class="external-link">https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance</a></p> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>ds</dt> <dd><p>A dataframe that must contain one variable called "time" with the time values specified by the <code>time</code> argument, one column called @@ -170,8 +140,8 @@ printing method).</p></dd> dissipation times.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>An list of class <code>nafta</code>. The list element named "mmkin" is the @@ -179,13 +149,13 @@ dissipation times.</p></dd> list element named "title" contains the title of the dataset used. The list element "data" contains the dataset used in the fits.</p> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span> <span class="va">nafta_evaluation</span> <span class="op"><-</span> <span class="fu">nafta</span><span class="op">(</span><span class="va">NAFTA_SOP_Appendix_D</span>, cores <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span></span> <span class="r-msg co"><span class="r-pr">#></span> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c</span> @@ -236,26 +206,22 @@ list element "data" contains the dataset used in the fits.</p> <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/nlme-1.png b/docs/reference/nlme-1.png Binary files differindex 0134107f..9583da2a 100644 --- a/docs/reference/nlme-1.png +++ b/docs/reference/nlme-1.png diff --git a/docs/reference/nlme-2.png b/docs/reference/nlme-2.png Binary files differindex 95739890..02aa0573 100644 --- a/docs/reference/nlme-2.png +++ b/docs/reference/nlme-2.png diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html index 26c56e54..d94e4bbe 100644 --- a/docs/reference/nlme.html +++ b/docs/reference/nlme.html @@ -1,137 +1,106 @@ <!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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<div class="hidden name"><code>nlme.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Helper functions to create nlme models from mmkin row objects</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/nlme.R" class="external-link"><code>R/nlme.R</code></a></small> + <div class="d-none name"><code>nlme.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>These functions facilitate setting up a nonlinear mixed effects model for an mmkin row object. An mmkin row object is essentially a list of mkinfit objects that have been obtained by fitting the same model to a list of datasets. They are used internally by the <code><a href="nlme.mmkin.html">nlme.mmkin()</a></code> method.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">nlme_function</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span> <span></span> <span><span class="fu">nlme_data</span><span class="op">(</span><span class="va">object</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>An mmkin row object containing several fits of the same model to different datasets</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>A function that can be used with nlme</p> @@ -139,13 +108,13 @@ datasets. They are used internally by the <code><a href="nlme.mmkin.html">nlme.m <p>A <code><a href="https://rdrr.io/pkg/nlme/man/groupedData.html" class="external-link">groupedData</a></code> object</p> </div> - <div id="see-also"> - <h2>See also</h2> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <div class="dont-index"><p><code><a href="nlme.mmkin.html">nlme.mmkin</a></code></p></div> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">m_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">d_SFO_1</span> <span class="op"><-</span> <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">m_SFO</span>,</span></span> @@ -221,26 +190,22 @@ datasets. They are used internally by the <code><a href="nlme.mmkin.html">nlme.m <span class="r-plt img"><img src="nlme-2.png" alt="" width="700" height="433"></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/nlme.mmkin-1.png b/docs/reference/nlme.mmkin-1.png Binary files differindex 7cabb086..762d5412 100644 --- a/docs/reference/nlme.mmkin-1.png +++ b/docs/reference/nlme.mmkin-1.png diff --git a/docs/reference/nlme.mmkin-2.png b/docs/reference/nlme.mmkin-2.png Binary files differindex b9a68e92..779adbdb 100644 --- a/docs/reference/nlme.mmkin-2.png +++ b/docs/reference/nlme.mmkin-2.png diff --git a/docs/reference/nlme.mmkin-3.png b/docs/reference/nlme.mmkin-3.png Binary files differindex ce7999bd..046d0238 100644 --- a/docs/reference/nlme.mmkin-3.png +++ b/docs/reference/nlme.mmkin-3.png diff --git a/docs/reference/nlme.mmkin.html b/docs/reference/nlme.mmkin.html index 05fbac5c..0e0412c6 100644 --- a/docs/reference/nlme.mmkin.html +++ b/docs/reference/nlme.mmkin.html @@ -1,122 +1,90 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Create an nlme model for an mmkin row object — nlme.mmkin • 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="Create an nlme model for an mmkin row object — nlme.mmkin"><meta property="og:description" content="This functions sets up a nonlinear mixed effects model for an mmkin row +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This functions sets up a nonlinear mixed effects model for an mmkin row +object. 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<div class="hidden name"><code>nlme.mmkin.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Create an nlme model for an mmkin row object</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/nlme.mmkin.R" class="external-link"><code>R/nlme.mmkin.R</code></a></small> + <div class="d-none name"><code>nlme.mmkin.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>This functions sets up a nonlinear mixed effects model for an mmkin row object. An mmkin row object is essentially a list of mkinfit objects that have been obtained by fitting the same model to a list of datasets.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mmkin</span></span> <span><span class="fu"><a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a></span><span class="op">(</span></span> <span> <span class="va">model</span>,</span> @@ -143,8 +111,8 @@ have been obtained by fitting the same model to a list of datasets.</p> <span><span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>model</dt> <dd><p>An <a href="mmkin.html">mmkin</a> row object.</p></dd> @@ -221,33 +189,33 @@ parameters taken from the mmkin object are used</p></dd> <dd><p>An nlme.mmkin object to update</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>Upon success, a fitted 'nlme.mmkin' object, which is an nlme object with additional elements. It also inherits from 'mixed.mmkin'.</p> </div> - <div id="details"> - <h2>Details</h2> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <p>Note that the convergence of the nlme algorithms depends on the quality of the data. In degradation kinetics, we often only have few datasets (e.g. data for few soils) and complicated degradation models, which may make it impossible to obtain convergence with nlme.</p> </div> - <div id="note"> - <h2>Note</h2> + <div class="section level2"> + <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2> <p>As the object inherits from <a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme::nlme</a>, there is a wealth of methods that will automatically work on 'nlme.mmkin' objects, such as <code><a href="https://rdrr.io/pkg/nlme/man/intervals.html" class="external-link">nlme::intervals()</a></code>, <code><a href="https://rdrr.io/pkg/nlme/man/anova.lme.html" class="external-link">nlme::anova.lme()</a></code> and <code><a href="https://rdrr.io/pkg/nlme/man/coef.lme.html" class="external-link">nlme::coef.lme()</a></code>.</p> </div> - <div id="see-also"> - <h2>See also</h2> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <div class="dont-index"><p><code><a href="nlme.html">nlme_function()</a></code>, <a href="plot.mixed.mmkin.html">plot.mixed.mmkin</a>, <a href="summary.nlme.mmkin.html">summary.nlme.mmkin</a></p></div> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span> <span class="r-in"><span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"name"</span>, <span class="st">"time"</span>, <span class="st">"value"</span><span class="op">)</span><span class="op">]</span>, <span class="va">name</span> <span class="op">==</span> <span class="st">"parent"</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span></span></span> @@ -438,26 +406,22 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav 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pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> + <a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> + <a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Performance</h6> + <a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a class="dropdown-item" 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alt=""><h1>Number of observations on which an mkinfit object was fitted</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/nobs.mkinfit.R" class="external-link"><code>R/nobs.mkinfit.R</code></a></small> + <div class="d-none name"><code>nobs.mkinfit.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Number of observations on which an mkinfit object was fitted</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> <span><span class="fu"><a href="https://rdrr.io/r/stats/nobs.html" class="external-link">nobs</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>An mkinfit object</p></dd> @@ -127,33 +93,29 @@ <dd><p>For compatibility with the generic method</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>The number of rows in the data included in the mkinfit object</p> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site 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models (nonlinear mixed-effects models)</h6> + <a class="dropdown-item" href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> + <a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> + <a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the 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href="https://github.com/jranke/mkin/blob/HEAD/R/saem.R" class="external-link"><code>R/saem.R</code></a></small> - <div class="hidden name"><code>parms.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Extract model parameters</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/parms.R" class="external-link"><code>R/parms.R</code></a>, <a href="https://github.com/jranke/mkin/blob/HEAD/R/saem.R" class="external-link"><code>R/saem.R</code></a></small> + <div class="d-none name"><code>parms.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>This function returns degradation model parameters as well as error model parameters per default, in order to avoid working with a fitted model without considering the error structure that was assumed for the fit.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">parms</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> <span><span class="co"># S3 method for mkinfit</span></span> @@ -132,8 +100,8 @@ without considering the error structure that was assumed for the fit.</p> <span><span class="fu">parms</span><span class="op">(</span><span class="va">object</span>, ci <span class="op">=</span> <span class="cn">FALSE</span>, covariates <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>A fitted model object.</p></dd> @@ -169,21 +137,21 @@ each column corresponding to a row of the data frame holding the covariates</p>< return parameter values. Only has an effect if 'ci' is FALSE.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>Depending on the object, a numeric vector of fitted model parameters, a matrix (e.g. for mmkin row objects), or a list of matrices (e.g. for mmkin objects with more than one row).</p> </div> - <div id="see-also"> - <h2>See also</h2> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <div class="dont-index"><p><a href="saem.html">saem</a>, <a href="multistart.html">multistart</a></p></div> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># mkinfit objects</span></span></span> <span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="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">parms</span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> @@ -273,26 +241,22 @@ mmkin objects with more than one row).</p> <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/parplot.html b/docs/reference/parplot.html index 2ae8d39f..5a4bada1 100644 --- a/docs/reference/parplot.html +++ b/docs/reference/parplot.html @@ -1,122 +1,90 @@ <!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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<div class="hidden name"><code>parplot.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Plot parameter variability of multistart objects</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/parplot.R" class="external-link"><code>R/parplot.R</code></a></small> + <div class="d-none name"><code>parplot.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Produces a boxplot with all parameters from the multiple runs, scaled either by the parameters of the run with the highest likelihood, or by their medians as proposed in the paper by Duchesne et al. (2021).</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">parplot</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> <span><span class="co"># S3 method for multistart.saem.mmkin</span></span> @@ -131,8 +99,8 @@ or by their medians as proposed in the paper by Duchesne et al. (2021).</p> <span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>The <a href="multistart.html">multistart</a> object</p></dd> @@ -164,44 +132,40 @@ If 'median', parameters are scaled using the median parameters from all fits.</p <dd><p>Title of the plot</p></dd> </dl></div> - <div id="details"> - <h2>Details</h2> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <p>Starting values of degradation model parameters and error model parameters are shown as green circles. The results obtained in the original run are shown as red circles.</p> </div> - <div id="references"> - <h2>References</h2> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>Duchesne R, Guillemin A, Gandrillon O, Crauste F. Practical identifiability in the frame of nonlinear mixed effects models: the example of the in vitro erythropoiesis. BMC Bioinformatics. 2021 Oct 4;22(1):478. doi: 10.1186/s12859-021-04373-4.</p> </div> - <div id="see-also"> - <h2>See also</h2> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <div class="dont-index"><p><a href="multistart.html">multistart</a></p></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git 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contents"> - <div class="page-header"> - <h1>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/plot.mixed.mmkin.R" class="external-link"><code>R/plot.mixed.mmkin.R</code></a></small> - <div class="hidden name"><code>plot.mixed.mmkin.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/plot.mixed.mmkin.R" class="external-link"><code>R/plot.mixed.mmkin.R</code></a></small> + <div class="d-none name"><code>plot.mixed.mmkin.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mixed.mmkin</span></span> <span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span></span> <span> <span class="va">x</span>,</span> @@ -143,8 +109,8 @@ <span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>x</dt> <dd><p>An object of class <a href="mixed.html">mixed.mmkin</a>, <a href="saem.html">saem.mmkin</a> or <a href="nlme.mmkin.html">nlme.mmkin</a></p></dd> @@ -265,23 +231,23 @@ corresponding model prediction lines for the different datasets.</p></dd> <dd><p>Further arguments passed to <code><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></code>.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>The function is called for its side effect.</p> </div> - <div id="note"> - <h2>Note</h2> + <div class="section level2"> + <h2 id="note">Note<a class="anchor" aria-label="anchor" href="#note"></a></h2> <p>Covariate models are currently only supported for saem.mmkin objects.</p> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span> <span class="r-in"><span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"name"</span>, <span class="st">"time"</span>, <span class="st">"value"</span><span class="op">)</span><span class="op">]</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/names.html" class="external-link">names</a></span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste0</a></span><span class="op">(</span><span class="st">"ds "</span>, <span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">)</span></span></span> @@ -319,26 +285,22 @@ corresponding model prediction lines for the different datasets.</p></dd> <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - 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name"><code>plot.mkinfit.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Plot the observed data and the fitted model of an mkinfit object</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/plot.mkinfit.R" class="external-link"><code>R/plot.mkinfit.R</code></a></small> + <div class="d-none name"><code>plot.mkinfit.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Solves the differential equations with the optimised and fixed parameters from a previous successful call to <code><a href="mkinfit.html">mkinfit</a></code> and plots the observed data together with the solution of the fitted model.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> <span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span></span> <span> <span class="va">x</span>,</span> @@ -163,8 +131,8 @@ observed data together with the solution of the fitted model.</p> <span><span class="fu">plot_err</span><span class="op">(</span><span class="va">fit</span>, sep_obs <span class="op">=</span> <span class="cn">FALSE</span>, show_errmin <span class="op">=</span> <span class="va">sep_obs</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>x</dt> <dd><p>Alias for fit introduced for compatibility with the generic S3 method.</p></dd> @@ -288,25 +256,25 @@ chi2 error percentage.</p></dd> standardized in the residual plot?</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>The function is called for its side effect.</p> </div> - <div id="details"> - <h2>Details</h2> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <p>If the current plot device is a <code><a href="https://rdrr.io/pkg/tikzDevice/man/tikz.html" class="external-link">tikz</a></code> device, then latex is being used for the formatting of the chi2 error level, if <code>show_errmin = TRUE</code>.</p> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># One parent compound, one metabolite, both single first order, path from</span></span></span> <span class="r-in"><span><span class="co"># parent to sink included</span></span></span> @@ -344,26 +312,22 @@ latex is being used for the formatting of the chi2 error level, if <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> 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<small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/plot.mmkin.R" class="external-link"><code>R/plot.mmkin.R</code></a></small> - <div class="hidden name"><code>plot.mmkin.Rd</code></div> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/plot.mmkin.R" class="external-link"><code>R/plot.mmkin.R</code></a></small> + <div class="d-none name"><code>plot.mmkin.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>When x is a row selected from an mmkin object (<code><a href="Extract.mmkin.html">[.mmkin</a></code>), the same model fitted for at least one dataset is shown. When it is a column, the fit of at least one model to the same dataset is shown.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mmkin</span></span> <span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span></span> <span> <span class="va">x</span>,</span> @@ -138,8 +106,8 @@ the fit of at least one model to the same dataset is shown.</p> <span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>x</dt> <dd><p>An object of class <code><a href="mmkin.html">mmkin</a></code>, with either one row or one column.</p></dd> @@ -202,24 +170,24 @@ than two rows of plots are shown.</p></dd> <code><a href="mkinresplot.html">mkinresplot</a></code>.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>The function is called for its side effect.</p> </div> - <div id="details"> - <h2>Details</h2> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <p>If the current plot device is a <code><a href="https://rdrr.io/pkg/tikzDevice/man/tikz.html" class="external-link">tikz</a></code> device, then latex is being used for the formatting of the chi2 error level.</p> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span> <span class="co"># \dontrun{</span></span></span> <span class="r-in"><span> <span class="co"># Only use one core not to offend CRAN checks</span></span></span> @@ -248,26 +216,22 @@ latex is being used for the formatting of the chi2 error level.</p> <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> 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</ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Plot the results of the three models used in the NAFTA scheme.</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/nafta.R" class="external-link"><code>R/nafta.R</code></a></small> + <div class="d-none name"><code>plot.nafta.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>The plots are ordered with increasing complexity of the model in this function (SFO, then IORE, then DFOP).</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for nafta</span></span> <span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">x</span>, legend <span class="op">=</span> <span class="cn">FALSE</span>, main <span class="op">=</span> <span class="st">"auto"</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>x</dt> <dd><p>An object of class <code><a href="nafta.html">nafta</a></code>.</p></dd> @@ -137,41 +104,37 @@ function (SFO, then IORE, then DFOP).</p> <dd><p>Further arguments passed to <code><a href="plot.mmkin.html">plot.mmkin</a></code>.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>The function is called for its side effect.</p> </div> - <div id="details"> - <h2>Details</h2> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <p>Calls <code><a href="plot.mmkin.html">plot.mmkin</a></code>.</p> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> 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These sheets are selected based on the contents of a sheet 'Datasets', with a column called 'Dataset Number', containing numbers identifying the dataset sheets to be read in. In the second column there must be a grouping @@ -7,110 +12,78 @@ variable, which will often be named 'Soil'. Optionally, time normalization factors can be given in columns named 'Temperature' and 'Moisture'."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--></head><body data-spy="scroll" data-target="#toc"> +<![endif]--></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - <div class="container template-reference-topic"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - 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</ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Read datasets and relevant meta information from a spreadsheet file</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/read_spreadsheet.R" class="external-link"><code>R/read_spreadsheet.R</code></a></small> - <div class="hidden name"><code>read_spreadsheet.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Read datasets and relevant meta information from a spreadsheet file</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/read_spreadsheet.R" class="external-link"><code>R/read_spreadsheet.R</code></a></small> + <div class="d-none name"><code>read_spreadsheet.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>This function imports one dataset from each sheet of a spreadsheet file. These sheets are selected based on the contents of a sheet 'Datasets', with a column called 'Dataset Number', containing numbers identifying the dataset @@ -119,7 +92,8 @@ variable, which will often be named 'Soil'. Optionally, time normalization factors can be given in columns named 'Temperature' and 'Moisture'.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">read_spreadsheet</span><span class="op">(</span></span> <span> <span class="va">path</span>,</span> <span> valid_datasets <span class="op">=</span> <span class="st">"all"</span>,</span> @@ -128,8 +102,8 @@ factors can be given in columns named 'Temperature' and 'Moisture'.</p> <span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>path</dt> <dd><p>Absolute or relative path to the spreadsheet file</p></dd> @@ -148,8 +122,8 @@ to use all datasets</p></dd> and moisture normalisation factors in the sheet 'Datasets'?</p></dd> </dl></div> - <div id="details"> - <h2>Details</h2> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <p>There must be a sheet 'Compounds', with columns 'Name' and 'Acronym'. The first row read after the header read in from this sheet is assumed to contain name and acronym of the parent compound.</p> @@ -170,26 +144,22 @@ so they can be easily used for specifying covariate models.</p> is probably more complicated to use.</p> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/reexports.html b/docs/reference/reexports.html index 847be2cb..e713acfe 100644 --- a/docs/reference/reexports.html +++ b/docs/reference/reexports.html @@ -1,5 +1,16 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Objects exported from other packages — reexports • 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="Objects exported from other packages — reexports"><meta property="og:description" content="These objects are imported from other packages. 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Follow the links below to see their documentation. lmtest @@ -13,113 +24,78 @@ intervals, nlme "><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--></head><body data-spy="scroll" data-target="#toc"> +<![endif]--></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - <div class="container template-reference-topic"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - 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<div class="hidden name"><code>reexports.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Objects exported from other packages</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/intervals.R" class="external-link"><code>R/intervals.R</code></a>, <a href="https://github.com/jranke/mkin/blob/HEAD/R/lrtest.mkinfit.R" class="external-link"><code>R/lrtest.mkinfit.R</code></a>, <a href="https://github.com/jranke/mkin/blob/HEAD/R/nlme.mmkin.R" class="external-link"><code>R/nlme.mmkin.R</code></a></small> + <div class="d-none name"><code>reexports.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>These objects are imported from other packages. Follow the links below to see their documentation.</p> <dl><dt>lmtest</dt> @@ -134,26 +110,21 @@ below to see their documentation.</p> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/residuals.mkinfit.html b/docs/reference/residuals.mkinfit.html index 0115cc3f..332f2bfd 100644 --- a/docs/reference/residuals.mkinfit.html +++ b/docs/reference/residuals.mkinfit.html @@ -1,124 +1,90 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html 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pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> + <a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> + <a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Performance</h6> + <a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a class="dropdown-item" 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alt=""><h1>Extract residuals from an mkinfit model</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/residuals.mkinfit.R" class="external-link"><code>R/residuals.mkinfit.R</code></a></small> + <div class="d-none name"><code>residuals.mkinfit.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Extract residuals from an mkinfit model</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> <span><span class="fu"><a href="https://rdrr.io/r/stats/residuals.html" class="external-link">residuals</a></span><span class="op">(</span><span class="va">object</span>, standardized <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>A <code><a href="mkinfit.html">mkinfit</a></code> object</p></dd> @@ -133,8 +99,8 @@ standard deviation obtained from the fitted error model?</p></dd> </dl></div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">f</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="va">FOCUS_2006_C</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/stats/residuals.html" class="external-link">residuals</a></span><span class="op">(</span><span class="va">f</span><span class="op">)</span></span></span> <span class="r-out co"><span class="r-pr">#></span> [1] 0.09726374 -0.13912142 -0.15351210 0.73388322 -0.08657004 -0.93204702</span> @@ -144,26 +110,22 @@ standard deviation obtained from the fitted error model?</p></dd> <span class="r-out co"><span class="r-pr">#></span> [7] -0.04695355 2.08761977 -1.27002287</span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div 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dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> + <a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> + <a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Performance</h6> + <a class="dropdown-item" 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class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Fit nonlinear mixed models with SAEM</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/saem.R" class="external-link"><code>R/saem.R</code></a></small> + <div class="d-none name"><code>saem.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>This function uses <code><a href="https://rdrr.io/pkg/saemix/man/saemix.html" class="external-link">saemix::saemix()</a></code> as a backend for fitting nonlinear mixed effects models created from <a href="mmkin.html">mmkin</a> row objects using the Stochastic Approximation Expectation Maximisation algorithm (SAEM).</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">saem</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> <span><span class="co"># S3 method for mmkin</span></span> @@ -166,8 +134,8 @@ Expectation Maximisation algorithm (SAEM).</p> <span><span class="fu">saemix_data</span><span class="op">(</span><span class="va">object</span>, covariates <span class="op">=</span> <span class="cn">NULL</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>An <a href="mmkin.html">mmkin</a> row object containing several fits of the same <a href="mkinmod.html">mkinmod</a> model to different datasets</p></dd> @@ -275,8 +243,8 @@ and the end of the optimisation process?</p></dd> <dd><p>Number of digits to use for printing</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>An S3 object of class 'saem.mmkin', containing the fitted @@ -289,21 +257,21 @@ object also inherits from 'mixed.mmkin'.</p> <p>An <a href="https://rdrr.io/pkg/saemix/man/SaemixData-class.html" class="external-link">saemix::SaemixData</a> object.</p> </div> - <div id="details"> - <h2>Details</h2> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <p>An mmkin row object is essentially a list of mkinfit objects that have been obtained by fitting the same model to a list of datasets using <a href="mkinfit.html">mkinfit</a>.</p> <p>Starting values for the fixed effects (population mean parameters, argument psi0 of <code><a href="https://rdrr.io/pkg/saemix/man/saemixModel.html" class="external-link">saemix::saemixModel()</a></code> are the mean values of the parameters found using <a href="mmkin.html">mmkin</a>.</p> </div> - <div id="see-also"> - <h2>See also</h2> + <div class="section level2"> + <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2> <div class="dont-index"><p><a href="summary.saem.mmkin.html">summary.saem.mmkin</a> <a href="plot.mixed.mmkin.html">plot.mixed.mmkin</a></p></div> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> <span class="r-in"><span><span class="va">ds</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">experimental_data_for_UBA_2019</span><span class="op">[</span><span class="fl">6</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span> <span class="r-in"><span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">x</span><span class="op">$</span><span class="va">data</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"name"</span>, <span class="st">"time"</span>, <span class="st">"value"</span><span class="op">)</span><span class="op">]</span><span class="op">)</span><span class="op">)</span></span></span> @@ -445,9 +413,9 @@ using <a href="mmkin.html">mmkin</a>.</p> <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: 1.2.6 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Oct 30 09:34:35 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Oct 30 09:34:35 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 16 04:17:34 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 16 04:17:34 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> @@ -462,7 +430,7 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted in 8.745 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 3.385 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> @@ -758,26 +726,22 @@ using <a href="mmkin.html">mmkin</a>.</p> <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/schaefer07_complex_case-1.png b/docs/reference/schaefer07_complex_case-1.png Binary files differindex a1d7d2f2..41665b13 100644 --- 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<div class="hidden name"><code>schaefer07_complex_case.Rd</code></div> + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Metabolism data set used for checking the software quality of KinGUI</h1> + + <div class="d-none name"><code>schaefer07_complex_case.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>This dataset was used for a comparison of KinGUI and ModelMaker to check the software quality of KinGUI in the original publication (Schäfer et al., 2007). The results from the fitting are also included.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">schaefer07_complex_case</span></span></code></pre></div> </div> - <div id="format"> - <h2>Format</h2> + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>The data set is a data frame with 8 observations on the following 6 variables.</p><dl><dt><code>time</code></dt> <dd><p>a numeric vector</p></dd> @@ -143,16 +111,16 @@ </dl><p>The results are a data frame with 14 results for different parameter values</p> </div> - <div id="references"> - <h2>References</h2> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>Schäfer D, Mikolasch B, Rainbird P and Harvey B (2007). KinGUI: a new kinetic software tool for evaluations according to FOCUS degradation kinetics. In: Del Re AAM, Capri E, Fragoulis G and Trevisan M (Eds.). Proceedings of the XIII Symposium Pesticide Chemistry, Piacenza, 2007, p. 916-923.</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">data</span> <span class="op"><-</span> <span class="fu"><a href="mkin_wide_to_long.html">mkin_wide_to_long</a></span><span class="op">(</span><span class="va">schaefer07_complex_case</span>, time <span class="op">=</span> <span class="st">"time"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">model</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> <span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"A1"</span>, <span class="st">"B1"</span>, <span class="st">"C1"</span><span class="op">)</span>, sink <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span>,</span></span> @@ -198,26 +166,22 @@ <span class="r-out co"><span class="r-pr">#></span> 14 metabolite A2 DT50 28.2400 28.4500 0.7</span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/set_nd_nq.html b/docs/reference/set_nd_nq.html index 249a7600..a2063d05 100644 --- a/docs/reference/set_nd_nq.html +++ b/docs/reference/set_nd_nq.html @@ -1,118 +1,87 @@ <!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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For time series, the function performs part of the residue processing proposed in the FOCUS kinetics guidance for parent compounds and metabolites. For two-dimensional residue series over time and depth, it automates the proposal of Boesten et al (2015)."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--></head><body data-spy="scroll" data-target="#toc"> +<![endif]--></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - <div class="container template-reference-topic"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - 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<div class="hidden name"><code>set_nd_nq.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Set non-detects and unquantified values in residue series without replicates</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/set_nd_nq.R" class="external-link"><code>R/set_nd_nq.R</code></a></small> + <div class="d-none name"><code>set_nd_nq.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>This function automates replacing unquantified values in residue time and depth series. For time series, the function performs part of the residue processing proposed in the FOCUS kinetics guidance for parent compounds @@ -120,7 +89,8 @@ and metabolites. For two-dimensional residue series over time and depth, it automates the proposal of Boesten et al (2015).</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">res_raw</span>, <span class="va">lod</span>, loq <span class="op">=</span> <span class="cn">NA</span>, time_zero_presence <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span> <span></span> <span><span class="fu">set_nd_nq_focus</span><span class="op">(</span></span> @@ -133,8 +103,8 @@ it automates the proposal of Boesten et al (2015).</p> <span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>res_raw</dt> <dd><p>Character vector of a residue time series, or matrix of residue values with rows representing depth profiles for a specific sampling @@ -174,19 +144,19 @@ in case it is a non-detection?</p></dd> non-detection that occurs after the quantified values?</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>A numeric vector, if a vector was supplied, or a numeric matrix otherwise</p> </div> - <div id="functions"> - <h2>Functions</h2> + <div class="section level2"> + <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functions"></a></h2> <ul><li><p><code>set_nd_nq_focus()</code>: Set non-detects in residue time series according to FOCUS rules</p></li> </ul></div> - <div id="references"> - <h2>References</h2> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>Boesten, J. J. T. I., van der Linden, A. M. A., Beltman, W. H. J. and Pol, J. W. (2015). Leaching of plant protection products and their transformation products; Proposals for improving the assessment of leaching @@ -197,8 +167,8 @@ Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Versi 18 December 2014, p. 251</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># FOCUS (2014) p. 75/76 and 131/132</span></span></span> <span class="r-in"><span><span class="va">parent_1</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">.12</span>, <span class="fl">.09</span>, <span class="fl">.05</span>, <span class="fl">.03</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span>, <span class="st">"nd"</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu">set_nd_nq</span><span class="op">(</span><span class="va">parent_1</span>, <span class="fl">0.02</span><span class="op">)</span></span></span> @@ -255,26 +225,22 @@ Kinetics from Environmental Fate Studies on Pesticides in EU Registration, Versi <span class="r-out co"><span class="r-pr">#></span> [7,] NA NA NA NA NA NA</span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> 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name"><code>sigma_twocomp.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Two-component error model</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/sigma_twocomp.R" class="external-link"><code>R/sigma_twocomp.R</code></a></small> + <div class="d-none name"><code>sigma_twocomp.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Function describing the standard deviation of the measurement error in dependence of the measured value \(y\):</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">sigma_twocomp</span><span class="op">(</span><span class="va">y</span>, <span class="va">sigma_low</span>, <span class="va">rsd_high</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>y</dt> <dd><p>The magnitude of the observed value</p></dd> @@ -134,14 +101,14 @@ observed values</p></dd> deviation with the magnitude of the observed value</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>The standard deviation of the response variable.</p> </div> - <div id="details"> - <h2>Details</h2> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <p>$$\sigma = \sqrt{ \sigma_{low}^2 + y^2 * {rsd}_{high}^2}$$ sigma = sqrt(sigma_low^2 + y^2 * rsd_high^2)</p> <p>This is the error model used for example by Werner et al. (1978). The model @@ -149,8 +116,8 @@ proposed by Rocke and Lorenzato (1995) can be written in this form as well, but assumes approximate lognormal distribution of errors for high values of y.</p> </div> - <div id="references"> - <h2>References</h2> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>Werner, Mario, Brooks, Samuel H., and Knott, Lancaster B. (1978) Additive, Multiplicative, and Mixed Analytical Errors. Clinical Chemistry 24(11), 1895-1898.</p> @@ -162,8 +129,8 @@ Degradation Data. <em>Environments</em> 6(12) 124 .</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">times</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">d_pred</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>time <span class="op">=</span> <span class="va">times</span>, parent <span class="op">=</span> <span class="fl">100</span> <span class="op">*</span> <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">exp</a></span><span class="op">(</span><span class="op">-</span> <span class="fl">0.03</span> <span class="op">*</span> <span class="va">times</span><span class="op">)</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">123456</span><span class="op">)</span></span></span> @@ -193,26 +160,22 @@ Degradation Data. <em>Environments</em> 6(12) 124 <span class="r-out co"><span class="r-pr">#></span> f_mkin_tc 4 101.6446</span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav 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href="https://github.com/jranke/mkin/blob/HEAD/R/status.R" class="external-link"><code>R/status.R</code></a></small> + <div class="d-none name"><code>status.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Method to get status information for fit array objects</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">status</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> <span><span class="co"># S3 method for mmkin</span></span> @@ -128,8 +94,8 @@ <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>The object to investigate</p></dd> @@ -142,16 +108,16 @@ <dd><p>The object to be printed</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>An object with the same dimensions as the fit array suitable printing method.</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> <span class="r-in"><span><span class="va">fits</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span><span class="op">)</span>,</span></span> @@ -170,26 +136,22 @@ suitable printing method.</p> <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a 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contents"> - <div class="page-header"> - <h1>Summary method for class "mkinfit"</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/summary.mkinfit.R" class="external-link"><code>R/summary.mkinfit.R</code></a></small> - <div class="hidden name"><code>summary.mkinfit.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Summary method for class "mkinfit"</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/summary.mkinfit.R" class="external-link"><code>R/summary.mkinfit.R</code></a></small> + <div class="d-none name"><code>summary.mkinfit.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Lists model equations, initial parameter values, optimised parameters with some uncertainty statistics, the chi2 error levels calculated according to FOCUS guidance (2006) as defined therein, formation fractions, DT50 values @@ -120,7 +89,8 @@ and optionally the data, consisting of observed, predicted and residual values.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> <span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">object</span>, data <span class="op">=</span> <span class="cn">TRUE</span>, distimes <span class="op">=</span> <span class="cn">TRUE</span>, alpha <span class="op">=</span> <span class="fl">0.05</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> @@ -128,8 +98,8 @@ values.</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="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>an object of class <a href="mkinfit.html">mkinfit</a>.</p></dd> @@ -161,8 +131,8 @@ distribution</p></dd> <dd><p>Number of digits to use for printing</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>The summary function returns a list with components, among others</p> @@ -217,34 +187,34 @@ g of SFORB systems in the model.</p></dd> </dl><p>The print method is called for its side effect, i.e. printing the summary.</p> </div> - <div id="references"> - <h2>References</h2> + <div class="section level2"> + <h2 id="references">References<a class="anchor" aria-label="anchor" href="#references"></a></h2> <p>FOCUS (2006) “Guidance Document on Estimating Persistence and Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics" class="external-link">http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></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: 1.2.6 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Oct 30 09:39:49 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Oct 30 09:39:49 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 16 04:19:39 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 16 04:19:39 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> <span class="r-out co"><span class="r-pr">#></span> </span> <span class="r-out co"><span class="r-pr">#></span> Model predictions using solution type analytical </span> <span class="r-out co"><span class="r-pr">#></span> </span> -<span class="r-out co"><span class="r-pr">#></span> Fitted using 131 model solutions performed in 0.02 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 131 model solutions performed in 0.009 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> @@ -311,26 +281,22 @@ EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/summary.mmkin.html b/docs/reference/summary.mmkin.html index 9b10a415..6f79cfe9 100644 --- a/docs/reference/summary.mmkin.html +++ b/docs/reference/summary.mmkin.html @@ -1,120 +1,87 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Summary method for class "mmkin" — summary.mmkin • mkin</title><!-- jquery --><script 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Dataset Z</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Example evaluations with hierarchical models (nonlinear mixed-effects models)</h6> + <a class="dropdown-item" href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_dmta_pathway.html">Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P</a> + <a class="dropdown-item" href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a> + <a class="dropdown-item" href="../articles/prebuilt/2022_cyan_pathway.html">Testing hierarchical pathway kinetics with residue data on cyantraniliprole</a> + <a class="dropdown-item" href="../articles/web_only/dimethenamid_2018.html">Comparison of saemix and nlme evaluations of dimethenamid data from 2018</a> + <a class="dropdown-item" href="../articles/web_only/multistart.html">Short demo of the multistart method</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Performance</h6> + <a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a> + <a class="dropdown-item" href="../articles/web_only/benchmarks.html">Benchmark timings for mkin</a> + <a class="dropdown-item" href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a> + <div class="dropdown-divider"></div> + <h6 class="dropdown-header" data-toc-skip>Miscellaneous</h6> + <a class="dropdown-item" href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a> + <a class="dropdown-item" href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a> + </div> </li> - </ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> +<li class="nav-item"> + <a class="nav-link" href="../news/index.html">News</a> +</li> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Summary method for class "mmkin"</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/summary.mmkin.R" class="external-link"><code>R/summary.mmkin.R</code></a></small> - <div class="hidden name"><code>summary.mmkin.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Summary method for class "mmkin"</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/summary.mmkin.R" class="external-link"><code>R/summary.mmkin.R</code></a></small> + <div class="d-none name"><code>summary.mmkin.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Shows status information on the <a href="mkinfit.html">mkinfit</a> objects contained in the object and gives an overview of ill-defined parameters calculated by <a href="illparms.html">illparms</a>.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mmkin</span></span> <span><span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">object</span>, conf.level <span class="op">=</span> <span class="fl">0.95</span>, <span class="va">...</span><span class="op">)</span></span> <span></span> @@ -122,8 +89,8 @@ and gives an overview of ill-defined parameters calculated by <a href="illparms. <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>an object of class <a href="mmkin.html">mmkin</a></p></dd> @@ -145,8 +112,8 @@ and gives an overview of ill-defined parameters calculated by <a href="illparms. </dl></div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span><span class="va">fits</span> <span class="op"><-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span></span></span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="st">"FOMC"</span><span class="op">)</span>,</span></span> @@ -157,7 +124,7 @@ and gives an overview of ill-defined parameters calculated by <a href="illparms. <span class="r-wrn co"><span class="r-pr">#></span> false convergence (8)</span> <span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/pkg/saemix/man/summary-methods.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">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 0.705 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.454 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> @@ -177,26 +144,22 @@ and gives an overview of ill-defined parameters calculated by <a href="illparms. <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/summary.nlme.mmkin.html b/docs/reference/summary.nlme.mmkin.html index 58eb3e21..e16b550a 100644 --- a/docs/reference/summary.nlme.mmkin.html +++ b/docs/reference/summary.nlme.mmkin.html @@ -1,118 +1,87 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Summary method for class "nlme.mmkin" — summary.nlme.mmkin • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" 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</ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Summary method for class "nlme.mmkin"</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/summary.nlme.mmkin.R" class="external-link"><code>R/summary.nlme.mmkin.R</code></a></small> - <div class="hidden name"><code>summary.nlme.mmkin.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Summary method for class "nlme.mmkin"</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/summary.nlme.mmkin.R" class="external-link"><code>R/summary.nlme.mmkin.R</code></a></small> + <div class="d-none name"><code>summary.nlme.mmkin.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Lists model equations, initial parameter values, optimised parameters for fixed effects (population), random effects (deviations from the population mean) and residual error model, as well as the resulting @@ -120,7 +89,8 @@ endpoints such as formation fractions and DT50 values. Optionally (default is FALSE), the data are listed in full.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for nlme.mmkin</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> <span> <span class="va">object</span>,</span> @@ -135,8 +105,8 @@ endpoints such as formation fractions and DT50 values. Optionally <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="va">x</span><span class="op">$</span><span class="va">verbose</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>an object of class <a href="nlme.mmkin.html">nlme.mmkin</a></p></dd> @@ -172,8 +142,8 @@ distribution</p></dd> <dd><p>Number of digits to use for printing</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>The summary function returns a list based on the <a href="https://rdrr.io/pkg/nlme/man/nlme.html" class="external-link">nlme</a> object @@ -212,14 +182,14 @@ model.</p></dd> </dl><p>The print method is called for its side effect, i.e. printing the summary.</p> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke for the mkin specific parts José Pinheiro and Douglas Bates for the components inherited from nlme</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span><span class="co"># Generate five datasets following SFO kinetics</span></span></span> <span class="r-in"><span><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span></span> @@ -256,9 +226,9 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <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: 3.1.163 </span> <span class="r-out co"><span class="r-pr">#></span> mkin version used for pre-fitting: 1.2.6 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Oct 30 09:39:53 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Oct 30 09:39:53 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 16 04:19:41 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 16 04:19:41 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> @@ -268,7 +238,7 @@ 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 0.451 s using 4 iterations</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 0.182 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> @@ -412,26 +382,22 @@ José Pinheiro and Douglas Bates for the components inherited from nlme</p> <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/summary.saem.mmkin.html b/docs/reference/summary.saem.mmkin.html index 54e5260b..bf42a4d9 100644 --- a/docs/reference/summary.saem.mmkin.html +++ b/docs/reference/summary.saem.mmkin.html @@ -1,118 +1,87 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Summary method for class "saem.mmkin" — summary.saem.mmkin • 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="Summary method for class " saem.mmkin summary.saem.mmkin><meta property="og:description" content="Lists model equations, initial parameter values, optimised parameters +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="Lists model equations, initial parameter values, optimised parameters +for fixed effects (population), random effects (deviations from the +population mean) and residual error model, as well as the resulting +endpoints such as formation fractions and DT50 values. 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</ul><ul class="nav navbar-nav navbar-right"><li> - <a href="https://github.com/jranke/mkin/" class="external-link"> - <span class="fab fa-github fa-lg"></span> + </ul><form class="form-inline my-2 my-lg-0" role="search"> + <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form> + + <ul class="navbar-nav"><li class="nav-item"> + <a class="external-link nav-link" href="https://github.com/jranke/mkin/" aria-label="github"> + <span class="fab fa fab fa-github fa-lg"></span> </a> </li> - </ul></div><!--/.nav-collapse --> - </div><!--/.container --> -</div><!--/.navbar --> - - - - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Summary method for class "saem.mmkin"</h1> - <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/summary.saem.mmkin.R" class="external-link"><code>R/summary.saem.mmkin.R</code></a></small> - <div class="hidden name"><code>summary.saem.mmkin.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Summary method for class "saem.mmkin"</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/summary.saem.mmkin.R" class="external-link"><code>R/summary.saem.mmkin.R</code></a></small> + <div class="d-none name"><code>summary.saem.mmkin.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>Lists model equations, initial parameter values, optimised parameters for fixed effects (population), random effects (deviations from the population mean) and residual error model, as well as the resulting @@ -120,7 +89,8 @@ endpoints such as formation fractions and DT50 values. Optionally (default is FALSE), the data are listed in full.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for saem.mmkin</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> <span> <span class="va">object</span>,</span> @@ -136,8 +106,8 @@ endpoints such as formation fractions and DT50 values. Optionally <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="va">x</span><span class="op">$</span><span class="va">verbose</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>an object of class <a href="saem.html">saem.mmkin</a></p></dd> @@ -179,8 +149,8 @@ included.</p></dd> <dd><p>Number of digits to use for printing</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>The summary function returns a list based on the <a href="https://rdrr.io/pkg/saemix/man/SaemixObject-class.html" class="external-link">saemix::SaemixObject</a></p> @@ -224,14 +194,14 @@ model.</p></dd> </dl><p>The print method is called for its side effect, i.e. printing the summary.</p> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke for the mkin specific parts saemix authors for the parts inherited from saemix.</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Generate five datasets following DFOP-SFO kinetics</span></span></span> <span class="r-in"><span><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="va">dfop_sfo</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"DFOP"</span>, <span class="st">"m1"</span><span class="op">)</span>,</span></span> @@ -334,9 +304,9 @@ saemix authors for the parts inherited from saemix.</p> <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: 1.2.6 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Oct 30 09:40:27 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Oct 30 09:40:27 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 16 04:19:57 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 16 04:19:57 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> @@ -351,7 +321,7 @@ 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 19.763 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted in 9.193 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> @@ -654,26 +624,22 @@ saemix authors for the parts inherited from saemix.</p> <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a 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class="external-link"><code>R/summary_listing.R</code></a></small> - <div class="hidden name"><code>summary_listing.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Display the output of a summary function according to the output format</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/summary_listing.R" class="external-link"><code>R/summary_listing.R</code></a></small> + <div class="d-none name"><code>summary_listing.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>This function is intended for use in a R markdown code chunk with the chunk option <code>results = "asis"</code>.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">summary_listing</span><span class="op">(</span><span class="va">object</span>, caption <span class="op">=</span> <span class="cn">NULL</span>, label <span class="op">=</span> <span class="cn">NULL</span>, clearpage <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> <span></span> <span><span class="fu">tex_listing</span><span class="op">(</span><span class="va">object</span>, caption <span class="op">=</span> <span class="cn">NULL</span>, label <span class="op">=</span> <span class="cn">NULL</span>, clearpage <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span> @@ -122,8 +89,8 @@ option <code>results = "asis"</code>.</p> <span><span class="fu">html_listing</span><span class="op">(</span><span class="va">object</span>, caption <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>The object for which the summary is to be listed</p></dd> @@ -141,26 +108,22 @@ option <code>results = "asis"</code>.</p> </dl></div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - 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synthetic_data_for_UBA_2014"><meta property="og:description" content="The 12 datasets were generated using four different models and three different +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="The 12 datasets were generated using four different models and three different + variance components. The four models are either the SFO or the DFOP model with either + two sequential or two parallel metabolites. +Variance component 'a' is based on a normal distribution with standard deviation of 3, + Variance component 'b' is also based on a normal distribution, but with a standard deviation of 7. + Variance component 'c' is based on the error model from Rocke and Lorenzato (1995), with the + minimum standard deviation (for small y values) of 0.5, and a proportionality constant of 0.07 + for the increase of the standard deviation with y. Note that this is a simplified version + of the error model proposed by Rocke and Lorenzato (1995), as in their model the error of the + measured values approximates lognormal distribution for high values, whereas we are using + normally distributed error components all along. +Initial concentrations for metabolites and all values where adding the variance component resulted + in a value below the assumed limit of detection of 0.1 were set to NA. +As an example, the first dataset has the title SFO_lin_a and is based on the SFO model + with two sequential metabolites (linear pathway), with added variance component 'a'. +Compare also the code in the example section to see the degradation models."><title>Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014 • mkin</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.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"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" 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><!-- 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><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014"><meta property="og:description" content="The 12 datasets were generated using four different models and three different variance components. The four models are either the SFO or the DFOP model with either two sequential or two parallel metabolites. Variance component 'a' is based on a normal distribution with standard deviation of 3, @@ -17,113 +32,78 @@ As an example, the first dataset has the title SFO_lin_a and is based on the SFO Compare also the code in the example section to see the degradation models."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--></head><body data-spy="scroll" data-target="#toc"> +<![endif]--></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - <div class="container template-reference-topic"> - 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<div class="ref-description"> + <div class="ref-description section level2"> <p>The 12 datasets were generated using four different models and three different variance components. The four models are either the SFO or the DFOP model with either two sequential or two parallel metabolites.</p> @@ -142,12 +122,13 @@ Compare also the code in the example section to see the degradation models."><!- <p>Compare also the code in the example section to see the degradation models.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">synthetic_data_for_UBA_2014</span></span></code></pre></div> </div> - <div id="format"> - <h2>Format</h2> + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>A list containing twelve datasets as an R6 class defined by <code><a href="mkinds.html">mkinds</a></code>, each containing, among others, the following components</p><dl><dt><code>title</code></dt> <dd><p>The name of the dataset, e.g. <code>SFO_lin_a</code></p></dd> @@ -157,16 +138,16 @@ Compare also the code in the example section to see the degradation models."><!- </dl></div> - <div id="source"> - <h2>Source</h2> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <p>Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452</p> <p>Rocke, David M. und Lorenzato, Stefan (1995) A two-component model for measurement error in analytical chemistry. Technometrics 37(2), 176-184.</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> <span class="r-in"><span><span class="co"># The data have been generated using the following kinetic models</span></span></span> <span class="r-in"><span><span class="va">m_synth_SFO_lin</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"M1"</span><span class="op">)</span>,</span></span> @@ -273,9 +254,9 @@ Compare also the code in the example section to see the degradation models."><!- <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: 1.2.6 </span> -<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.1 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of fit: Mon Oct 30 09:40:49 2023 </span> -<span class="r-out co"><span class="r-pr">#></span> Date of summary: Mon Oct 30 09:40:49 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> R version used for fitting: 4.3.2 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of fit: Thu Nov 16 04:20:07 2023 </span> +<span class="r-out co"><span class="r-pr">#></span> Date of summary: Thu Nov 16 04:20:07 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> @@ -284,7 +265,7 @@ Compare also the code in the example section to see the degradation models."><!- <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 848 model solutions performed in 0.408 s</span> +<span class="r-out co"><span class="r-pr">#></span> Fitted using 848 model solutions performed in 0.166 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> @@ -423,26 +404,22 @@ Compare also the code in the example section to see the degradation models."><!- <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/test_data_from_UBA_2014-1.png 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--> - </div><!--/.container --> -</div><!--/.navbar --> - - + </ul></div> - </header><div class="row"> - <div class="col-md-9 contents"> - <div class="page-header"> - <h1>Three experimental datasets from two water sediment systems and one soil</h1> - <div class="hidden name"><code>test_data_from_UBA_2014.Rd</code></div> + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Three experimental datasets from two water sediment systems and one soil</h1> + + <div class="d-none name"><code>test_data_from_UBA_2014.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>The datasets were used for the comparative validation of several kinetic evaluation software packages (Ranke, 2014).</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">test_data_from_UBA_2014</span></span></code></pre></div> </div> - <div id="format"> - <h2>Format</h2> + <div class="section level2"> + <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2> <p>A list containing three datasets as an R6 class defined by <code><a href="mkinds.html">mkinds</a></code>. Each dataset has, among others, the following components</p><dl><dt><code>title</code></dt> <dd><p>The name of the dataset, e.g. <code>UBA_2014_WS_river</code></p></dd> @@ -129,14 +96,14 @@ </dl></div> - <div id="source"> - <h2>Source</h2> + <div class="section level2"> + <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2> <p>Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="co"># \dontrun{</span></span></span> <span class="r-in"><span> <span class="co"># This is a level P-II evaluation of the dataset according to the FOCUS kinetics</span></span></span> <span class="r-in"><span> <span class="co"># guidance. Due to the strong correlation of the parameter estimates, the</span></span></span> @@ -213,26 +180,22 @@ <span class="r-in"><span> <span class="co"># }</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index aade8415..1e28ddc2 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -1,5 +1,10 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" 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="Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms"><meta property="og:description" content="The transformations are intended to map parameters that should only take on +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="The transformations are intended to map parameters that should only take on +restricted values to the full scale of real numbers. For kinetic rate +constants and other parameters that can only take on positive values, a +simple log transformation is used. 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For kinetic rate constants and other parameters that can only take on positive values, a simple log transformation is used. 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<div class="hidden name"><code>transform_odeparms.Rd</code></div> + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Functions to transform and backtransform kinetic parameters for fitting</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/transform_odeparms.R" class="external-link"><code>R/transform_odeparms.R</code></a></small> + <div class="d-none name"><code>transform_odeparms.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>The transformations are intended to map parameters that should only take on restricted values to the full scale of real numbers. For kinetic rate constants and other parameters that can only take on positive values, a @@ -122,7 +92,8 @@ formations fractions that should always sum up to 1 and can not be negative, the <a href="ilr.html">ilr</a> transformation is used.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">transform_odeparms</span><span class="op">(</span></span> <span> <span class="va">parms</span>,</span> <span> <span class="va">mkinmod</span>,</span> @@ -138,8 +109,8 @@ the <a href="ilr.html">ilr</a> transformation is used.</p> <span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>parms</dt> <dd><p>Parameters of kinetic models as used in the differential equations.</p></dd> @@ -179,25 +150,25 @@ exceed one, the <a href="ilr.html">ilr</a> transformation is used.</p></dd> fitting procedure.</p></dd> </dl></div> - <div id="value"> - <h2>Value</h2> + <div class="section level2"> + <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2> <p>A vector of transformed or backtransformed parameters</p> </div> - <div id="details"> - <h2>Details</h2> + <div class="section level2"> + <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2> <p>The transformation of sets of formation fractions is fragile, as it supposes the same ordering of the components in forward and backward transformation. This is no problem for the internal use in <a href="mkinfit.html">mkinfit</a>.</p> </div> - <div id="author"> - <h2>Author</h2> + <div class="section level2"> + <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2> <p>Johannes Ranke</p> </div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span></span></span> <span class="r-in"><span><span class="va">SFO_SFO</span> <span class="op"><-</span> <span class="fu"><a href="mkinmod.html">mkinmod</a></span><span class="op">(</span></span></span> <span class="r-in"><span> parent <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>type <span class="op">=</span> <span class="st">"SFO"</span>, to <span class="op">=</span> <span class="st">"m1"</span>, sink <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>,</span></span> @@ -313,26 +284,22 @@ This is no problem for the internal use in <a href="mkinfit.html">mkinfit</a>.</ <span class="r-in"><span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/reference/update.mkinfit-1.png b/docs/reference/update.mkinfit-1.png Binary files differindex 12fe1f5b..9278aefd 100644 --- a/docs/reference/update.mkinfit-1.png +++ b/docs/reference/update.mkinfit-1.png diff --git a/docs/reference/update.mkinfit-2.png b/docs/reference/update.mkinfit-2.png Binary files differindex 21817f94..f73a6180 100644 --- a/docs/reference/update.mkinfit-2.png +++ b/docs/reference/update.mkinfit-2.png diff --git a/docs/reference/update.mkinfit.html b/docs/reference/update.mkinfit.html index 10f9e8a2..5d4812bf 100644 --- a/docs/reference/update.mkinfit.html +++ b/docs/reference/update.mkinfit.html @@ -1,130 +1,99 @@ <!DOCTYPE html> -<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Update an mkinfit model with different arguments — update.mkinfit • mkin</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Update an mkinfit model with different arguments — update.mkinfit"><meta property="og:description" content="This function will return an updated mkinfit object. The fitted degradation +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="This function will return an updated mkinfit object. The fitted degradation +model parameters from the old fit are used as starting values for the +updated fit. 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Values specified as 'parms.ini' and/or 'state.ini' will override these starting values."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--></head><body data-spy="scroll" data-target="#toc"> +<![endif]--></head><body> + <a href="#main" class="visually-hidden-focusable">Skip to contents</a> - <div class="container template-reference-topic"> - <header><div class="navbar navbar-default navbar-fixed-top" role="navigation"> - <div class="container"> - <div class="navbar-header"> - 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<div class="hidden name"><code>update.mkinfit.Rd</code></div> + </ul></div> + + + </div> +</nav><div class="container template-reference-topic"> +<div class="row"> + <main id="main" class="col-md-9"><div class="page-header"> + <img src="" class="logo" alt=""><h1>Update an mkinfit model with different arguments</h1> + <small class="dont-index">Source: <a href="https://github.com/jranke/mkin/blob/HEAD/R/update.mkinfit.R" class="external-link"><code>R/update.mkinfit.R</code></a></small> + <div class="d-none name"><code>update.mkinfit.Rd</code></div> </div> - <div class="ref-description"> + <div class="ref-description section level2"> <p>This function will return an updated mkinfit object. The fitted degradation model parameters from the old fit are used as starting values for the updated fit. Values specified as 'parms.ini' and/or 'state.ini' will override these starting values.</p> </div> - <div id="ref-usage"> + <div class="section level2"> + <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S3 method for mkinfit</span></span> <span><span class="fu"><a href="https://rdrr.io/r/stats/update.html" class="external-link">update</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span>, evaluate <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div> </div> - <div id="arguments"> - <h2>Arguments</h2> + <div class="section level2"> + <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2> <dl><dt>object</dt> <dd><p>An mkinfit object to be updated</p></dd> @@ -140,8 +109,8 @@ remove arguments given in the original call</p></dd> </dl></div> - <div id="ref-examples"> - <h2>Examples</h2> + <div class="section level2"> + <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2> <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \dontrun{</span></span></span> <span class="r-in"><span><span class="va">fit</span> <span class="op"><-</span> <span class="fu"><a href="mkinfit.html">mkinfit</a></span><span class="op">(</span><span class="st">"SFO"</span>, <span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">FOCUS_2006_D</span>, <span class="va">value</span> <span class="op">!=</span> <span class="fl">0</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span> <span class="r-in"><span><span class="fu"><a href="parms.html">parms</a></span><span class="op">(</span><span class="va">fit</span><span class="op">)</span></span></span> @@ -158,26 +127,22 @@ remove arguments given in the original call</p></dd> <span class="r-in"><span><span class="co"># }</span></span></span> </code></pre></div> </div> - </div> - <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> - <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2> - </nav></div> -</div> + </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2> + </nav></aside></div> - <footer><div class="copyright"> + <footer><div class="pkgdown-footer-left"> <p></p><p>Developed by Johannes Ranke.</p> </div> -<div class="pkgdown"> +<div class="pkgdown-footer-right"> <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer></div> + </footer></div> - </body></html> diff --git a/docs/search.json b/docs/search.json new file mode 100644 index 00000000..23e2fc64 --- /dev/null +++ b/docs/search.json @@ -0,0 +1 @@ +[{"path":"https://pkgdown.jrwb.de/mkin/articles/FOCUS_L.html","id":"laboratory-data-l1","dir":"Articles","previous_headings":"","what":"Laboratory Data L1","title":"Example evaluation of FOCUS Laboratory Data L1 to L3","text":"following code defines example dataset L1 FOCUS kinetics report, p. 284: use assumptions simple first order (SFO), case declining rate constant time (FOMC) case two different phases kinetics (DFOP). detailed discussion models, please see FOCUS kinetics report. Since mkin version 0.9-32 (July 2014), can use shorthand notation like \"SFO\" parent degradation models. following two lines fit model produce summary report model fit. covers numerical analysis given FOCUS report. plot fit obtained plot function mkinfit objects. residual plot can easily obtained comparison, FOMC model fitted well, \\(\\chi^2\\) error level checked. get warning default optimisation algorithm Port converge, indication model overparameterised, .e. contains many parameters ill-defined consequence. fact, due higher number parameters, lower number degrees freedom fit, \\(\\chi^2\\) error level actually higher FOMC model (3.6%) SFO model (3.4%). Additionally, parameters log_alpha log_beta internally fitted model excessive confidence intervals, span 25 orders magnitude (!) backtransformed scale alpha beta. Also, t-test significant difference zero indicate significant difference, p-values greater 0.1, finally, parameter correlation log_alpha log_beta 1.000, clearly indicating model overparameterised. \\(\\chi^2\\) error levels reported Appendix 3 Appendix 7 FOCUS kinetics report rounded integer percentages partly deviate one percentage point results calculated mkin. reason known. However, mkin gives \\(\\chi^2\\) error levels kinfit package calculation routines kinfit package extensively compared results obtained KinGUI software, documented kinfit package vignette. KinGUI first widely used standard package field. Also, calculation \\(\\chi^2\\) error levels compared KinGUII, CAKE DegKin manager project sponsored German Umweltbundesamt (Ranke 2014).","code":"library(\"mkin\", quietly = TRUE) FOCUS_2006_L1 = data.frame( t = rep(c(0, 1, 2, 3, 5, 7, 14, 21, 30), each = 2), parent = c(88.3, 91.4, 85.6, 84.5, 78.9, 77.6, 72.0, 71.9, 50.3, 59.4, 47.0, 45.1, 27.7, 27.3, 10.0, 10.4, 2.9, 4.0)) FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1) m.L1.SFO <- mkinfit(\"SFO\", FOCUS_2006_L1_mkin, quiet = TRUE) summary(m.L1.SFO) ## mkin version used for fitting: 1.2.6 ## R version used for fitting: 4.3.2 ## Date of fit: Thu Nov 16 04:20:13 2023 ## Date of summary: Thu Nov 16 04:20:13 2023 ## ## Equations: ## d_parent/dt = - k_parent * parent ## ## Model predictions using solution type analytical ## ## Fitted using 133 model solutions performed in 0.011 s ## ## Error model: Constant variance ## ## Error model algorithm: OLS ## ## Starting values for parameters to be optimised: ## value type ## parent_0 89.85 state ## k_parent 0.10 deparm ## ## Starting values for the transformed parameters actually optimised: ## value lower upper ## parent_0 89.850000 -Inf Inf ## log_k_parent -2.302585 -Inf Inf ## ## Fixed parameter values: ## None ## ## Results: ## ## AIC BIC logLik ## 93.88778 96.5589 -43.94389 ## ## Optimised, transformed parameters with symmetric confidence intervals: ## Estimate Std. Error Lower Upper ## parent_0 92.470 1.28200 89.740 95.200 ## log_k_parent -2.347 0.03763 -2.428 -2.267 ## sigma 2.780 0.46330 1.792 3.767 ## ## Parameter correlation: ## parent_0 log_k_parent sigma ## parent_0 1.000e+00 6.186e-01 -1.516e-09 ## log_k_parent 6.186e-01 1.000e+00 -3.124e-09 ## sigma -1.516e-09 -3.124e-09 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. ## t-test (unrealistically) based on the assumption of normal distribution ## for estimators of untransformed parameters. ## Estimate t value Pr(>t) Lower Upper ## parent_0 92.47000 72.13 8.824e-21 89.74000 95.2000 ## k_parent 0.09561 26.57 2.487e-14 0.08824 0.1036 ## sigma 2.78000 6.00 1.216e-05 1.79200 3.7670 ## ## FOCUS Chi2 error levels in percent: ## err.min n.optim df ## All data 3.424 2 7 ## parent 3.424 2 7 ## ## Estimated disappearance times: ## DT50 DT90 ## parent 7.249 24.08 ## ## Data: ## time variable observed predicted residual ## 0 parent 88.3 92.471 -4.1710 ## 0 parent 91.4 92.471 -1.0710 ## 1 parent 85.6 84.039 1.5610 ## 1 parent 84.5 84.039 0.4610 ## 2 parent 78.9 76.376 2.5241 ## 2 parent 77.6 76.376 1.2241 ## 3 parent 72.0 69.412 2.5884 ## 3 parent 71.9 69.412 2.4884 ## 5 parent 50.3 57.330 -7.0301 ## 5 parent 59.4 57.330 2.0699 ## 7 parent 47.0 47.352 -0.3515 ## 7 parent 45.1 47.352 -2.2515 ## 14 parent 27.7 24.247 3.4528 ## 14 parent 27.3 24.247 3.0528 ## 21 parent 10.0 12.416 -2.4163 ## 21 parent 10.4 12.416 -2.0163 ## 30 parent 2.9 5.251 -2.3513 ## 30 parent 4.0 5.251 -1.2513 plot(m.L1.SFO, show_errmin = TRUE, main = \"FOCUS L1 - SFO\") mkinresplot(m.L1.SFO, ylab = \"Observed\", xlab = \"Time\") m.L1.FOMC <- mkinfit(\"FOMC\", FOCUS_2006_L1_mkin, quiet=TRUE) ## Warning in mkinfit(\"FOMC\", FOCUS_2006_L1_mkin, quiet = TRUE): Optimisation did not converge: ## false convergence (8) plot(m.L1.FOMC, show_errmin = TRUE, main = \"FOCUS L1 - FOMC\") summary(m.L1.FOMC, data = FALSE) ## Warning in sqrt(diag(covar)): NaNs produced ## Warning in sqrt(1/diag(V)): NaNs produced ## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result ## is doubtful ## mkin version used for fitting: 1.2.6 ## R version used for fitting: 4.3.2 ## Date of fit: Thu Nov 16 04:20:13 2023 ## Date of summary: Thu Nov 16 04:20:13 2023 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## ## Fitted using 342 model solutions performed in 0.023 s ## ## Error model: Constant variance ## ## Error model algorithm: OLS ## ## Starting values for parameters to be optimised: ## value type ## parent_0 89.85 state ## alpha 1.00 deparm ## beta 10.00 deparm ## ## Starting values for the transformed parameters actually optimised: ## value lower upper ## parent_0 89.850000 -Inf Inf ## log_alpha 0.000000 -Inf Inf ## log_beta 2.302585 -Inf Inf ## ## Fixed parameter values: ## None ## ## ## Warning(s): ## Optimisation did not converge: ## false convergence (8) ## ## Results: ## ## AIC BIC logLik ## 95.88782 99.44931 -43.94391 ## ## Optimised, transformed parameters with symmetric confidence intervals: ## Estimate Std. Error Lower Upper ## parent_0 92.47 1.2820 89.720 95.220 ## log_alpha 13.20 NaN NaN NaN ## log_beta 15.54 NaN NaN NaN ## sigma 2.78 0.4607 1.792 3.768 ## ## Parameter correlation: ## parent_0 log_alpha log_beta sigma ## parent_0 1.000000 NaN NaN 0.000603 ## log_alpha NaN 1 NaN NaN ## log_beta NaN NaN 1 NaN ## sigma 0.000603 NaN NaN 1.000000 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. ## t-test (unrealistically) based on the assumption of normal distribution ## for estimators of untransformed parameters. ## Estimate t value Pr(>t) Lower Upper ## parent_0 9.247e+01 NA NA 89.720 95.220 ## alpha 5.386e+05 NA NA NA NA ## beta 5.633e+06 NA NA NA NA ## sigma 2.780e+00 NA NA 1.792 3.768 ## ## FOCUS Chi2 error levels in percent: ## err.min n.optim df ## All data 3.619 3 6 ## parent 3.619 3 6 ## ## Estimated disappearance times: ## DT50 DT90 DT50back ## parent 7.249 24.08 7.249"},{"path":"https://pkgdown.jrwb.de/mkin/articles/FOCUS_L.html","id":"laboratory-data-l2","dir":"Articles","previous_headings":"","what":"Laboratory Data L2","title":"Example evaluation of FOCUS Laboratory Data L1 to L3","text":"following code defines example dataset L2 FOCUS kinetics report, p. 287:","code":"FOCUS_2006_L2 = data.frame( t = rep(c(0, 1, 3, 7, 14, 28), each = 2), parent = c(96.1, 91.8, 41.4, 38.7, 19.3, 22.3, 4.6, 4.6, 2.6, 1.2, 0.3, 0.6)) FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2)"},{"path":"https://pkgdown.jrwb.de/mkin/articles/FOCUS_L.html","id":"sfo-fit-for-l2","dir":"Articles","previous_headings":"Laboratory Data L2","what":"SFO fit for L2","title":"Example evaluation of FOCUS Laboratory Data L1 to L3","text":", SFO model fitted result plotted. residual plot can obtained simply adding argument show_residuals plot command. \\(\\chi^2\\) error level 14% suggests model fit well. also obvious plots fit, included residual plot. FOCUS kinetics report, stated apparent systematic error observed residual plot measured DT90 (approximately day 5), underestimation beyond point. may add difficult judge random nature residuals just three samplings days 0, 1 3. Also, clear priori consistent underestimation approximate DT90 irrelevant. However, can rationalised fact FOCUS fate models generally implement SFO kinetics.","code":"m.L2.SFO <- mkinfit(\"SFO\", FOCUS_2006_L2_mkin, quiet=TRUE) plot(m.L2.SFO, show_residuals = TRUE, show_errmin = TRUE, main = \"FOCUS L2 - SFO\")"},{"path":"https://pkgdown.jrwb.de/mkin/articles/FOCUS_L.html","id":"fomc-fit-for-l2","dir":"Articles","previous_headings":"Laboratory Data L2","what":"FOMC fit for L2","title":"Example evaluation of FOCUS Laboratory Data L1 to L3","text":"comparison, FOMC model fitted well, \\(\\chi^2\\) error level checked. error level \\(\\chi^2\\) test passes much lower case. Therefore, FOMC model provides better description data, less experimental error assumed order explain data.","code":"m.L2.FOMC <- mkinfit(\"FOMC\", FOCUS_2006_L2_mkin, quiet = TRUE) plot(m.L2.FOMC, show_residuals = TRUE, main = \"FOCUS L2 - FOMC\") summary(m.L2.FOMC, data = FALSE) ## mkin version used for fitting: 1.2.6 ## R version used for fitting: 4.3.2 ## Date of fit: Thu Nov 16 04:20:13 2023 ## Date of summary: Thu Nov 16 04:20:14 2023 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## ## Fitted using 239 model solutions performed in 0.014 s ## ## Error model: Constant variance ## ## Error model algorithm: OLS ## ## Starting values for parameters to be optimised: ## value type ## parent_0 93.95 state ## alpha 1.00 deparm ## beta 10.00 deparm ## ## Starting values for the transformed parameters actually optimised: ## value lower upper ## parent_0 93.950000 -Inf Inf ## log_alpha 0.000000 -Inf Inf ## log_beta 2.302585 -Inf Inf ## ## Fixed parameter values: ## None ## ## Results: ## ## AIC BIC logLik ## 61.78966 63.72928 -26.89483 ## ## Optimised, transformed parameters with symmetric confidence intervals: ## Estimate Std. Error Lower Upper ## parent_0 93.7700 1.6130 90.05000 97.4900 ## log_alpha 0.3180 0.1559 -0.04149 0.6776 ## log_beta 0.2102 0.2493 -0.36460 0.7850 ## sigma 2.2760 0.4645 1.20500 3.3470 ## ## Parameter correlation: ## parent_0 log_alpha log_beta sigma ## parent_0 1.000e+00 -1.151e-01 -2.085e-01 -7.436e-09 ## log_alpha -1.151e-01 1.000e+00 9.741e-01 -1.617e-07 ## log_beta -2.085e-01 9.741e-01 1.000e+00 -1.386e-07 ## sigma -7.436e-09 -1.617e-07 -1.386e-07 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. ## t-test (unrealistically) based on the assumption of normal distribution ## for estimators of untransformed parameters. ## Estimate t value Pr(>t) Lower Upper ## parent_0 93.770 58.120 4.267e-12 90.0500 97.490 ## alpha 1.374 6.414 1.030e-04 0.9594 1.969 ## beta 1.234 4.012 1.942e-03 0.6945 2.192 ## sigma 2.276 4.899 5.977e-04 1.2050 3.347 ## ## FOCUS Chi2 error levels in percent: ## err.min n.optim df ## All data 6.205 3 3 ## parent 6.205 3 3 ## ## Estimated disappearance times: ## DT50 DT90 DT50back ## parent 0.8092 5.356 1.612"},{"path":"https://pkgdown.jrwb.de/mkin/articles/FOCUS_L.html","id":"dfop-fit-for-l2","dir":"Articles","previous_headings":"Laboratory Data L2","what":"DFOP fit for L2","title":"Example evaluation of FOCUS Laboratory Data L1 to L3","text":"Fitting four parameter DFOP model reduces \\(\\chi^2\\) error level. , DFOP model clearly best-fit model dataset L2 based chi^2 error level criterion.","code":"m.L2.DFOP <- mkinfit(\"DFOP\", FOCUS_2006_L2_mkin, quiet = TRUE) plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE, main = \"FOCUS L2 - DFOP\") summary(m.L2.DFOP, data = FALSE) ## mkin version used for fitting: 1.2.6 ## R version used for fitting: 4.3.2 ## Date of fit: Thu Nov 16 04:20:14 2023 ## Date of summary: Thu Nov 16 04:20:14 2023 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * ## time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) ## * parent ## ## Model predictions using solution type analytical ## ## Fitted using 581 model solutions performed in 0.041 s ## ## Error model: Constant variance ## ## Error model algorithm: OLS ## ## Starting values for parameters to be optimised: ## value type ## parent_0 93.95 state ## k1 0.10 deparm ## k2 0.01 deparm ## g 0.50 deparm ## ## Starting values for the transformed parameters actually optimised: ## value lower upper ## parent_0 93.950000 -Inf Inf ## log_k1 -2.302585 -Inf Inf ## log_k2 -4.605170 -Inf Inf ## g_qlogis 0.000000 -Inf Inf ## ## Fixed parameter values: ## None ## ## Results: ## ## AIC BIC logLik ## 52.36695 54.79148 -21.18347 ## ## Optimised, transformed parameters with symmetric confidence intervals: ## Estimate Std. Error Lower Upper ## parent_0 93.950 9.998e-01 91.5900 96.3100 ## log_k1 3.113 1.849e+03 -4369.0000 4375.0000 ## log_k2 -1.088 6.285e-02 -1.2370 -0.9394 ## g_qlogis -0.399 9.946e-02 -0.6342 -0.1638 ## sigma 1.414 2.886e-01 0.7314 2.0960 ## ## Parameter correlation: ## parent_0 log_k1 log_k2 g_qlogis sigma ## parent_0 1.000e+00 6.763e-07 -8.944e-10 2.665e-01 -1.083e-09 ## log_k1 6.763e-07 1.000e+00 1.112e-04 -2.187e-04 -1.027e-05 ## log_k2 -8.944e-10 1.112e-04 1.000e+00 -7.903e-01 9.464e-09 ## g_qlogis 2.665e-01 -2.187e-04 -7.903e-01 1.000e+00 -1.532e-08 ## sigma -1.083e-09 -1.027e-05 9.464e-09 -1.532e-08 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. ## t-test (unrealistically) based on the assumption of normal distribution ## for estimators of untransformed parameters. ## Estimate t value Pr(>t) Lower Upper ## parent_0 93.9500 9.397e+01 2.036e-12 91.5900 96.3100 ## k1 22.4900 5.533e-04 4.998e-01 0.0000 Inf ## k2 0.3369 1.591e+01 4.697e-07 0.2904 0.3909 ## g 0.4016 1.680e+01 3.238e-07 0.3466 0.4591 ## sigma 1.4140 4.899e+00 8.776e-04 0.7314 2.0960 ## ## FOCUS Chi2 error levels in percent: ## err.min n.optim df ## All data 2.53 4 2 ## parent 2.53 4 2 ## ## Estimated disappearance times: ## DT50 DT90 DT50back DT50_k1 DT50_k2 ## parent 0.5335 5.311 1.599 0.03083 2.058"},{"path":"https://pkgdown.jrwb.de/mkin/articles/FOCUS_L.html","id":"laboratory-data-l3","dir":"Articles","previous_headings":"","what":"Laboratory Data L3","title":"Example evaluation of FOCUS Laboratory Data L1 to L3","text":"following code defines example dataset L3 FOCUS kinetics report, p. 290.","code":"FOCUS_2006_L3 = data.frame( t = c(0, 3, 7, 14, 30, 60, 91, 120), parent = c(97.8, 60, 51, 43, 35, 22, 15, 12)) FOCUS_2006_L3_mkin <- mkin_wide_to_long(FOCUS_2006_L3)"},{"path":"https://pkgdown.jrwb.de/mkin/articles/FOCUS_L.html","id":"fit-multiple-models","dir":"Articles","previous_headings":"Laboratory Data L3","what":"Fit multiple models","title":"Example evaluation of FOCUS Laboratory Data L1 to L3","text":"mkin version 0.9-39 (June 2015), can fit several models one datasets one call function mmkin. datasets passed list, case named list holding L3 dataset prepared . \\(\\chi^2\\) error level 21% well plot suggest SFO model fit well. FOMC model performs better, error level \\(\\chi^2\\) test passes 7%. Fitting four parameter DFOP model reduces \\(\\chi^2\\) error level considerably.","code":"# Only use one core here, not to offend the CRAN checks mm.L3 <- mmkin(c(\"SFO\", \"FOMC\", \"DFOP\"), cores = 1, list(\"FOCUS L3\" = FOCUS_2006_L3_mkin), quiet = TRUE) plot(mm.L3)"},{"path":"https://pkgdown.jrwb.de/mkin/articles/FOCUS_L.html","id":"accessing-mmkin-objects","dir":"Articles","previous_headings":"Laboratory Data L3","what":"Accessing mmkin objects","title":"Example evaluation of FOCUS Laboratory Data L1 to L3","text":"objects returned mmkin arranged like matrix, models row index datasets column index. can extract summary plot e.g. DFOP fit, using square brackets indexing result use summary plot functions working mkinfit objects. , look model plot, confidence intervals parameters correlation matrix suggest parameter estimates reliable, DFOP model can used best-fit model based \\(\\chi^2\\) error level criterion laboratory data L3. also example standard t-test parameter g_ilr misleading, tests significant difference zero. case, zero appears correct value parameter, confidence interval backtransformed parameter g quite narrow.","code":"summary(mm.L3[[\"DFOP\", 1]]) ## mkin version used for fitting: 1.2.6 ## R version used for fitting: 4.3.2 ## Date of fit: Thu Nov 16 04:20:14 2023 ## Date of summary: Thu Nov 16 04:20:14 2023 ## ## Equations: ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * ## time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) ## * parent ## ## Model predictions using solution type analytical ## ## Fitted using 376 model solutions performed in 0.024 s ## ## Error model: Constant variance ## ## Error model algorithm: OLS ## ## Starting values for parameters to be optimised: ## value type ## parent_0 97.80 state ## k1 0.10 deparm ## k2 0.01 deparm ## g 0.50 deparm ## ## Starting values for the transformed parameters actually optimised: ## value lower upper ## parent_0 97.800000 -Inf Inf ## log_k1 -2.302585 -Inf Inf ## log_k2 -4.605170 -Inf Inf ## g_qlogis 0.000000 -Inf Inf ## ## Fixed parameter values: ## None ## ## Results: ## ## AIC BIC logLik ## 32.97732 33.37453 -11.48866 ## ## Optimised, transformed parameters with symmetric confidence intervals: ## Estimate Std. Error Lower Upper ## parent_0 97.7500 1.01900 94.5000 101.000000 ## log_k1 -0.6612 0.10050 -0.9812 -0.341300 ## log_k2 -4.2860 0.04322 -4.4230 -4.148000 ## g_qlogis -0.1739 0.05270 -0.3416 -0.006142 ## sigma 1.0170 0.25430 0.2079 1.827000 ## ## Parameter correlation: ## parent_0 log_k1 log_k2 g_qlogis sigma ## parent_0 1.000e+00 1.732e-01 2.282e-02 4.009e-01 -9.696e-08 ## log_k1 1.732e-01 1.000e+00 4.945e-01 -5.809e-01 7.148e-07 ## log_k2 2.282e-02 4.945e-01 1.000e+00 -6.812e-01 1.022e-06 ## g_qlogis 4.009e-01 -5.809e-01 -6.812e-01 1.000e+00 -7.930e-07 ## sigma -9.696e-08 7.148e-07 1.022e-06 -7.930e-07 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. ## t-test (unrealistically) based on the assumption of normal distribution ## for estimators of untransformed parameters. ## Estimate t value Pr(>t) Lower Upper ## parent_0 97.75000 95.960 1.248e-06 94.50000 101.00000 ## k1 0.51620 9.947 1.081e-03 0.37490 0.71090 ## k2 0.01376 23.140 8.840e-05 0.01199 0.01579 ## g 0.45660 34.920 2.581e-05 0.41540 0.49850 ## sigma 1.01700 4.000 1.400e-02 0.20790 1.82700 ## ## FOCUS Chi2 error levels in percent: ## err.min n.optim df ## All data 2.225 4 4 ## parent 2.225 4 4 ## ## Estimated disappearance times: ## DT50 DT90 DT50back DT50_k1 DT50_k2 ## parent 7.464 123 37.03 1.343 50.37 ## ## Data: ## time variable observed predicted residual ## 0 parent 97.8 97.75 0.05396 ## 3 parent 60.0 60.45 -0.44933 ## 7 parent 51.0 49.44 1.56338 ## 14 parent 43.0 43.84 -0.83632 ## 30 parent 35.0 35.15 -0.14707 ## 60 parent 22.0 23.26 -1.25919 ## 91 parent 15.0 15.18 -0.18181 ## 120 parent 12.0 10.19 1.81395 plot(mm.L3[[\"DFOP\", 1]], show_errmin = TRUE)"},{"path":"https://pkgdown.jrwb.de/mkin/articles/FOCUS_L.html","id":"laboratory-data-l4","dir":"Articles","previous_headings":"","what":"Laboratory Data L4","title":"Example evaluation of FOCUS Laboratory Data L1 to L3","text":"following code defines example dataset L4 FOCUS kinetics report, p. 293: Fits SFO FOMC models, plots summaries produced : \\(\\chi^2\\) error level 3.3% well plot suggest SFO model fits well. error level \\(\\chi^2\\) test passes slightly lower FOMC model. However, difference appears negligible.","code":"FOCUS_2006_L4 = data.frame( t = c(0, 3, 7, 14, 30, 60, 91, 120), parent = c(96.6, 96.3, 94.3, 88.8, 74.9, 59.9, 53.5, 49.0)) FOCUS_2006_L4_mkin <- mkin_wide_to_long(FOCUS_2006_L4) # Only use one core here, not to offend the CRAN checks mm.L4 <- mmkin(c(\"SFO\", \"FOMC\"), cores = 1, list(\"FOCUS L4\" = FOCUS_2006_L4_mkin), quiet = TRUE) plot(mm.L4) summary(mm.L4[[\"SFO\", 1]], data = FALSE) ## mkin version used for fitting: 1.2.6 ## R version used for fitting: 4.3.2 ## Date of fit: Thu Nov 16 04:20:14 2023 ## Date of summary: Thu Nov 16 04:20:15 2023 ## ## Equations: ## d_parent/dt = - k_parent * parent ## ## Model predictions using solution type analytical ## ## Fitted using 142 model solutions performed in 0.01 s ## ## Error model: Constant variance ## ## Error model algorithm: OLS ## ## Starting values for parameters to be optimised: ## value type ## parent_0 96.6 state ## k_parent 0.1 deparm ## ## Starting values for the transformed parameters actually optimised: ## value lower upper ## parent_0 96.600000 -Inf Inf ## log_k_parent -2.302585 -Inf Inf ## ## Fixed parameter values: ## None ## ## Results: ## ## AIC BIC logLik ## 47.12133 47.35966 -20.56067 ## ## Optimised, transformed parameters with symmetric confidence intervals: ## Estimate Std. Error Lower Upper ## parent_0 96.440 1.69900 92.070 100.800 ## log_k_parent -5.030 0.07059 -5.211 -4.848 ## sigma 3.162 0.79050 1.130 5.194 ## ## Parameter correlation: ## parent_0 log_k_parent sigma ## parent_0 1.000e+00 5.938e-01 3.430e-07 ## log_k_parent 5.938e-01 1.000e+00 5.885e-07 ## sigma 3.430e-07 5.885e-07 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. ## t-test (unrealistically) based on the assumption of normal distribution ## for estimators of untransformed parameters. ## Estimate t value Pr(>t) Lower Upper ## parent_0 96.440000 56.77 1.604e-08 92.070000 1.008e+02 ## k_parent 0.006541 14.17 1.578e-05 0.005455 7.842e-03 ## sigma 3.162000 4.00 5.162e-03 1.130000 5.194e+00 ## ## FOCUS Chi2 error levels in percent: ## err.min n.optim df ## All data 3.287 2 6 ## parent 3.287 2 6 ## ## Estimated disappearance times: ## DT50 DT90 ## parent 106 352 summary(mm.L4[[\"FOMC\", 1]], data = FALSE) ## mkin version used for fitting: 1.2.6 ## R version used for fitting: 4.3.2 ## Date of fit: Thu Nov 16 04:20:15 2023 ## Date of summary: Thu Nov 16 04:20:15 2023 ## ## Equations: ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent ## ## Model predictions using solution type analytical ## ## Fitted using 224 model solutions performed in 0.014 s ## ## Error model: Constant variance ## ## Error model algorithm: OLS ## ## Starting values for parameters to be optimised: ## value type ## parent_0 96.6 state ## alpha 1.0 deparm ## beta 10.0 deparm ## ## Starting values for the transformed parameters actually optimised: ## value lower upper ## parent_0 96.600000 -Inf Inf ## log_alpha 0.000000 -Inf Inf ## log_beta 2.302585 -Inf Inf ## ## Fixed parameter values: ## None ## ## Results: ## ## AIC BIC logLik ## 40.37255 40.69032 -16.18628 ## ## Optimised, transformed parameters with symmetric confidence intervals: ## Estimate Std. Error Lower Upper ## parent_0 99.1400 1.2670 95.6300 102.7000 ## log_alpha -0.3506 0.2616 -1.0770 0.3756 ## log_beta 4.1740 0.3938 3.0810 5.2670 ## sigma 1.8300 0.4575 0.5598 3.1000 ## ## Parameter correlation: ## parent_0 log_alpha log_beta sigma ## parent_0 1.000e+00 -4.696e-01 -5.543e-01 -2.447e-07 ## log_alpha -4.696e-01 1.000e+00 9.889e-01 2.198e-08 ## log_beta -5.543e-01 9.889e-01 1.000e+00 4.923e-08 ## sigma -2.447e-07 2.198e-08 4.923e-08 1.000e+00 ## ## Backtransformed parameters: ## Confidence intervals for internally transformed parameters are asymmetric. ## t-test (unrealistically) based on the assumption of normal distribution ## for estimators of untransformed parameters. ## Estimate t value Pr(>t) Lower Upper ## parent_0 99.1400 78.250 7.993e-08 95.6300 102.700 ## alpha 0.7042 3.823 9.365e-03 0.3407 1.456 ## beta 64.9800 2.540 3.201e-02 21.7800 193.900 ## sigma 1.8300 4.000 8.065e-03 0.5598 3.100 ## ## FOCUS Chi2 error levels in percent: ## err.min n.optim df ## All data 2.029 3 5 ## parent 2.029 3 5 ## ## Estimated disappearance times: ## DT50 DT90 DT50back ## parent 108.9 1644 494.9"},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/articles/mkin.html","id":"abstract","dir":"Articles","previous_headings":"","what":"Abstract","title":"Short introduction to mkin","text":"regulatory evaluation chemical substances like plant protection products (pesticides), biocides chemicals, degradation data play important role. evaluation pesticide degradation experiments, detailed guidance developed, based nonlinear optimisation. R add-package mkin implements fitting models recommended guidance within R calculates statistical measures data series within one compartments, parent metabolites.","code":"library(\"mkin\", quietly = TRUE) # Define the kinetic model m_SFO_SFO_SFO <- mkinmod(parent = mkinsub(\"SFO\", \"M1\"), M1 = mkinsub(\"SFO\", \"M2\"), M2 = mkinsub(\"SFO\"), use_of_ff = \"max\", quiet = TRUE) # Produce model predictions using some arbitrary parameters sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) d_SFO_SFO_SFO <- mkinpredict(m_SFO_SFO_SFO, c(k_parent = 0.03, f_parent_to_M1 = 0.5, k_M1 = log(2)/100, f_M1_to_M2 = 0.9, k_M2 = log(2)/50), c(parent = 100, M1 = 0, M2 = 0), sampling_times) # Generate a dataset by adding normally distributed errors with # standard deviation 3, for two replicates at each sampling time d_SFO_SFO_SFO_err <- add_err(d_SFO_SFO_SFO, reps = 2, sdfunc = function(x) 3, n = 1, seed = 123456789 ) # Fit the model to the dataset f_SFO_SFO_SFO <- mkinfit(m_SFO_SFO_SFO, d_SFO_SFO_SFO_err[[1]], quiet = TRUE) # Plot the results separately for parent and metabolites plot_sep(f_SFO_SFO_SFO, lpos = c(\"topright\", \"bottomright\", \"bottomright\"))"},{"path":"https://pkgdown.jrwb.de/mkin/articles/mkin.html","id":"background","dir":"Articles","previous_headings":"","what":"Background","title":"Short introduction to mkin","text":"mkin package (J. Ranke 2021) implements approach degradation kinetics recommended kinetics report provided FOrum Co-ordination pesticide fate models USe (FOCUS Work Group Degradation Kinetics 2006, 2014). covers data series describing decline one compound, data series transformation products (commonly termed metabolites) data series one compartment. possible include back reactions. Therefore, equilibrium reactions equilibrium partitioning can specified, although often leads overparameterisation model. first mkin code published 2010, commonly used tools fitting complex kinetic degradation models experimental data KinGUI (Schäfer et al. 2007), MATLAB based tool graphical user interface specifically tailored task included output proposed FOCUS Kinetics Workgroup, ModelMaker, general purpose compartment based tool providing infrastructure fitting dynamic simulation models based differential equations data. ‘mkin’ code first uploaded BerliOS development platform. taken , version control history imported R-Forge site (see e.g. initial commit 11 May 2010), code still updated. time, R package FME (Flexible Modelling Environment) (Soetaert Petzoldt 2010) already available, provided good basis developing package specifically tailored task. remaining challenge make easy possible users (including author vignette) specify system differential equations include output requested FOCUS guidance, \\(\\chi^2\\) error level defined guidance. Also, mkin introduced using analytical solutions parent kinetics improved optimization speed. Later, Eigenvalue based solutions introduced mkin case linear differential equations (.e. FOMC DFOP models used parent compound), greatly improving optimization speed cases. , become somehow obsolete, use compiled code described gives even faster execution times. possibility specify back-reactions biphasic model (SFORB) metabolites present mkin beginning.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/articles/mkin.html","id":"derived-software-tools","dir":"Articles","previous_headings":"Background","what":"Derived software tools","title":"Short introduction to mkin","text":"Soon publication mkin, two derived tools published, namely KinGUII (developed Bayer Crop Science) CAKE (commissioned Tessella Syngenta), added graphical user interface (GUI), added fitting iteratively reweighted least squares (IRLS) characterisation likely parameter distributions Markov Chain Monte Carlo (MCMC) sampling. CAKE focuses smooth use experience, sacrificing flexibility model definition, originally allowing two primary metabolites parallel. current version 3.4 CAKE released May 2020 uses scheme six metabolites flexible arrangement supports biphasic modelling metabolites, support back-reactions (non-instantaneous equilibria). KinGUI offers even flexible widget specifying complex kinetic models. Back-reactions (non-instantaneous equilibria) supported early , 2014, simple first-order models specified transformation products. Starting KinGUII version 2.1, biphasic modelling metabolites also available KinGUII. graphical user interface (GUI) recently brought decent degree maturity browser based GUI named gmkin. Please see documentation page manual information. comparison scope, usability numerical results obtained tools recently published Johannes Ranke, Wöltjen, Meinecke (2018).","code":""},{"path":"https://pkgdown.jrwb.de/mkin/articles/mkin.html","id":"unique-features","dir":"Articles","previous_headings":"","what":"Unique features","title":"Short introduction to mkin","text":"Currently, main unique features available mkin speed increase using compiled code compiler present, parallel model fitting multicore machines using mmkin function, estimation parameter confidence intervals based transformed parameters (see ) possibility use two-component error model iteratively reweighted least squares fitting different variances variable introduced Gao et al. (2011) available mkin since version 0.9-22. release 0.9.49.5, IRLS algorithm complemented direct step-wise maximisation likelihood function, makes possible fit variance variable error model also two-component error model inspired error models developed analytical chemistry (Johannes Ranke Meinecke 2019).","code":""},{"path":"https://pkgdown.jrwb.de/mkin/articles/mkin.html","id":"internal-parameter-transformations","dir":"Articles","previous_headings":"","what":"Internal parameter transformations","title":"Short introduction to mkin","text":"rate constants, log transformation used, proposed Bates Watts (1988, 77, 149). Approximate intervals constructed transformed rate constants (compare Bates Watts 1988, 135), .e. logarithms. Confidence intervals rate constants obtained using appropriate backtransformation using exponential function. first version mkin allowing specifying models using formation fractions, home-made reparameterisation used order ensure sum formation fractions exceed unity. method still used current version KinGUII (v2.1 April 2014), modification allows fixing pathway sink zero. CAKE uses penalties objective function order enforce constraint. 2012, alternative reparameterisation formation fractions proposed together René Lehmann (J. Ranke Lehmann 2012), based isometric logratio transformation (ILR). aim improve validity linear approximation objective function parameter estimation procedure well subsequent calculation parameter confidence intervals. current version mkin, logit transformation used parameters bound 0 1, g parameter DFOP model.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/articles/mkin.html","id":"confidence-intervals-based-on-transformed-parameters","dir":"Articles","previous_headings":"Internal parameter transformations","what":"Confidence intervals based on transformed parameters","title":"Short introduction to mkin","text":"first attempt providing improved parameter confidence intervals introduced mkin 2013, confidence intervals obtained FME transformed parameters simply backtransformed one one yield asymmetric confidence intervals backtransformed parameters. However, 1:1 relation rate constants model transformed parameters fitted model, parameters obtained isometric logratio transformation calculated set formation fractions quantify paths compounds formed specific parent compound, 1:1 relation exists. Therefore, parameter confidence intervals formation fractions obtained method appear valid case single transformation product, currently logit transformation used formation fraction. confidence intervals obtained backtransformation cases 1:1 relation transformed original parameter exist considered author vignette accurate obtained using re-estimation Hessian matrix backtransformation, implemented FME package.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/articles/mkin.html","id":"parameter-t-test-based-on-untransformed-parameters","dir":"Articles","previous_headings":"Internal parameter transformations","what":"Parameter t-test based on untransformed parameters","title":"Short introduction to mkin","text":"standard output many nonlinear regression software packages includes results test significant difference zero parameters. test also recommended check validity rate constants FOCUS guidance (FOCUS Work Group Degradation Kinetics 2014, 96ff). argued precondition test, .e. normal distribution estimator parameters, fulfilled case nonlinear regression (J. Ranke Lehmann 2015). However, test commonly used industry, consultants national authorities order decide reliability parameter estimates, based FOCUS guidance mentioned . Therefore, results one-sided t-test included summary output mkin. reasonable test significant difference transformed parameters (e.g. \\(log(k)\\)) zero, t-test calculated based model definition parameter transformation, .e. similar way packages apply internal parameter transformation. note included mkin output, pointing fact t-test based unjustified assumption normal distribution parameter estimators.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_cyan_pathway.html","id":"introduction","dir":"Articles > Prebuilt","previous_headings":"","what":"Introduction","title":"Testing hierarchical pathway kinetics with residue data on cyantraniliprole","text":"purpose document test demonstrate nonlinear hierarchical models (NLHM) based parent degradation models SFO, FOMC, DFOP HS, serial formation two metabolites can fitted mkin package. assembled course work package 1.2 Project Number 173340 (Application nonlinear hierarchical models kinetic evaluation chemical degradation data) German Environment Agency carried 2022 2023. mkin package used version 1.2.6 currently development. newly introduced functionality used simplification excluding random effects set fits based related set fits reduced model, documentation starting parameters fit, starting parameters saem fits now listed summary. saemix package used backend fitting NLHM, also loaded make convergence plot function available. document processed knitr package, also provides kable function used improve display tabular data R markdown documents. parallel processing, parallel package used.","code":"library(mkin) library(knitr) library(saemix) library(parallel) n_cores <- detectCores() # We need to start a new cluster after defining a compiled model that is # saved as a DLL to the user directory, therefore we define a function # This is used again after defining the pathway model start_cluster <- function(n_cores) { if (Sys.info()[\"sysname\"] == \"Windows\") { ret <- makePSOCKcluster(n_cores) } else { ret <- makeForkCluster(n_cores) } return(ret) } cl <- start_cluster(n_cores)"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_cyan_pathway.html","id":"test-data","dir":"Articles > Prebuilt","previous_headings":"Introduction","what":"Test data","title":"Testing hierarchical pathway kinetics with residue data on cyantraniliprole","text":"example data taken final addendum DAR 2014 distributed mkin package. Residue data time step normalisation factors read using function read_spreadsheet mkin package. function also performs time step normalisation. following tables show covariate data 5 datasets read spreadsheet file. Covariate data Dataset Nambsheim Dataset Tama Dataset Gross-Umstadt Dataset Sassafras Dataset Lleida","code":"data_file <- system.file( \"testdata\", \"cyantraniliprole_soil_efsa_2014.xlsx\", package = \"mkin\") cyan_ds <- read_spreadsheet(data_file, parent_only = FALSE) pH <- attr(cyan_ds, \"covariates\") kable(pH, caption = \"Covariate data\") for (ds_name in names(cyan_ds)) { print( kable(mkin_long_to_wide(cyan_ds[[ds_name]]), caption = paste(\"Dataset\", ds_name), booktabs = TRUE, row.names = FALSE)) cat(\"\\n\\\\clearpage\\n\") }"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_cyan_pathway.html","id":"parent-only-evaluations","dir":"Articles > Prebuilt","previous_headings":"","what":"Parent only evaluations","title":"Testing hierarchical pathway kinetics with residue data on cyantraniliprole","text":"pathway fits long run times, evaluations parent data performed first, order determine hierarchical parent degradation model random effects degradation model parameters ill-defined. fits converged successfully. almost models, random effect initial concentration parent compound ill-defined. biexponential models DFOP SFORB, random effect one additional parameter ill-defined two-component error model used. Model comparison based AIC BIC indicates two-component error model preferable parent models exception DFOP. lowest AIC BIC values obtained FOMC model, followed SFORB DFOP.","code":"cyan_sep_const <- mmkin(c(\"SFO\", \"FOMC\", \"DFOP\", \"SFORB\", \"HS\"), cyan_ds, quiet = TRUE, cores = n_cores) cyan_sep_tc <- update(cyan_sep_const, error_model = \"tc\") cyan_saem_full <- mhmkin(list(cyan_sep_const, cyan_sep_tc)) status(cyan_saem_full) |> kable() illparms(cyan_saem_full) |> kable() anova(cyan_saem_full) |> kable(digits = 1) stopCluster(cl)"},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_cyan_pathway.html","id":"evaluations-with-pathway-established-previously","dir":"Articles > Prebuilt","previous_headings":"Pathway fits","what":"Evaluations with pathway established previously","title":"Testing hierarchical pathway kinetics with residue data on cyantraniliprole","text":"test technical feasibility coupling relevant parent degradation models different transformation pathway models, list mkinmod models set . EU evaluation, parallel formation metabolites JCZ38 J9Z38 secondary formation metabolite JSE76 JCZ38 used. obtain suitable starting values NLHM fits, separate pathway fits performed datasets. separate fits converged successfully. biggest convergence problems seen using HS model constant variance. hierarchical pathway fits, random effects quantified corresponding parent data analyses excluded. code , output illparms function parent fits used argument no_random_effect mhmkin function. possibility introduced mkin version 1.2.2 currently development. status information individual fits shows fits completed successfully. matrix entries Fth FO indicate Fisher Information Matrix inverted fixed effects (theta) random effects (Omega), respectively. affected fits, ill-defined parameters determined using illparms function, relies Fisher Information Matrix. model comparison suggests pathway fits using DFOP SFORB parent compound provide best fit. two parent model, successful fits shown . Plots fits parent models shown Appendix. DFOP pathway fit two-component error SFORB pathway fit two-component error closer graphical analysis Figures shows residues transformation product JCZ38 soils Tama Nambsheim observed later time points strongly systematically underestimated.","code":"if (!dir.exists(\"cyan_dlls\")) dir.create(\"cyan_dlls\") cyan_path_1 <- list( sfo_path_1 = mkinmod( cyan = mkinsub(\"SFO\", c(\"JCZ38\", \"J9Z38\")), JCZ38 = mkinsub(\"SFO\", \"JSE76\"), J9Z38 = mkinsub(\"SFO\"), JSE76 = mkinsub(\"SFO\"), quiet = TRUE, name = \"sfo_path_1\", dll_dir = \"cyan_dlls\", overwrite = TRUE), fomc_path_1 = mkinmod( cyan = mkinsub(\"FOMC\", c(\"JCZ38\", \"J9Z38\")), JCZ38 = mkinsub(\"SFO\", \"JSE76\"), J9Z38 = mkinsub(\"SFO\"), JSE76 = mkinsub(\"SFO\"), quiet = TRUE, name = \"fomc_path_1\", dll_dir = \"cyan_dlls\", overwrite = TRUE), dfop_path_1 = mkinmod( cyan = mkinsub(\"DFOP\", c(\"JCZ38\", \"J9Z38\")), JCZ38 = mkinsub(\"SFO\", \"JSE76\"), J9Z38 = mkinsub(\"SFO\"), JSE76 = mkinsub(\"SFO\"), quiet = TRUE, name = \"dfop_path_1\", dll_dir = \"cyan_dlls\", overwrite = TRUE), sforb_path_1 = mkinmod( cyan = mkinsub(\"SFORB\", c(\"JCZ38\", \"J9Z38\")), JCZ38 = mkinsub(\"SFO\", \"JSE76\"), J9Z38 = mkinsub(\"SFO\"), JSE76 = mkinsub(\"SFO\"), quiet = TRUE, name = \"sforb_path_1\", dll_dir = \"cyan_dlls\", overwrite = TRUE), hs_path_1 = mkinmod( cyan = mkinsub(\"HS\", c(\"JCZ38\", \"J9Z38\")), JCZ38 = mkinsub(\"SFO\", \"JSE76\"), J9Z38 = mkinsub(\"SFO\"), JSE76 = mkinsub(\"SFO\"), quiet = TRUE, name = \"hs_path_1\", dll_dir = \"cyan_dlls\", overwrite = TRUE) ) cl_path_1 <- start_cluster(n_cores) f_sep_1_const <- mmkin( cyan_path_1, cyan_ds, error_model = \"const\", cluster = cl_path_1, quiet = TRUE) status(f_sep_1_const) |> kable() f_sep_1_tc <- update(f_sep_1_const, error_model = \"tc\") status(f_sep_1_tc) |> kable() f_saem_1 <- mhmkin(list(f_sep_1_const, f_sep_1_tc), no_random_effect = illparms(cyan_saem_full), cluster = cl_path_1) status(f_saem_1) |> kable() illparms(f_saem_1) |> kable() anova(f_saem_1) |> kable(digits = 1) plot(f_saem_1[[\"dfop_path_1\", \"tc\"]]) plot(f_saem_1[[\"sforb_path_1\", \"tc\"]]) stopCluster(cl_path_1)"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_cyan_pathway.html","id":"alternative-pathway-fits","dir":"Articles > Prebuilt","previous_headings":"Pathway fits","what":"Alternative pathway fits","title":"Testing hierarchical pathway kinetics with residue data on cyantraniliprole","text":"improve fit JCZ38, back-reaction JSE76 JCZ38 introduced alternative version transformation pathway, analogy back-reaction K5A78 K5A77. pairs transformation products pairs organic acid corresponding amide (Addendum 2014, p. 109). FOMC provided best fit parent, biexponential models DFOP SFORB provided best initial pathway fits, three parent models used alternative pathway fits. Using constant variance, separate fits converge exception fits Sassafras soil data. Using two-component error model, separate fits converge exception alternative pathway fit DFOP used parent Sassafras dataset. hierarchical fits alternative pathway completed successfully. fits, random effects formation fractions pathways JCZ38 JSE76, reverse pathway JSE76 JCZ38 ill-defined. variants using biexponential models DFOP SFORB parent compound two-component error model give lowest AIC BIC values plotted . Compared original pathway, AIC BIC values indicate large improvement. confirmed plots, show metabolite JCZ38 fitted much better model. FOMC pathway fit two-component error, alternative pathway DFOP pathway fit two-component error, alternative pathway SFORB pathway fit two-component error, alternative pathway","code":"cyan_path_2 <- list( fomc_path_2 = mkinmod( cyan = mkinsub(\"FOMC\", c(\"JCZ38\", \"J9Z38\")), JCZ38 = mkinsub(\"SFO\", \"JSE76\"), J9Z38 = mkinsub(\"SFO\"), JSE76 = mkinsub(\"SFO\", \"JCZ38\"), name = \"fomc_path_2\", quiet = TRUE, dll_dir = \"cyan_dlls\", overwrite = TRUE ), dfop_path_2 = mkinmod( cyan = mkinsub(\"DFOP\", c(\"JCZ38\", \"J9Z38\")), JCZ38 = mkinsub(\"SFO\", \"JSE76\"), J9Z38 = mkinsub(\"SFO\"), JSE76 = mkinsub(\"SFO\", \"JCZ38\"), name = \"dfop_path_2\", quiet = TRUE, dll_dir = \"cyan_dlls\", overwrite = TRUE ), sforb_path_2 = mkinmod( cyan = mkinsub(\"SFORB\", c(\"JCZ38\", \"J9Z38\")), JCZ38 = mkinsub(\"SFO\", \"JSE76\"), J9Z38 = mkinsub(\"SFO\"), JSE76 = mkinsub(\"SFO\", \"JCZ38\"), name = \"sforb_path_2\", quiet = TRUE, dll_dir = \"cyan_dlls\", overwrite = TRUE ) ) cl_path_2 <- start_cluster(n_cores) f_sep_2_const <- mmkin( cyan_path_2, cyan_ds, error_model = \"const\", cluster = cl_path_2, quiet = TRUE) status(f_sep_2_const) |> kable() f_sep_2_tc <- update(f_sep_2_const, error_model = \"tc\") status(f_sep_2_tc) |> kable() f_saem_2 <- mhmkin(list(f_sep_2_const, f_sep_2_tc), no_random_effect = illparms(cyan_saem_full[2:4, ]), cluster = cl_path_2) status(f_saem_2) |> kable() illparms(f_saem_2) |> kable() anova(f_saem_2) |> kable(digits = 1) plot(f_saem_2[[\"fomc_path_2\", \"tc\"]]) plot(f_saem_2[[\"dfop_path_2\", \"tc\"]]) plot(f_saem_2[[\"sforb_path_2\", \"tc\"]])"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_cyan_pathway.html","id":"refinement-of-alternative-pathway-fits","dir":"Articles > Prebuilt","previous_headings":"Pathway fits","what":"Refinement of alternative pathway fits","title":"Testing hierarchical pathway kinetics with residue data on cyantraniliprole","text":"ill-defined random effects identified parent fits pathway fits, excluded final evaluations . purpose, list character vectors created can indexed row column indices, contains degradation parameter names random effects excluded hierarchical fits contained f_saem_2. exception FOMC pathway fit constant variance, updated fits completed successfully. However, Fisher Information Matrix fixed effects (Fth) inverted, confidence intervals optimised parameters available. AIC BIC values best fit (DFOP pathway fit two-component error) lower previous fits alternative pathway, practical value refined evaluations limited confidence intervals obtained.","code":"no_ranef <- matrix(list(), nrow = 3, ncol = 2, dimnames = dimnames(f_saem_2)) no_ranef[[\"fomc_path_2\", \"const\"]] <- c(\"log_beta\", \"f_JCZ38_qlogis\", \"f_JSE76_qlogis\") no_ranef[[\"fomc_path_2\", \"tc\"]] <- c(\"cyan_0\", \"f_JCZ38_qlogis\", \"f_JSE76_qlogis\") no_ranef[[\"dfop_path_2\", \"const\"]] <- c(\"cyan_0\", \"f_JCZ38_qlogis\", \"f_JSE76_qlogis\") no_ranef[[\"dfop_path_2\", \"tc\"]] <- c(\"cyan_0\", \"log_k1\", \"f_JCZ38_qlogis\", \"f_JSE76_qlogis\") no_ranef[[\"sforb_path_2\", \"const\"]] <- c(\"cyan_free_0\", \"f_JCZ38_qlogis\", \"f_JSE76_qlogis\") no_ranef[[\"sforb_path_2\", \"tc\"]] <- c(\"cyan_free_0\", \"log_k_cyan_free_bound\", \"f_JCZ38_qlogis\", \"f_JSE76_qlogis\") clusterExport(cl_path_2, \"no_ranef\") f_saem_3 <- update(f_saem_2, no_random_effect = no_ranef, cluster = cl_path_2) status(f_saem_3) |> kable() illparms(f_saem_3) |> kable() anova(f_saem_3) |> kable(digits = 1) stopCluster(cl_path_2)"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_cyan_pathway.html","id":"conclusion","dir":"Articles > Prebuilt","previous_headings":"","what":"Conclusion","title":"Testing hierarchical pathway kinetics with residue data on cyantraniliprole","text":"demonstrated relatively complex transformation pathway parallel formation two primary metabolites one secondary metabolite can fitted even data individual datasets quite different partly cover formation phase. run times pathway fits several hours, limiting practical feasibility iterative refinements based ill-defined parameters alternative checks parameter identifiability based multistart runs.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_cyan_pathway.html","id":"acknowledgements","dir":"Articles > Prebuilt","previous_headings":"","what":"Acknowledgements","title":"Testing hierarchical pathway kinetics with residue data on cyantraniliprole","text":"helpful comments Janina Wöltjen German Environment Agency gratefully acknowledged.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_cyan_pathway.html","id":"plots-of-fits-that-were-not-refined-further","dir":"Articles > Prebuilt","previous_headings":"Appendix","what":"Plots of fits that were not refined further","title":"Testing hierarchical pathway kinetics with residue data on cyantraniliprole","text":"SFO pathway fit two-component error FOMC pathway fit two-component error HS pathway fit two-component error","code":"plot(f_saem_1[[\"sfo_path_1\", \"tc\"]]) plot(f_saem_1[[\"fomc_path_1\", \"tc\"]]) plot(f_saem_1[[\"sforb_path_1\", \"tc\"]])"},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_cyan_pathway.html","id":"pathway-1","dir":"Articles > Prebuilt","previous_headings":"Appendix > Hierarchical fit listings","what":"Pathway 1","title":"Testing hierarchical pathway kinetics with residue data on cyantraniliprole","text":"Hierarchical SFO path 1 fit constant variance Hierarchical SFO path 1 fit two-component error Hierarchical FOMC path 1 fit constant variance Hierarchical FOMC path 1 fit two-component error Hierarchical DFOP path 1 fit constant variance Hierarchical DFOP path 1 fit two-component error Hierarchical SFORB path 1 fit constant variance Hierarchical SFORB path 1 fit two-component error Hierarchical HS path 1 fit constant variance","code":"saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 R version used for fitting: 4.3.2 Date of fit: Thu Nov 16 04:27:41 2023 Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - k_cyan * cyan d_JCZ38/dt = + f_cyan_to_JCZ38 * k_cyan * cyan - k_JCZ38 * JCZ38 d_J9Z38/dt = + f_cyan_to_J9Z38 * k_cyan * cyan - k_J9Z38 * J9Z38 d_JSE76/dt = + f_JCZ38_to_JSE76 * k_JCZ38 * JCZ38 - k_JSE76 * JSE76 Data: 433 observations of 4 variable(s) grouped in 5 datasets Model predictions using solution type deSolve Fitted in 421.347 s Using 300, 100 iterations and 10 chains Variance model: Constant variance Starting values for degradation parameters: cyan_0 log_k_cyan log_k_JCZ38 log_k_J9Z38 log_k_JSE76 95.3304 -3.8459 -3.1305 -5.0678 -5.3196 f_cyan_ilr_1 f_cyan_ilr_2 f_JCZ38_qlogis 0.8158 23.5335 11.8774 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): cyan_0 log_k_cyan log_k_JCZ38 log_k_J9Z38 log_k_JSE76 cyan_0 4.797 0.0000 0.000 0.000 0.0000 log_k_cyan 0.000 0.9619 0.000 0.000 0.0000 log_k_JCZ38 0.000 0.0000 2.139 0.000 0.0000 log_k_J9Z38 0.000 0.0000 0.000 1.639 0.0000 log_k_JSE76 0.000 0.0000 0.000 0.000 0.7894 f_cyan_ilr_1 0.000 0.0000 0.000 0.000 0.0000 f_cyan_ilr_2 0.000 0.0000 0.000 0.000 0.0000 f_JCZ38_qlogis 0.000 0.0000 0.000 0.000 0.0000 f_cyan_ilr_1 f_cyan_ilr_2 f_JCZ38_qlogis cyan_0 0.0000 0.000 0.00 log_k_cyan 0.0000 0.000 0.00 log_k_JCZ38 0.0000 0.000 0.00 log_k_J9Z38 0.0000 0.000 0.00 log_k_JSE76 0.0000 0.000 0.00 f_cyan_ilr_1 0.7714 0.000 0.00 f_cyan_ilr_2 0.0000 9.247 0.00 f_JCZ38_qlogis 0.0000 0.000 16.61 Starting values for error model parameters: a.1 1 Results: Likelihood computed by importance sampling AIC BIC logLik 2693 2687 -1331 Optimised parameters: est. lower upper cyan_0 95.1279 9.354e+01 9.671e+01 log_k_cyan -3.8527 -4.367e+00 -3.338e+00 log_k_JCZ38 -3.0381 -4.187e+00 -1.889e+00 log_k_J9Z38 -5.0095 -5.623e+00 -4.396e+00 log_k_JSE76 -5.3357 -6.025e+00 -4.646e+00 f_cyan_ilr_1 0.8050 5.174e-01 1.093e+00 f_cyan_ilr_2 12.4820 -1.050e+06 1.051e+06 f_JCZ38_qlogis 1.2912 3.561e-01 2.226e+00 a.1 4.8393 NA NA SD.log_k_cyan 0.5840 NA NA SD.log_k_JCZ38 1.2740 NA NA SD.log_k_J9Z38 0.3172 NA NA SD.log_k_JSE76 0.5677 NA NA SD.f_cyan_ilr_1 0.2623 NA NA SD.f_cyan_ilr_2 1.3724 NA NA SD.f_JCZ38_qlogis 0.1464 NA NA Correlation is not available Random effects: est. lower upper SD.log_k_cyan 0.5840 NA NA SD.log_k_JCZ38 1.2740 NA NA SD.log_k_J9Z38 0.3172 NA NA SD.log_k_JSE76 0.5677 NA NA SD.f_cyan_ilr_1 0.2623 NA NA SD.f_cyan_ilr_2 1.3724 NA NA SD.f_JCZ38_qlogis 0.1464 NA NA Variance model: est. lower upper a.1 4.839 NA NA Backtransformed parameters: est. lower upper cyan_0 95.127935 93.542456 96.713413 k_cyan 0.021221 0.012687 0.035497 k_JCZ38 0.047924 0.015189 0.151213 k_J9Z38 0.006674 0.003612 0.012332 k_JSE76 0.004817 0.002417 0.009601 f_cyan_to_JCZ38 0.757402 NA NA f_cyan_to_J9Z38 0.242597 NA NA f_JCZ38_to_JSE76 0.784347 0.588098 0.902582 Resulting formation fractions: ff cyan_JCZ38 7.574e-01 cyan_J9Z38 2.426e-01 cyan_sink 9.839e-08 JCZ38_JSE76 7.843e-01 JCZ38_sink 2.157e-01 Estimated disappearance times: DT50 DT90 cyan 32.66 108.50 JCZ38 14.46 48.05 J9Z38 103.86 345.00 JSE76 143.91 478.04 saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 R version used for fitting: 4.3.2 Date of fit: Thu Nov 16 04:27:55 2023 Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - k_cyan * cyan d_JCZ38/dt = + f_cyan_to_JCZ38 * k_cyan * cyan - k_JCZ38 * JCZ38 d_J9Z38/dt = + f_cyan_to_J9Z38 * k_cyan * cyan - k_J9Z38 * J9Z38 d_JSE76/dt = + f_JCZ38_to_JSE76 * k_JCZ38 * JCZ38 - k_JSE76 * JSE76 Data: 433 observations of 4 variable(s) grouped in 5 datasets Model predictions using solution type deSolve Fitted in 435.122 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function Starting values for degradation parameters: cyan_0 log_k_cyan log_k_JCZ38 log_k_J9Z38 log_k_JSE76 96.0039 -3.8907 -3.1276 -5.0069 -4.9367 f_cyan_ilr_1 f_cyan_ilr_2 f_JCZ38_qlogis 0.7937 22.3422 17.8932 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): cyan_0 log_k_cyan log_k_JCZ38 log_k_J9Z38 log_k_JSE76 cyan_0 4.859 0.000 0.00 0.00 0.0000 log_k_cyan 0.000 0.962 0.00 0.00 0.0000 log_k_JCZ38 0.000 0.000 2.04 0.00 0.0000 log_k_J9Z38 0.000 0.000 0.00 1.72 0.0000 log_k_JSE76 0.000 0.000 0.00 0.00 0.9076 f_cyan_ilr_1 0.000 0.000 0.00 0.00 0.0000 f_cyan_ilr_2 0.000 0.000 0.00 0.00 0.0000 f_JCZ38_qlogis 0.000 0.000 0.00 0.00 0.0000 f_cyan_ilr_1 f_cyan_ilr_2 f_JCZ38_qlogis cyan_0 0.0000 0.000 0.00 log_k_cyan 0.0000 0.000 0.00 log_k_JCZ38 0.0000 0.000 0.00 log_k_J9Z38 0.0000 0.000 0.00 log_k_JSE76 0.0000 0.000 0.00 f_cyan_ilr_1 0.7598 0.000 0.00 f_cyan_ilr_2 0.0000 8.939 0.00 f_JCZ38_qlogis 0.0000 0.000 14.49 Starting values for error model parameters: a.1 b.1 1 1 Results: Likelihood computed by importance sampling AIC BIC logLik 2658 2651 -1312 Optimised parameters: est. lower upper cyan_0 94.81681 NA NA log_k_cyan -3.91558 NA NA log_k_JCZ38 -3.12715 NA NA log_k_J9Z38 -5.04840 NA NA log_k_JSE76 -5.10443 NA NA f_cyan_ilr_1 0.80760 NA NA f_cyan_ilr_2 48.66960 NA NA f_JCZ38_qlogis 3.03397 NA NA a.1 3.93879 NA NA b.1 0.08057 NA NA SD.log_k_cyan 0.58921 NA NA SD.log_k_JCZ38 1.29813 NA NA SD.log_k_J9Z38 0.68372 NA NA SD.log_k_JSE76 0.35128 NA NA SD.f_cyan_ilr_1 0.38352 NA NA SD.f_cyan_ilr_2 4.98884 NA NA SD.f_JCZ38_qlogis 1.75636 NA NA Correlation is not available Random effects: est. lower upper SD.log_k_cyan 0.5892 NA NA SD.log_k_JCZ38 1.2981 NA NA SD.log_k_J9Z38 0.6837 NA NA SD.log_k_JSE76 0.3513 NA NA SD.f_cyan_ilr_1 0.3835 NA NA SD.f_cyan_ilr_2 4.9888 NA NA SD.f_JCZ38_qlogis 1.7564 NA NA Variance model: est. lower upper a.1 3.93879 NA NA b.1 0.08057 NA NA Backtransformed parameters: est. lower upper cyan_0 94.81681 NA NA k_cyan 0.01993 NA NA k_JCZ38 0.04384 NA NA k_J9Z38 0.00642 NA NA k_JSE76 0.00607 NA NA f_cyan_to_JCZ38 0.75807 NA NA f_cyan_to_J9Z38 0.24193 NA NA f_JCZ38_to_JSE76 0.95409 NA NA Resulting formation fractions: ff cyan_JCZ38 0.75807 cyan_J9Z38 0.24193 cyan_sink 0.00000 JCZ38_JSE76 0.95409 JCZ38_sink 0.04591 Estimated disappearance times: DT50 DT90 cyan 34.78 115.54 JCZ38 15.81 52.52 J9Z38 107.97 358.68 JSE76 114.20 379.35 saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 R version used for fitting: 4.3.2 Date of fit: Thu Nov 16 04:28:33 2023 Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan d_JCZ38/dt = + f_cyan_to_JCZ38 * (alpha/beta) * 1/((time/beta) + 1) * cyan - k_JCZ38 * JCZ38 d_J9Z38/dt = + f_cyan_to_J9Z38 * (alpha/beta) * 1/((time/beta) + 1) * cyan - k_J9Z38 * J9Z38 d_JSE76/dt = + f_JCZ38_to_JSE76 * k_JCZ38 * JCZ38 - k_JSE76 * JSE76 Data: 433 observations of 4 variable(s) grouped in 5 datasets Model predictions using solution type deSolve Fitted in 473.357 s Using 300, 100 iterations and 10 chains Variance model: Constant variance Starting values for degradation parameters: cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 101.2314 -3.3680 -5.1108 -5.9416 0.7144 f_cyan_ilr_2 f_JCZ38_qlogis log_alpha log_beta 7.0229 14.9234 -0.1791 2.9811 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 cyan_0 5.416 0.000 0.0 0.000 0.0000 log_k_JCZ38 0.000 2.439 0.0 0.000 0.0000 log_k_J9Z38 0.000 0.000 1.7 0.000 0.0000 log_k_JSE76 0.000 0.000 0.0 1.856 0.0000 f_cyan_ilr_1 0.000 0.000 0.0 0.000 0.7164 f_cyan_ilr_2 0.000 0.000 0.0 0.000 0.0000 f_JCZ38_qlogis 0.000 0.000 0.0 0.000 0.0000 log_alpha 0.000 0.000 0.0 0.000 0.0000 log_beta 0.000 0.000 0.0 0.000 0.0000 f_cyan_ilr_2 f_JCZ38_qlogis log_alpha log_beta cyan_0 0.00 0.00 0.0000 0.0000 log_k_JCZ38 0.00 0.00 0.0000 0.0000 log_k_J9Z38 0.00 0.00 0.0000 0.0000 log_k_JSE76 0.00 0.00 0.0000 0.0000 f_cyan_ilr_1 0.00 0.00 0.0000 0.0000 f_cyan_ilr_2 11.57 0.00 0.0000 0.0000 f_JCZ38_qlogis 0.00 18.81 0.0000 0.0000 log_alpha 0.00 0.00 0.4144 0.0000 log_beta 0.00 0.00 0.0000 0.5077 Starting values for error model parameters: a.1 1 Results: Likelihood computed by importance sampling AIC BIC logLik 2428 2421 -1196 Optimised parameters: est. lower upper cyan_0 101.1664 98.51265 103.8202 log_k_JCZ38 -3.3883 -4.78250 -1.9941 log_k_J9Z38 -5.3087 -5.91564 -4.7017 log_k_JSE76 -6.1313 -7.30061 -4.9619 f_cyan_ilr_1 0.7456 0.43782 1.0534 f_cyan_ilr_2 0.8181 0.24956 1.3866 f_JCZ38_qlogis 2.0467 0.61165 3.4817 log_alpha -0.2391 -0.62806 0.1499 log_beta 2.8739 2.67664 3.0711 a.1 3.4160 3.17960 3.6525 SD.cyan_0 2.4355 0.40399 4.4671 SD.log_k_JCZ38 1.5654 0.57311 2.5576 SD.log_k_J9Z38 0.4645 -0.06533 0.9943 SD.log_k_JSE76 0.9841 0.10738 1.8609 SD.f_cyan_ilr_1 0.3285 0.10546 0.5515 SD.f_cyan_ilr_2 0.2276 -0.38711 0.8424 SD.f_JCZ38_qlogis 0.8340 -0.20970 1.8777 SD.log_alpha 0.4250 0.16017 0.6898 Correlation: cyan_0 l__JCZ3 l__J9Z3 l__JSE7 f_cy__1 f_cy__2 f_JCZ38 log_lph log_k_JCZ38 -0.0159 log_k_J9Z38 -0.0546 0.0080 log_k_JSE76 -0.0337 0.0016 0.0074 f_cyan_ilr_1 -0.0095 0.0194 -0.1573 0.0003 f_cyan_ilr_2 -0.2733 0.0799 0.3059 0.0263 0.0125 f_JCZ38_qlogis 0.0755 -0.0783 -0.0516 0.1222 -0.1155 -0.5231 log_alpha -0.0567 0.0120 0.0351 0.0189 0.0040 0.0829 -0.0502 log_beta -0.2980 0.0461 0.1382 0.0758 0.0209 0.4079 -0.2053 0.2759 Random effects: est. lower upper SD.cyan_0 2.4355 0.40399 4.4671 SD.log_k_JCZ38 1.5654 0.57311 2.5576 SD.log_k_J9Z38 0.4645 -0.06533 0.9943 SD.log_k_JSE76 0.9841 0.10738 1.8609 SD.f_cyan_ilr_1 0.3285 0.10546 0.5515 SD.f_cyan_ilr_2 0.2276 -0.38711 0.8424 SD.f_JCZ38_qlogis 0.8340 -0.20970 1.8777 SD.log_alpha 0.4250 0.16017 0.6898 Variance model: est. lower upper a.1 3.416 3.18 3.652 Backtransformed parameters: est. lower upper cyan_0 1.012e+02 9.851e+01 103.82023 k_JCZ38 3.377e-02 8.375e-03 0.13614 k_J9Z38 4.948e-03 2.697e-03 0.00908 k_JSE76 2.174e-03 6.751e-04 0.00700 f_cyan_to_JCZ38 6.389e-01 NA NA f_cyan_to_J9Z38 2.226e-01 NA NA f_JCZ38_to_JSE76 8.856e-01 6.483e-01 0.97016 alpha 7.873e-01 5.336e-01 1.16166 beta 1.771e+01 1.454e+01 21.56509 Resulting formation fractions: ff cyan_JCZ38 0.6389 cyan_J9Z38 0.2226 cyan_sink 0.1385 JCZ38_JSE76 0.8856 JCZ38_sink 0.1144 Estimated disappearance times: DT50 DT90 DT50back cyan 25.00 312.06 93.94 JCZ38 20.53 68.19 NA J9Z38 140.07 465.32 NA JSE76 318.86 1059.22 NA saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 R version used for fitting: 4.3.2 Date of fit: Thu Nov 16 04:28:46 2023 Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan d_JCZ38/dt = + f_cyan_to_JCZ38 * (alpha/beta) * 1/((time/beta) + 1) * cyan - k_JCZ38 * JCZ38 d_J9Z38/dt = + f_cyan_to_J9Z38 * (alpha/beta) * 1/((time/beta) + 1) * cyan - k_J9Z38 * J9Z38 d_JSE76/dt = + f_JCZ38_to_JSE76 * k_JCZ38 * JCZ38 - k_JSE76 * JSE76 Data: 433 observations of 4 variable(s) grouped in 5 datasets Model predictions using solution type deSolve Fitted in 486.031 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function Starting values for degradation parameters: cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 101.13294 -3.32499 -5.09097 -5.93566 0.71359 f_cyan_ilr_2 f_JCZ38_qlogis log_alpha log_beta 10.30315 14.62272 -0.09633 3.10634 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 cyan_0 5.649 0.000 0.00 0.00 0.0000 log_k_JCZ38 0.000 2.319 0.00 0.00 0.0000 log_k_J9Z38 0.000 0.000 1.73 0.00 0.0000 log_k_JSE76 0.000 0.000 0.00 1.86 0.0000 f_cyan_ilr_1 0.000 0.000 0.00 0.00 0.7183 f_cyan_ilr_2 0.000 0.000 0.00 0.00 0.0000 f_JCZ38_qlogis 0.000 0.000 0.00 0.00 0.0000 log_alpha 0.000 0.000 0.00 0.00 0.0000 log_beta 0.000 0.000 0.00 0.00 0.0000 f_cyan_ilr_2 f_JCZ38_qlogis log_alpha log_beta cyan_0 0.00 0.00 0.0000 0.0000 log_k_JCZ38 0.00 0.00 0.0000 0.0000 log_k_J9Z38 0.00 0.00 0.0000 0.0000 log_k_JSE76 0.00 0.00 0.0000 0.0000 f_cyan_ilr_1 0.00 0.00 0.0000 0.0000 f_cyan_ilr_2 12.85 0.00 0.0000 0.0000 f_JCZ38_qlogis 0.00 18.54 0.0000 0.0000 log_alpha 0.00 0.00 0.3142 0.0000 log_beta 0.00 0.00 0.0000 0.7333 Starting values for error model parameters: a.1 b.1 1 1 Results: Likelihood computed by importance sampling AIC BIC logLik 2424 2416 -1193 Optimised parameters: est. lower upper cyan_0 100.65667 NA NA log_k_JCZ38 -3.45782 NA NA log_k_J9Z38 -5.23476 NA NA log_k_JSE76 -5.71827 NA NA f_cyan_ilr_1 0.68389 NA NA f_cyan_ilr_2 0.61027 NA NA f_JCZ38_qlogis 116.27482 NA NA log_alpha -0.14484 NA NA log_beta 3.03220 NA NA a.1 3.11051 NA NA b.1 0.04508 NA NA SD.log_k_JCZ38 1.39961 NA NA SD.log_k_J9Z38 0.57920 NA NA SD.log_k_JSE76 0.68364 NA NA SD.f_cyan_ilr_1 0.31477 NA NA SD.f_cyan_ilr_2 0.37716 NA NA SD.f_JCZ38_qlogis 5.52695 NA NA SD.log_alpha 0.22823 NA NA SD.log_beta 0.39161 NA NA Correlation is not available Random effects: est. lower upper SD.log_k_JCZ38 1.3996 NA NA SD.log_k_J9Z38 0.5792 NA NA SD.log_k_JSE76 0.6836 NA NA SD.f_cyan_ilr_1 0.3148 NA NA SD.f_cyan_ilr_2 0.3772 NA NA SD.f_JCZ38_qlogis 5.5270 NA NA SD.log_alpha 0.2282 NA NA SD.log_beta 0.3916 NA NA Variance model: est. lower upper a.1 3.11051 NA NA b.1 0.04508 NA NA Backtransformed parameters: est. lower upper cyan_0 1.007e+02 NA NA k_JCZ38 3.150e-02 NA NA k_J9Z38 5.328e-03 NA NA k_JSE76 3.285e-03 NA NA f_cyan_to_JCZ38 5.980e-01 NA NA f_cyan_to_J9Z38 2.273e-01 NA NA f_JCZ38_to_JSE76 1.000e+00 NA NA alpha 8.652e-01 NA NA beta 2.074e+01 NA NA Resulting formation fractions: ff cyan_JCZ38 0.5980 cyan_J9Z38 0.2273 cyan_sink 0.1746 JCZ38_JSE76 1.0000 JCZ38_sink 0.0000 Estimated disappearance times: DT50 DT90 DT50back cyan 25.48 276.2 83.15 JCZ38 22.01 73.1 NA J9Z38 130.09 432.2 NA JSE76 210.98 700.9 NA saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 R version used for fitting: 4.3.2 Date of fit: Thu Nov 16 04:29:15 2023 Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * cyan d_JCZ38/dt = + f_cyan_to_JCZ38 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * cyan - k_JCZ38 * JCZ38 d_J9Z38/dt = + f_cyan_to_J9Z38 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * cyan - k_J9Z38 * J9Z38 d_JSE76/dt = + f_JCZ38_to_JSE76 * k_JCZ38 * JCZ38 - k_JSE76 * JSE76 Data: 433 observations of 4 variable(s) grouped in 5 datasets Model predictions using solution type deSolve Fitted in 514.477 s Using 300, 100 iterations and 10 chains Variance model: Constant variance Starting values for degradation parameters: cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 102.0643 -3.4008 -5.0024 -5.8612 0.6855 f_cyan_ilr_2 f_JCZ38_qlogis log_k1 log_k2 g_qlogis 1.2366 13.6901 -1.8641 -4.5063 -0.6468 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 cyan_0 4.466 0.000 0.000 0.000 0.0000 log_k_JCZ38 0.000 2.382 0.000 0.000 0.0000 log_k_J9Z38 0.000 0.000 1.595 0.000 0.0000 log_k_JSE76 0.000 0.000 0.000 1.245 0.0000 f_cyan_ilr_1 0.000 0.000 0.000 0.000 0.6852 f_cyan_ilr_2 0.000 0.000 0.000 0.000 0.0000 f_JCZ38_qlogis 0.000 0.000 0.000 0.000 0.0000 log_k1 0.000 0.000 0.000 0.000 0.0000 log_k2 0.000 0.000 0.000 0.000 0.0000 g_qlogis 0.000 0.000 0.000 0.000 0.0000 f_cyan_ilr_2 f_JCZ38_qlogis log_k1 log_k2 g_qlogis cyan_0 0.00 0.00 0.0000 0.0000 0.000 log_k_JCZ38 0.00 0.00 0.0000 0.0000 0.000 log_k_J9Z38 0.00 0.00 0.0000 0.0000 0.000 log_k_JSE76 0.00 0.00 0.0000 0.0000 0.000 f_cyan_ilr_1 0.00 0.00 0.0000 0.0000 0.000 f_cyan_ilr_2 1.28 0.00 0.0000 0.0000 0.000 f_JCZ38_qlogis 0.00 16.08 0.0000 0.0000 0.000 log_k1 0.00 0.00 0.9866 0.0000 0.000 log_k2 0.00 0.00 0.0000 0.5953 0.000 g_qlogis 0.00 0.00 0.0000 0.0000 1.583 Starting values for error model parameters: a.1 1 Results: Likelihood computed by importance sampling AIC BIC logLik 2403 2395 -1182 Optimised parameters: est. lower upper cyan_0 102.5565 NA NA log_k_JCZ38 -3.4729 NA NA log_k_J9Z38 -5.1533 NA NA log_k_JSE76 -5.6669 NA NA f_cyan_ilr_1 0.6665 NA NA f_cyan_ilr_2 0.5191 NA NA f_JCZ38_qlogis 37.0113 NA NA log_k1 -1.8497 NA NA log_k2 -4.4931 NA NA g_qlogis -0.6383 NA NA a.1 3.2397 NA NA SD.log_k_JCZ38 1.4286 NA NA SD.log_k_J9Z38 0.5312 NA NA SD.log_k_JSE76 0.6627 NA NA SD.f_cyan_ilr_1 0.3013 NA NA SD.f_cyan_ilr_2 0.2980 NA NA SD.f_JCZ38_qlogis 0.1637 NA NA SD.log_k1 0.5069 NA NA SD.log_k2 0.3828 NA NA SD.g_qlogis 0.8641 NA NA Correlation is not available Random effects: est. lower upper SD.log_k_JCZ38 1.4286 NA NA SD.log_k_J9Z38 0.5312 NA NA SD.log_k_JSE76 0.6627 NA NA SD.f_cyan_ilr_1 0.3013 NA NA SD.f_cyan_ilr_2 0.2980 NA NA SD.f_JCZ38_qlogis 0.1637 NA NA SD.log_k1 0.5069 NA NA SD.log_k2 0.3828 NA NA SD.g_qlogis 0.8641 NA NA Variance model: est. lower upper a.1 3.24 NA NA Backtransformed parameters: est. lower upper cyan_0 1.026e+02 NA NA k_JCZ38 3.103e-02 NA NA k_J9Z38 5.780e-03 NA NA k_JSE76 3.459e-03 NA NA f_cyan_to_JCZ38 5.813e-01 NA NA f_cyan_to_J9Z38 2.265e-01 NA NA f_JCZ38_to_JSE76 1.000e+00 NA NA k1 1.573e-01 NA NA k2 1.119e-02 NA NA g 3.456e-01 NA NA Resulting formation fractions: ff cyan_JCZ38 0.5813 cyan_J9Z38 0.2265 cyan_sink 0.1922 JCZ38_JSE76 1.0000 JCZ38_sink 0.0000 Estimated disappearance times: DT50 DT90 DT50back DT50_k1 DT50_k2 cyan 25.23 167.94 50.55 4.407 61.97 JCZ38 22.34 74.22 NA NA NA J9Z38 119.92 398.36 NA NA NA JSE76 200.41 665.76 NA NA NA saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 R version used for fitting: 4.3.2 Date of fit: Thu Nov 16 04:31:58 2023 Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * cyan d_JCZ38/dt = + f_cyan_to_JCZ38 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * cyan - k_JCZ38 * JCZ38 d_J9Z38/dt = + f_cyan_to_J9Z38 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * cyan - k_J9Z38 * J9Z38 d_JSE76/dt = + f_JCZ38_to_JSE76 * k_JCZ38 * JCZ38 - k_JSE76 * JSE76 Data: 433 observations of 4 variable(s) grouped in 5 datasets Model predictions using solution type deSolve Fitted in 677.928 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function Starting values for degradation parameters: cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 101.3964 -3.3626 -4.9792 -5.8727 0.6814 f_cyan_ilr_2 f_JCZ38_qlogis log_k1 log_k2 g_qlogis 6.8713 13.6901 -1.9222 -4.5035 -0.7172 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 cyan_0 5.317 0.000 0.000 0.000 0.0000 log_k_JCZ38 0.000 2.272 0.000 0.000 0.0000 log_k_J9Z38 0.000 0.000 1.633 0.000 0.0000 log_k_JSE76 0.000 0.000 0.000 1.271 0.0000 f_cyan_ilr_1 0.000 0.000 0.000 0.000 0.6839 f_cyan_ilr_2 0.000 0.000 0.000 0.000 0.0000 f_JCZ38_qlogis 0.000 0.000 0.000 0.000 0.0000 log_k1 0.000 0.000 0.000 0.000 0.0000 log_k2 0.000 0.000 0.000 0.000 0.0000 g_qlogis 0.000 0.000 0.000 0.000 0.0000 f_cyan_ilr_2 f_JCZ38_qlogis log_k1 log_k2 g_qlogis cyan_0 0.00 0.00 0.0000 0.0000 0.000 log_k_JCZ38 0.00 0.00 0.0000 0.0000 0.000 log_k_J9Z38 0.00 0.00 0.0000 0.0000 0.000 log_k_JSE76 0.00 0.00 0.0000 0.0000 0.000 f_cyan_ilr_1 0.00 0.00 0.0000 0.0000 0.000 f_cyan_ilr_2 11.95 0.00 0.0000 0.0000 0.000 f_JCZ38_qlogis 0.00 16.08 0.0000 0.0000 0.000 log_k1 0.00 0.00 0.9496 0.0000 0.000 log_k2 0.00 0.00 0.0000 0.5846 0.000 g_qlogis 0.00 0.00 0.0000 0.0000 1.719 Starting values for error model parameters: a.1 b.1 1 1 Results: Likelihood computed by importance sampling AIC BIC logLik 2398 2390 -1179 Optimised parameters: est. lower upper cyan_0 100.69709 NA NA log_k_JCZ38 -3.46669 NA NA log_k_J9Z38 -5.05076 NA NA log_k_JSE76 -5.55558 NA NA f_cyan_ilr_1 0.66045 NA NA f_cyan_ilr_2 0.84275 NA NA f_JCZ38_qlogis 64.22404 NA NA log_k1 -2.17715 NA NA log_k2 -4.55002 NA NA g_qlogis -0.55920 NA NA a.1 2.95785 NA NA b.1 0.04456 NA NA SD.log_k_JCZ38 1.39881 NA NA SD.log_k_J9Z38 0.67788 NA NA SD.log_k_JSE76 0.52603 NA NA SD.f_cyan_ilr_1 0.32490 NA NA SD.f_cyan_ilr_2 0.53923 NA NA SD.f_JCZ38_qlogis 2.75576 NA NA SD.log_k2 0.30694 NA NA SD.g_qlogis 0.83619 NA NA Correlation is not available Random effects: est. lower upper SD.log_k_JCZ38 1.3988 NA NA SD.log_k_J9Z38 0.6779 NA NA SD.log_k_JSE76 0.5260 NA NA SD.f_cyan_ilr_1 0.3249 NA NA SD.f_cyan_ilr_2 0.5392 NA NA SD.f_JCZ38_qlogis 2.7558 NA NA SD.log_k2 0.3069 NA NA SD.g_qlogis 0.8362 NA NA Variance model: est. lower upper a.1 2.95785 NA NA b.1 0.04456 NA NA Backtransformed parameters: est. lower upper cyan_0 1.007e+02 NA NA k_JCZ38 3.122e-02 NA NA k_J9Z38 6.404e-03 NA NA k_JSE76 3.866e-03 NA NA f_cyan_to_JCZ38 6.187e-01 NA NA f_cyan_to_J9Z38 2.431e-01 NA NA f_JCZ38_to_JSE76 1.000e+00 NA NA k1 1.134e-01 NA NA k2 1.057e-02 NA NA g 3.637e-01 NA NA Resulting formation fractions: ff cyan_JCZ38 0.6187 cyan_J9Z38 0.2431 cyan_sink 0.1382 JCZ38_JSE76 1.0000 JCZ38_sink 0.0000 Estimated disappearance times: DT50 DT90 DT50back DT50_k1 DT50_k2 cyan 26.35 175.12 52.72 6.114 65.6 JCZ38 22.20 73.75 NA NA NA J9Z38 108.23 359.53 NA NA NA JSE76 179.30 595.62 NA NA NA saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 R version used for fitting: 4.3.2 Date of fit: Thu Nov 16 04:29:33 2023 Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * cyan_free + k_cyan_bound_free * cyan_bound d_cyan_bound/dt = + k_cyan_free_bound * cyan_free - k_cyan_bound_free * cyan_bound d_JCZ38/dt = + f_cyan_free_to_JCZ38 * k_cyan_free * cyan_free - k_JCZ38 * JCZ38 d_J9Z38/dt = + f_cyan_free_to_J9Z38 * k_cyan_free * cyan_free - k_J9Z38 * J9Z38 d_JSE76/dt = + f_JCZ38_to_JSE76 * k_JCZ38 * JCZ38 - k_JSE76 * JSE76 Data: 433 observations of 4 variable(s) grouped in 5 datasets Model predictions using solution type deSolve Fitted in 532.937 s Using 300, 100 iterations and 10 chains Variance model: Constant variance Starting values for degradation parameters: cyan_free_0 log_k_cyan_free log_k_cyan_free_bound 102.0643 -2.8987 -2.7077 log_k_cyan_bound_free log_k_JCZ38 log_k_J9Z38 -3.4717 -3.4008 -5.0024 log_k_JSE76 f_cyan_ilr_1 f_cyan_ilr_2 -5.8613 0.6855 1.2366 f_JCZ38_qlogis 13.7395 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): cyan_free_0 log_k_cyan_free log_k_cyan_free_bound cyan_free_0 4.466 0.0000 0.000 log_k_cyan_free 0.000 0.6158 0.000 log_k_cyan_free_bound 0.000 0.0000 1.463 log_k_cyan_bound_free 0.000 0.0000 0.000 log_k_JCZ38 0.000 0.0000 0.000 log_k_J9Z38 0.000 0.0000 0.000 log_k_JSE76 0.000 0.0000 0.000 f_cyan_ilr_1 0.000 0.0000 0.000 f_cyan_ilr_2 0.000 0.0000 0.000 f_JCZ38_qlogis 0.000 0.0000 0.000 log_k_cyan_bound_free log_k_JCZ38 log_k_J9Z38 log_k_JSE76 cyan_free_0 0.000 0.000 0.000 0.000 log_k_cyan_free 0.000 0.000 0.000 0.000 log_k_cyan_free_bound 0.000 0.000 0.000 0.000 log_k_cyan_bound_free 1.058 0.000 0.000 0.000 log_k_JCZ38 0.000 2.382 0.000 0.000 log_k_J9Z38 0.000 0.000 1.595 0.000 log_k_JSE76 0.000 0.000 0.000 1.245 f_cyan_ilr_1 0.000 0.000 0.000 0.000 f_cyan_ilr_2 0.000 0.000 0.000 0.000 f_JCZ38_qlogis 0.000 0.000 0.000 0.000 f_cyan_ilr_1 f_cyan_ilr_2 f_JCZ38_qlogis cyan_free_0 0.0000 0.00 0.00 log_k_cyan_free 0.0000 0.00 0.00 log_k_cyan_free_bound 0.0000 0.00 0.00 log_k_cyan_bound_free 0.0000 0.00 0.00 log_k_JCZ38 0.0000 0.00 0.00 log_k_J9Z38 0.0000 0.00 0.00 log_k_JSE76 0.0000 0.00 0.00 f_cyan_ilr_1 0.6852 0.00 0.00 f_cyan_ilr_2 0.0000 1.28 0.00 f_JCZ38_qlogis 0.0000 0.00 16.13 Starting values for error model parameters: a.1 1 Results: Likelihood computed by importance sampling AIC BIC logLik 2401 2394 -1181 Optimised parameters: est. lower upper cyan_free_0 102.8136 NA NA log_k_cyan_free -2.7935 NA NA log_k_cyan_free_bound -2.5440 NA NA log_k_cyan_bound_free -3.4303 NA NA log_k_JCZ38 -3.5010 NA NA log_k_J9Z38 -5.1226 NA NA log_k_JSE76 -5.6314 NA NA f_cyan_ilr_1 0.6609 NA NA f_cyan_ilr_2 0.5085 NA NA f_JCZ38_qlogis 44.0153 NA NA a.1 3.2318 NA NA SD.log_k_cyan_free 0.3211 NA NA SD.log_k_cyan_free_bound 0.8408 NA NA SD.log_k_cyan_bound_free 0.5724 NA NA SD.log_k_JCZ38 1.4925 NA NA SD.log_k_J9Z38 0.5816 NA NA SD.log_k_JSE76 0.6037 NA NA SD.f_cyan_ilr_1 0.3115 NA NA SD.f_cyan_ilr_2 0.3436 NA NA SD.f_JCZ38_qlogis 4.8937 NA NA Correlation is not available Random effects: est. lower upper SD.log_k_cyan_free 0.3211 NA NA SD.log_k_cyan_free_bound 0.8408 NA NA SD.log_k_cyan_bound_free 0.5724 NA NA SD.log_k_JCZ38 1.4925 NA NA SD.log_k_J9Z38 0.5816 NA NA SD.log_k_JSE76 0.6037 NA NA SD.f_cyan_ilr_1 0.3115 NA NA SD.f_cyan_ilr_2 0.3436 NA NA SD.f_JCZ38_qlogis 4.8937 NA NA Variance model: est. lower upper a.1 3.232 NA NA Backtransformed parameters: est. lower upper cyan_free_0 1.028e+02 NA NA k_cyan_free 6.120e-02 NA NA k_cyan_free_bound 7.855e-02 NA NA k_cyan_bound_free 3.238e-02 NA NA k_JCZ38 3.017e-02 NA NA k_J9Z38 5.961e-03 NA NA k_JSE76 3.584e-03 NA NA f_cyan_free_to_JCZ38 5.784e-01 NA NA f_cyan_free_to_J9Z38 2.271e-01 NA NA f_JCZ38_to_JSE76 1.000e+00 NA NA Estimated Eigenvalues of SFORB model(s): cyan_b1 cyan_b2 cyan_g 0.15973 0.01241 0.33124 Resulting formation fractions: ff cyan_free_JCZ38 0.5784 cyan_free_J9Z38 0.2271 cyan_free_sink 0.1945 cyan_free 1.0000 JCZ38_JSE76 1.0000 JCZ38_sink 0.0000 Estimated disappearance times: DT50 DT90 DT50back DT50_cyan_b1 DT50_cyan_b2 cyan 24.51 153.18 46.11 4.34 55.87 JCZ38 22.98 76.33 NA NA NA J9Z38 116.28 386.29 NA NA NA JSE76 193.42 642.53 NA NA NA saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 R version used for fitting: 4.3.2 Date of fit: Thu Nov 16 04:31:58 2023 Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * cyan_free + k_cyan_bound_free * cyan_bound d_cyan_bound/dt = + k_cyan_free_bound * cyan_free - k_cyan_bound_free * cyan_bound d_JCZ38/dt = + f_cyan_free_to_JCZ38 * k_cyan_free * cyan_free - k_JCZ38 * JCZ38 d_J9Z38/dt = + f_cyan_free_to_J9Z38 * k_cyan_free * cyan_free - k_J9Z38 * J9Z38 d_JSE76/dt = + f_JCZ38_to_JSE76 * k_JCZ38 * JCZ38 - k_JSE76 * JSE76 Data: 433 observations of 4 variable(s) grouped in 5 datasets Model predictions using solution type deSolve Fitted in 677.936 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function Starting values for degradation parameters: cyan_free_0 log_k_cyan_free log_k_cyan_free_bound 101.3964 -2.9881 -2.7949 log_k_cyan_bound_free log_k_JCZ38 log_k_J9Z38 -3.4376 -3.3626 -4.9792 log_k_JSE76 f_cyan_ilr_1 f_cyan_ilr_2 -5.8727 0.6814 6.7399 f_JCZ38_qlogis 13.7395 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): cyan_free_0 log_k_cyan_free log_k_cyan_free_bound cyan_free_0 5.317 0.0000 0.000 log_k_cyan_free 0.000 0.7301 0.000 log_k_cyan_free_bound 0.000 0.0000 1.384 log_k_cyan_bound_free 0.000 0.0000 0.000 log_k_JCZ38 0.000 0.0000 0.000 log_k_J9Z38 0.000 0.0000 0.000 log_k_JSE76 0.000 0.0000 0.000 f_cyan_ilr_1 0.000 0.0000 0.000 f_cyan_ilr_2 0.000 0.0000 0.000 f_JCZ38_qlogis 0.000 0.0000 0.000 log_k_cyan_bound_free log_k_JCZ38 log_k_J9Z38 log_k_JSE76 cyan_free_0 0.000 0.000 0.000 0.000 log_k_cyan_free 0.000 0.000 0.000 0.000 log_k_cyan_free_bound 0.000 0.000 0.000 0.000 log_k_cyan_bound_free 1.109 0.000 0.000 0.000 log_k_JCZ38 0.000 2.272 0.000 0.000 log_k_J9Z38 0.000 0.000 1.633 0.000 log_k_JSE76 0.000 0.000 0.000 1.271 f_cyan_ilr_1 0.000 0.000 0.000 0.000 f_cyan_ilr_2 0.000 0.000 0.000 0.000 f_JCZ38_qlogis 0.000 0.000 0.000 0.000 f_cyan_ilr_1 f_cyan_ilr_2 f_JCZ38_qlogis cyan_free_0 0.0000 0.00 0.00 log_k_cyan_free 0.0000 0.00 0.00 log_k_cyan_free_bound 0.0000 0.00 0.00 log_k_cyan_bound_free 0.0000 0.00 0.00 log_k_JCZ38 0.0000 0.00 0.00 log_k_J9Z38 0.0000 0.00 0.00 log_k_JSE76 0.0000 0.00 0.00 f_cyan_ilr_1 0.6838 0.00 0.00 f_cyan_ilr_2 0.0000 11.69 0.00 f_JCZ38_qlogis 0.0000 0.00 16.13 Starting values for error model parameters: a.1 b.1 1 1 Results: Likelihood computed by importance sampling AIC BIC logLik 2400 2392 -1180 Optimised parameters: est. lower upper cyan_free_0 100.56004 NA NA log_k_cyan_free -3.12657 NA NA log_k_cyan_free_bound -3.16825 NA NA log_k_cyan_bound_free -3.66003 NA NA log_k_JCZ38 -3.47278 NA NA log_k_J9Z38 -5.06823 NA NA log_k_JSE76 -5.54327 NA NA f_cyan_ilr_1 0.66631 NA NA f_cyan_ilr_2 0.82898 NA NA f_JCZ38_qlogis 38.31115 NA NA a.1 2.98352 NA NA b.1 0.04388 NA NA SD.log_k_cyan_free 0.49145 NA NA SD.log_k_cyan_bound_free 0.27347 NA NA SD.log_k_JCZ38 1.41193 NA NA SD.log_k_J9Z38 0.66073 NA NA SD.log_k_JSE76 0.55885 NA NA SD.f_cyan_ilr_1 0.33020 NA NA SD.f_cyan_ilr_2 0.51367 NA NA SD.f_JCZ38_qlogis 5.52122 NA NA Correlation is not available Random effects: est. lower upper SD.log_k_cyan_free 0.4914 NA NA SD.log_k_cyan_bound_free 0.2735 NA NA SD.log_k_JCZ38 1.4119 NA NA SD.log_k_J9Z38 0.6607 NA NA SD.log_k_JSE76 0.5589 NA NA SD.f_cyan_ilr_1 0.3302 NA NA SD.f_cyan_ilr_2 0.5137 NA NA SD.f_JCZ38_qlogis 5.5212 NA NA Variance model: est. lower upper a.1 2.98352 NA NA b.1 0.04388 NA NA Backtransformed parameters: est. lower upper cyan_free_0 1.006e+02 NA NA k_cyan_free 4.387e-02 NA NA k_cyan_free_bound 4.208e-02 NA NA k_cyan_bound_free 2.573e-02 NA NA k_JCZ38 3.103e-02 NA NA k_J9Z38 6.294e-03 NA NA k_JSE76 3.914e-03 NA NA f_cyan_free_to_JCZ38 6.188e-01 NA NA f_cyan_free_to_J9Z38 2.412e-01 NA NA f_JCZ38_to_JSE76 1.000e+00 NA NA Estimated Eigenvalues of SFORB model(s): cyan_b1 cyan_b2 cyan_g 0.10044 0.01124 0.36580 Resulting formation fractions: ff cyan_free_JCZ38 0.6188 cyan_free_J9Z38 0.2412 cyan_free_sink 0.1400 cyan_free 1.0000 JCZ38_JSE76 1.0000 JCZ38_sink 0.0000 Estimated disappearance times: DT50 DT90 DT50back DT50_cyan_b1 DT50_cyan_b2 cyan 26.05 164.4 49.48 6.901 61.67 JCZ38 22.34 74.2 NA NA NA J9Z38 110.14 365.9 NA NA NA JSE76 177.11 588.3 NA NA NA saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 R version used for fitting: 4.3.2 Date of fit: Thu Nov 16 04:29:18 2023 Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - ifelse(time <= tb, k1, k2) * cyan d_JCZ38/dt = + f_cyan_to_JCZ38 * ifelse(time <= tb, k1, k2) * cyan - k_JCZ38 * JCZ38 d_J9Z38/dt = + f_cyan_to_J9Z38 * ifelse(time <= tb, k1, k2) * cyan - k_J9Z38 * J9Z38 d_JSE76/dt = + f_JCZ38_to_JSE76 * k_JCZ38 * JCZ38 - k_JSE76 * JSE76 Data: 433 observations of 4 variable(s) grouped in 5 datasets Model predictions using solution type deSolve Fitted in 518.128 s Using 300, 100 iterations and 10 chains Variance model: Constant variance Starting values for degradation parameters: cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 102.8845 -3.4495 -4.9355 -5.6040 0.6468 f_cyan_ilr_2 f_JCZ38_qlogis log_k1 log_k2 log_tb 1.2396 9.7220 -2.9079 -4.1810 1.7813 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 cyan_0 5.406 0.00 0.00 0.000 0.0000 log_k_JCZ38 0.000 2.33 0.00 0.000 0.0000 log_k_J9Z38 0.000 0.00 1.59 0.000 0.0000 log_k_JSE76 0.000 0.00 0.00 1.013 0.0000 f_cyan_ilr_1 0.000 0.00 0.00 0.000 0.6367 f_cyan_ilr_2 0.000 0.00 0.00 0.000 0.0000 f_JCZ38_qlogis 0.000 0.00 0.00 0.000 0.0000 log_k1 0.000 0.00 0.00 0.000 0.0000 log_k2 0.000 0.00 0.00 0.000 0.0000 log_tb 0.000 0.00 0.00 0.000 0.0000 f_cyan_ilr_2 f_JCZ38_qlogis log_k1 log_k2 log_tb cyan_0 0.000 0.00 0.0000 0.0000 0.0000 log_k_JCZ38 0.000 0.00 0.0000 0.0000 0.0000 log_k_J9Z38 0.000 0.00 0.0000 0.0000 0.0000 log_k_JSE76 0.000 0.00 0.0000 0.0000 0.0000 f_cyan_ilr_1 0.000 0.00 0.0000 0.0000 0.0000 f_cyan_ilr_2 2.038 0.00 0.0000 0.0000 0.0000 f_JCZ38_qlogis 0.000 10.33 0.0000 0.0000 0.0000 log_k1 0.000 0.00 0.7006 0.0000 0.0000 log_k2 0.000 0.00 0.0000 0.8928 0.0000 log_tb 0.000 0.00 0.0000 0.0000 0.6773 Starting values for error model parameters: a.1 1 Results: Likelihood computed by importance sampling AIC BIC logLik 2427 2419 -1194 Optimised parameters: est. lower upper cyan_0 101.9660 1.005e+02 1.035e+02 log_k_JCZ38 -3.4698 -4.716e+00 -2.224e+00 log_k_J9Z38 -5.0947 -5.740e+00 -4.450e+00 log_k_JSE76 -5.5977 -6.321e+00 -4.875e+00 f_cyan_ilr_1 0.6595 3.734e-01 9.456e-01 f_cyan_ilr_2 0.5905 1.664e-01 1.015e+00 f_JCZ38_qlogis 25.8627 -4.224e+05 4.225e+05 log_k1 -3.0884 -3.453e+00 -2.723e+00 log_k2 -4.3877 -4.778e+00 -3.998e+00 log_tb 2.3057 1.715e+00 2.896e+00 a.1 3.3228 NA NA SD.log_k_JCZ38 1.4071 NA NA SD.log_k_J9Z38 0.5774 NA NA SD.log_k_JSE76 0.6214 NA NA SD.f_cyan_ilr_1 0.3058 NA NA SD.f_cyan_ilr_2 0.3470 NA NA SD.f_JCZ38_qlogis 0.0644 NA NA SD.log_k1 0.3994 NA NA SD.log_k2 0.4373 NA NA SD.log_tb 0.6419 NA NA Correlation is not available Random effects: est. lower upper SD.log_k_JCZ38 1.4071 NA NA SD.log_k_J9Z38 0.5774 NA NA SD.log_k_JSE76 0.6214 NA NA SD.f_cyan_ilr_1 0.3058 NA NA SD.f_cyan_ilr_2 0.3470 NA NA SD.f_JCZ38_qlogis 0.0644 NA NA SD.log_k1 0.3994 NA NA SD.log_k2 0.4373 NA NA SD.log_tb 0.6419 NA NA Variance model: est. lower upper a.1 3.323 NA NA Backtransformed parameters: est. lower upper cyan_0 1.020e+02 1.005e+02 1.035e+02 k_JCZ38 3.112e-02 8.951e-03 1.082e-01 k_J9Z38 6.129e-03 3.216e-03 1.168e-02 k_JSE76 3.706e-03 1.798e-03 7.639e-03 f_cyan_to_JCZ38 5.890e-01 NA NA f_cyan_to_J9Z38 2.318e-01 NA NA f_JCZ38_to_JSE76 1.000e+00 0.000e+00 1.000e+00 k1 4.558e-02 3.164e-02 6.565e-02 k2 1.243e-02 8.417e-03 1.835e-02 tb 1.003e+01 5.557e+00 1.811e+01 Resulting formation fractions: ff cyan_JCZ38 5.890e-01 cyan_J9Z38 2.318e-01 cyan_sink 1.793e-01 JCZ38_JSE76 1.000e+00 JCZ38_sink 5.861e-12 Estimated disappearance times: DT50 DT90 DT50back DT50_k1 DT50_k2 cyan 29.02 158.51 47.72 15.21 55.77 JCZ38 22.27 73.98 NA NA NA J9Z38 113.09 375.69 NA NA NA JSE76 187.01 621.23 NA NA NA"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_cyan_pathway.html","id":"pathway-2","dir":"Articles > Prebuilt","previous_headings":"Appendix > Hierarchical fit listings","what":"Pathway 2","title":"Testing hierarchical pathway kinetics with residue data on cyantraniliprole","text":"Hierarchical FOMC path 2 fit two-component error Hierarchical DFOP path 2 fit constant variance Hierarchical DFOP path 2 fit two-component error Hierarchical SFORB path 2 fit constant variance Hierarchical SFORB path 2 fit two-component error","code":"saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 R version used for fitting: 4.3.2 Date of fit: Thu Nov 16 04:40:28 2023 Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan d_JCZ38/dt = + f_cyan_to_JCZ38 * (alpha/beta) * 1/((time/beta) + 1) * cyan - k_JCZ38 * JCZ38 + f_JSE76_to_JCZ38 * k_JSE76 * JSE76 d_J9Z38/dt = + f_cyan_to_J9Z38 * (alpha/beta) * 1/((time/beta) + 1) * cyan - k_J9Z38 * J9Z38 d_JSE76/dt = + f_JCZ38_to_JSE76 * k_JCZ38 * JCZ38 - k_JSE76 * JSE76 Data: 433 observations of 4 variable(s) grouped in 5 datasets Model predictions using solution type deSolve Fitted in 499.317 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function Starting values for degradation parameters: cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 102.4477 -1.8631 -5.1087 -2.5114 0.6826 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_alpha log_beta 4.7944 15.9616 13.1566 -0.1564 2.9781 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 cyan_0 7.701 0.000 0.000 0.000 0.0000 log_k_JCZ38 0.000 1.448 0.000 0.000 0.0000 log_k_J9Z38 0.000 0.000 1.724 0.000 0.0000 log_k_JSE76 0.000 0.000 0.000 3.659 0.0000 f_cyan_ilr_1 0.000 0.000 0.000 0.000 0.6356 f_cyan_ilr_2 0.000 0.000 0.000 0.000 0.0000 f_JCZ38_qlogis 0.000 0.000 0.000 0.000 0.0000 f_JSE76_qlogis 0.000 0.000 0.000 0.000 0.0000 log_alpha 0.000 0.000 0.000 0.000 0.0000 log_beta 0.000 0.000 0.000 0.000 0.0000 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_alpha log_beta cyan_0 0.00 0.00 0.00 0.0000 0.0000 log_k_JCZ38 0.00 0.00 0.00 0.0000 0.0000 log_k_J9Z38 0.00 0.00 0.00 0.0000 0.0000 log_k_JSE76 0.00 0.00 0.00 0.0000 0.0000 f_cyan_ilr_1 0.00 0.00 0.00 0.0000 0.0000 f_cyan_ilr_2 10.32 0.00 0.00 0.0000 0.0000 f_JCZ38_qlogis 0.00 12.23 0.00 0.0000 0.0000 f_JSE76_qlogis 0.00 0.00 14.99 0.0000 0.0000 log_alpha 0.00 0.00 0.00 0.3924 0.0000 log_beta 0.00 0.00 0.00 0.0000 0.5639 Starting values for error model parameters: a.1 b.1 1 1 Results: Likelihood computed by importance sampling AIC BIC logLik 2249 2241 -1104 Optimised parameters: est. lower upper cyan_0 101.55265 9.920e+01 103.90593 log_k_JCZ38 -2.32302 -2.832e+00 -1.81416 log_k_J9Z38 -5.13082 -5.942e+00 -4.31990 log_k_JSE76 -3.01756 -4.262e+00 -1.77360 f_cyan_ilr_1 0.70850 3.657e-01 1.05135 f_cyan_ilr_2 0.95775 2.612e-01 1.65432 f_JCZ38_qlogis 3.86105 9.248e-01 6.79733 f_JSE76_qlogis 7.51583 -1.120e+02 127.03921 log_alpha -0.15308 -4.508e-01 0.14462 log_beta 2.99165 2.711e+00 3.27202 a.1 2.04034 1.811e+00 2.26968 b.1 0.06924 5.745e-02 0.08104 SD.log_k_JCZ38 0.50818 1.390e-01 0.87736 SD.log_k_J9Z38 0.86597 2.652e-01 1.46671 SD.log_k_JSE76 1.38092 4.864e-01 2.27541 SD.f_cyan_ilr_1 0.38204 1.354e-01 0.62864 SD.f_cyan_ilr_2 0.55129 7.198e-02 1.03060 SD.f_JCZ38_qlogis 1.88457 1.710e-02 3.75205 SD.f_JSE76_qlogis 2.64018 -2.450e+03 2455.27887 SD.log_alpha 0.31860 1.047e-01 0.53249 SD.log_beta 0.24195 1.273e-02 0.47117 Correlation: cyan_0 l__JCZ3 l__J9Z3 l__JSE7 f_cy__1 f_cy__2 f_JCZ38 f_JSE76 log_k_JCZ38 -0.0235 log_k_J9Z38 -0.0442 0.0047 log_k_JSE76 -0.0023 0.0966 0.0006 f_cyan_ilr_1 -0.0032 0.0070 -0.0536 -0.0001 f_cyan_ilr_2 -0.5189 0.0452 0.1152 0.0013 -0.0304 f_JCZ38_qlogis 0.1088 -0.0848 -0.0240 0.0040 -0.0384 -0.2303 f_JSE76_qlogis -0.0545 0.1315 0.0195 0.0020 0.0252 0.1737 -0.5939 log_alpha -0.0445 0.0056 0.0261 0.0019 -0.0055 0.0586 -0.0239 -0.0284 log_beta -0.2388 0.0163 0.0566 0.0040 -0.0078 0.2183 -0.0714 -0.0332 log_lph log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_alpha log_beta 0.2135 Random effects: est. lower upper SD.log_k_JCZ38 0.5082 1.390e-01 0.8774 SD.log_k_J9Z38 0.8660 2.652e-01 1.4667 SD.log_k_JSE76 1.3809 4.864e-01 2.2754 SD.f_cyan_ilr_1 0.3820 1.354e-01 0.6286 SD.f_cyan_ilr_2 0.5513 7.198e-02 1.0306 SD.f_JCZ38_qlogis 1.8846 1.710e-02 3.7520 SD.f_JSE76_qlogis 2.6402 -2.450e+03 2455.2789 SD.log_alpha 0.3186 1.047e-01 0.5325 SD.log_beta 0.2420 1.273e-02 0.4712 Variance model: est. lower upper a.1 2.04034 1.81101 2.26968 b.1 0.06924 0.05745 0.08104 Backtransformed parameters: est. lower upper cyan_0 1.016e+02 9.920e+01 103.9059 k_JCZ38 9.798e-02 5.890e-02 0.1630 k_J9Z38 5.912e-03 2.627e-03 0.0133 k_JSE76 4.892e-02 1.410e-02 0.1697 f_cyan_to_JCZ38 6.432e-01 NA NA f_cyan_to_J9Z38 2.362e-01 NA NA f_JCZ38_to_JSE76 9.794e-01 7.160e-01 0.9989 f_JSE76_to_JCZ38 9.995e-01 2.268e-49 1.0000 alpha 8.581e-01 6.371e-01 1.1556 beta 1.992e+01 1.505e+01 26.3646 Resulting formation fractions: ff cyan_JCZ38 0.6432301 cyan_J9Z38 0.2361657 cyan_sink 0.1206042 JCZ38_JSE76 0.9793879 JCZ38_sink 0.0206121 JSE76_JCZ38 0.9994559 JSE76_sink 0.0005441 Estimated disappearance times: DT50 DT90 DT50back cyan 24.759 271.61 81.76 JCZ38 7.075 23.50 NA J9Z38 117.249 389.49 NA JSE76 14.169 47.07 NA saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 R version used for fitting: 4.3.2 Date of fit: Thu Nov 16 04:41:25 2023 Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * cyan d_JCZ38/dt = + f_cyan_to_JCZ38 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * cyan - k_JCZ38 * JCZ38 + f_JSE76_to_JCZ38 * k_JSE76 * JSE76 d_J9Z38/dt = + f_cyan_to_J9Z38 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * cyan - k_J9Z38 * J9Z38 d_JSE76/dt = + f_JCZ38_to_JSE76 * k_JCZ38 * JCZ38 - k_JSE76 * JSE76 Data: 433 observations of 4 variable(s) grouped in 5 datasets Model predictions using solution type deSolve Fitted in 555.724 s Using 300, 100 iterations and 10 chains Variance model: Constant variance Starting values for degradation parameters: cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 102.4380 -2.3107 -5.3123 -3.7120 0.6757 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_k1 log_k2 1.1439 13.1194 12.3492 -1.9317 -4.4557 g_qlogis -0.5644 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 cyan_0 4.591 0.0000 0.000 0.0 0.0000 log_k_JCZ38 0.000 0.7966 0.000 0.0 0.0000 log_k_J9Z38 0.000 0.0000 1.561 0.0 0.0000 log_k_JSE76 0.000 0.0000 0.000 0.8 0.0000 f_cyan_ilr_1 0.000 0.0000 0.000 0.0 0.6349 f_cyan_ilr_2 0.000 0.0000 0.000 0.0 0.0000 f_JCZ38_qlogis 0.000 0.0000 0.000 0.0 0.0000 f_JSE76_qlogis 0.000 0.0000 0.000 0.0 0.0000 log_k1 0.000 0.0000 0.000 0.0 0.0000 log_k2 0.000 0.0000 0.000 0.0 0.0000 g_qlogis 0.000 0.0000 0.000 0.0 0.0000 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_k1 log_k2 cyan_0 0.000 0.00 0.00 0.000 0.0000 log_k_JCZ38 0.000 0.00 0.00 0.000 0.0000 log_k_J9Z38 0.000 0.00 0.00 0.000 0.0000 log_k_JSE76 0.000 0.00 0.00 0.000 0.0000 f_cyan_ilr_1 0.000 0.00 0.00 0.000 0.0000 f_cyan_ilr_2 1.797 0.00 0.00 0.000 0.0000 f_JCZ38_qlogis 0.000 13.86 0.00 0.000 0.0000 f_JSE76_qlogis 0.000 0.00 13.91 0.000 0.0000 log_k1 0.000 0.00 0.00 1.106 0.0000 log_k2 0.000 0.00 0.00 0.000 0.6141 g_qlogis 0.000 0.00 0.00 0.000 0.0000 g_qlogis cyan_0 0.000 log_k_JCZ38 0.000 log_k_J9Z38 0.000 log_k_JSE76 0.000 f_cyan_ilr_1 0.000 f_cyan_ilr_2 0.000 f_JCZ38_qlogis 0.000 f_JSE76_qlogis 0.000 log_k1 0.000 log_k2 0.000 g_qlogis 1.595 Starting values for error model parameters: a.1 1 Results: Likelihood computed by importance sampling AIC BIC logLik 2288 2280 -1122 Optimised parameters: est. lower upper cyan_0 102.7204 1.014e+02 1.040e+02 log_k_JCZ38 -2.8925 -4.044e+00 -1.741e+00 log_k_J9Z38 -5.1430 -5.828e+00 -4.457e+00 log_k_JSE76 -3.5577 -4.174e+00 -2.941e+00 f_cyan_ilr_1 0.6929 3.788e-01 1.007e+00 f_cyan_ilr_2 0.6066 5.342e-02 1.160e+00 f_JCZ38_qlogis 9.8071 -2.819e+03 2.838e+03 f_JSE76_qlogis 2.2229 5.684e-01 3.877e+00 log_k1 -1.9339 -2.609e+00 -1.258e+00 log_k2 -4.4709 -4.935e+00 -4.007e+00 g_qlogis -0.4987 -1.373e+00 3.757e-01 a.1 2.7368 2.545e+00 2.928e+00 SD.log_k_JCZ38 1.2747 4.577e-01 2.092e+00 SD.log_k_J9Z38 0.6758 1.418e-01 1.210e+00 SD.log_k_JSE76 0.5869 1.169e-01 1.057e+00 SD.f_cyan_ilr_1 0.3392 1.161e-01 5.622e-01 SD.f_cyan_ilr_2 0.4200 8.501e-02 7.550e-01 SD.f_JCZ38_qlogis 0.8511 -1.137e+06 1.137e+06 SD.f_JSE76_qlogis 0.3767 -5.238e-01 1.277e+00 SD.log_k1 0.7475 2.601e-01 1.235e+00 SD.log_k2 0.5179 1.837e-01 8.521e-01 SD.g_qlogis 0.9817 3.553e-01 1.608e+00 Correlation: cyan_0 l__JCZ3 l__J9Z3 l__JSE7 f_cy__1 f_cy__2 f_JCZ38 f_JSE76 log_k_JCZ38 -0.0351 log_k_J9Z38 -0.0541 0.0043 log_k_JSE76 -0.0078 0.0900 -0.0014 f_cyan_ilr_1 -0.0249 0.0268 -0.0962 0.0000 f_cyan_ilr_2 -0.3560 0.0848 0.1545 -0.0022 0.0463 f_JCZ38_qlogis 0.2005 -0.1226 -0.0347 0.0514 -0.1840 -0.5906 f_JSE76_qlogis -0.1638 0.1307 0.0266 0.0001 0.1645 0.5181 -0.9297 log_k1 0.0881 -0.0071 0.0005 -0.0070 -0.0064 -0.0346 0.0316 -0.0341 log_k2 0.0238 -0.0003 0.0082 -0.0022 -0.0017 -0.0017 -0.0002 -0.0076 g_qlogis 0.0198 -0.0002 -0.0109 0.0034 0.0017 -0.0176 0.0044 0.0051 log_k1 log_k2 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_k1 log_k2 0.0276 g_qlogis -0.0283 -0.0309 Random effects: est. lower upper SD.log_k_JCZ38 1.2747 4.577e-01 2.092e+00 SD.log_k_J9Z38 0.6758 1.418e-01 1.210e+00 SD.log_k_JSE76 0.5869 1.169e-01 1.057e+00 SD.f_cyan_ilr_1 0.3392 1.161e-01 5.622e-01 SD.f_cyan_ilr_2 0.4200 8.501e-02 7.550e-01 SD.f_JCZ38_qlogis 0.8511 -1.137e+06 1.137e+06 SD.f_JSE76_qlogis 0.3767 -5.238e-01 1.277e+00 SD.log_k1 0.7475 2.601e-01 1.235e+00 SD.log_k2 0.5179 1.837e-01 8.521e-01 SD.g_qlogis 0.9817 3.553e-01 1.608e+00 Variance model: est. lower upper a.1 2.737 2.545 2.928 Backtransformed parameters: est. lower upper cyan_0 102.72037 1.014e+02 104.00464 k_JCZ38 0.05544 1.752e-02 0.17539 k_J9Z38 0.00584 2.942e-03 0.01159 k_JSE76 0.02850 1.539e-02 0.05279 f_cyan_to_JCZ38 0.59995 NA NA f_cyan_to_J9Z38 0.22519 NA NA f_JCZ38_to_JSE76 0.99994 0.000e+00 1.00000 f_JSE76_to_JCZ38 0.90229 6.384e-01 0.97971 k1 0.14459 7.357e-02 0.28414 k2 0.01144 7.192e-03 0.01819 g 0.37784 2.021e-01 0.59284 Resulting formation fractions: ff cyan_JCZ38 5.999e-01 cyan_J9Z38 2.252e-01 cyan_sink 1.749e-01 JCZ38_JSE76 9.999e-01 JCZ38_sink 5.506e-05 JSE76_JCZ38 9.023e-01 JSE76_sink 9.771e-02 Estimated disappearance times: DT50 DT90 DT50back DT50_k1 DT50_k2 cyan 21.93 159.83 48.11 4.794 60.6 JCZ38 12.50 41.53 NA NA NA J9Z38 118.69 394.27 NA NA NA JSE76 24.32 80.78 NA NA NA saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 R version used for fitting: 4.3.2 Date of fit: Thu Nov 16 04:44:08 2023 Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * cyan d_JCZ38/dt = + f_cyan_to_JCZ38 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * cyan - k_JCZ38 * JCZ38 + f_JSE76_to_JCZ38 * k_JSE76 * JSE76 d_J9Z38/dt = + f_cyan_to_J9Z38 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * cyan - k_J9Z38 * J9Z38 d_JSE76/dt = + f_JCZ38_to_JSE76 * k_JCZ38 * JCZ38 - k_JSE76 * JSE76 Data: 433 observations of 4 variable(s) grouped in 5 datasets Model predictions using solution type deSolve Fitted in 718.988 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function Starting values for degradation parameters: cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 101.7393 -1.4493 -5.0118 -2.1269 0.6720 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_k1 log_k2 7.3362 13.4423 13.2659 -2.0061 -4.5527 g_qlogis -0.5806 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 cyan_0 5.604 0.00 0.000 0.000 0.0000 log_k_JCZ38 0.000 2.77 0.000 0.000 0.0000 log_k_J9Z38 0.000 0.00 1.662 0.000 0.0000 log_k_JSE76 0.000 0.00 0.000 5.021 0.0000 f_cyan_ilr_1 0.000 0.00 0.000 0.000 0.6519 f_cyan_ilr_2 0.000 0.00 0.000 0.000 0.0000 f_JCZ38_qlogis 0.000 0.00 0.000 0.000 0.0000 f_JSE76_qlogis 0.000 0.00 0.000 0.000 0.0000 log_k1 0.000 0.00 0.000 0.000 0.0000 log_k2 0.000 0.00 0.000 0.000 0.0000 g_qlogis 0.000 0.00 0.000 0.000 0.0000 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_k1 log_k2 cyan_0 0.00 0.00 0.00 0.0000 0.0000 log_k_JCZ38 0.00 0.00 0.00 0.0000 0.0000 log_k_J9Z38 0.00 0.00 0.00 0.0000 0.0000 log_k_JSE76 0.00 0.00 0.00 0.0000 0.0000 f_cyan_ilr_1 0.00 0.00 0.00 0.0000 0.0000 f_cyan_ilr_2 13.37 0.00 0.00 0.0000 0.0000 f_JCZ38_qlogis 0.00 14.21 0.00 0.0000 0.0000 f_JSE76_qlogis 0.00 0.00 14.58 0.0000 0.0000 log_k1 0.00 0.00 0.00 0.8453 0.0000 log_k2 0.00 0.00 0.00 0.0000 0.5969 g_qlogis 0.00 0.00 0.00 0.0000 0.0000 g_qlogis cyan_0 0.00 log_k_JCZ38 0.00 log_k_J9Z38 0.00 log_k_JSE76 0.00 f_cyan_ilr_1 0.00 f_cyan_ilr_2 0.00 f_JCZ38_qlogis 0.00 f_JSE76_qlogis 0.00 log_k1 0.00 log_k2 0.00 g_qlogis 1.69 Starting values for error model parameters: a.1 b.1 1 1 Results: Likelihood computed by importance sampling AIC BIC logLik 2234 2226 -1095 Optimised parameters: est. lower upper cyan_0 101.25496 99.14662 103.36331 log_k_JCZ38 -2.55593 -3.32972 -1.78215 log_k_J9Z38 -5.07103 -5.85423 -4.28783 log_k_JSE76 -3.25468 -4.17577 -2.33360 f_cyan_ilr_1 0.70139 0.35924 1.04355 f_cyan_ilr_2 1.07712 0.17789 1.97636 f_JCZ38_qlogis 3.57483 0.05990 7.08976 f_JSE76_qlogis 4.54884 -7.25628 16.35395 log_k1 -2.38201 -2.51639 -2.24763 log_k2 -4.66741 -4.91865 -4.41617 g_qlogis -0.28446 -1.14192 0.57300 a.1 2.05925 1.83267 2.28582 b.1 0.06172 0.05076 0.07268 SD.log_k_JCZ38 0.81137 0.25296 1.36977 SD.log_k_J9Z38 0.83542 0.25396 1.41689 SD.log_k_JSE76 0.97903 0.30100 1.65707 SD.f_cyan_ilr_1 0.37878 0.13374 0.62382 SD.f_cyan_ilr_2 0.67274 0.10102 1.24446 SD.f_JCZ38_qlogis 1.35327 -0.42361 3.13015 SD.f_JSE76_qlogis 1.43956 -19.15140 22.03052 SD.log_k2 0.25329 0.07521 0.43138 SD.g_qlogis 0.95167 0.35149 1.55184 Correlation: cyan_0 l__JCZ3 l__J9Z3 l__JSE7 f_cy__1 f_cy__2 f_JCZ38 f_JSE76 log_k_JCZ38 -0.0265 log_k_J9Z38 -0.0392 0.0024 log_k_JSE76 0.0011 0.1220 -0.0016 f_cyan_ilr_1 -0.0161 0.0217 -0.0552 0.0034 f_cyan_ilr_2 -0.4718 0.0829 0.1102 0.0042 0.0095 f_JCZ38_qlogis 0.1609 -0.1318 -0.0277 0.0081 -0.1040 -0.4559 f_JSE76_qlogis -0.1289 0.1494 0.0219 0.0012 0.1004 0.4309 -0.8543 log_k1 0.2618 -0.0739 -0.0167 -0.0148 -0.0444 -0.2768 0.3518 -0.3818 log_k2 0.0603 -0.0217 0.0174 -0.0058 -0.0197 -0.0533 0.0923 -0.1281 g_qlogis 0.0362 0.0115 -0.0111 0.0040 0.0095 -0.0116 -0.0439 0.0651 log_k1 log_k2 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_k1 log_k2 0.3269 g_qlogis -0.1656 -0.0928 Random effects: est. lower upper SD.log_k_JCZ38 0.8114 0.25296 1.3698 SD.log_k_J9Z38 0.8354 0.25396 1.4169 SD.log_k_JSE76 0.9790 0.30100 1.6571 SD.f_cyan_ilr_1 0.3788 0.13374 0.6238 SD.f_cyan_ilr_2 0.6727 0.10102 1.2445 SD.f_JCZ38_qlogis 1.3533 -0.42361 3.1301 SD.f_JSE76_qlogis 1.4396 -19.15140 22.0305 SD.log_k2 0.2533 0.07521 0.4314 SD.g_qlogis 0.9517 0.35149 1.5518 Variance model: est. lower upper a.1 2.05925 1.83267 2.28582 b.1 0.06172 0.05076 0.07268 Backtransformed parameters: est. lower upper cyan_0 1.013e+02 9.915e+01 103.36331 k_JCZ38 7.762e-02 3.580e-02 0.16828 k_J9Z38 6.276e-03 2.868e-03 0.01373 k_JSE76 3.859e-02 1.536e-02 0.09695 f_cyan_to_JCZ38 6.520e-01 NA NA f_cyan_to_J9Z38 2.418e-01 NA NA f_JCZ38_to_JSE76 9.727e-01 5.150e-01 0.99917 f_JSE76_to_JCZ38 9.895e-01 7.052e-04 1.00000 k1 9.236e-02 8.075e-02 0.10565 k2 9.397e-03 7.309e-03 0.01208 g 4.294e-01 2.420e-01 0.63945 Resulting formation fractions: ff cyan_JCZ38 0.65203 cyan_J9Z38 0.24181 cyan_sink 0.10616 JCZ38_JSE76 0.97274 JCZ38_sink 0.02726 JSE76_JCZ38 0.98953 JSE76_sink 0.01047 Estimated disappearance times: DT50 DT90 DT50back DT50_k1 DT50_k2 cyan 24.26 185.34 55.79 7.504 73.77 JCZ38 8.93 29.66 NA NA NA J9Z38 110.45 366.89 NA NA NA JSE76 17.96 59.66 NA NA NA saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 R version used for fitting: 4.3.2 Date of fit: Thu Nov 16 04:41:22 2023 Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * cyan_free + k_cyan_bound_free * cyan_bound d_cyan_bound/dt = + k_cyan_free_bound * cyan_free - k_cyan_bound_free * cyan_bound d_JCZ38/dt = + f_cyan_free_to_JCZ38 * k_cyan_free * cyan_free - k_JCZ38 * JCZ38 + f_JSE76_to_JCZ38 * k_JSE76 * JSE76 d_J9Z38/dt = + f_cyan_free_to_J9Z38 * k_cyan_free * cyan_free - k_J9Z38 * J9Z38 d_JSE76/dt = + f_JCZ38_to_JSE76 * k_JCZ38 * JCZ38 - k_JSE76 * JSE76 Data: 433 observations of 4 variable(s) grouped in 5 datasets Model predictions using solution type deSolve Fitted in 553.276 s Using 300, 100 iterations and 10 chains Variance model: Constant variance Starting values for degradation parameters: cyan_free_0 log_k_cyan_free log_k_cyan_free_bound 102.4395 -2.7673 -2.8942 log_k_cyan_bound_free log_k_JCZ38 log_k_J9Z38 -3.6201 -2.3107 -5.3123 log_k_JSE76 f_cyan_ilr_1 f_cyan_ilr_2 -3.7120 0.6754 1.1448 f_JCZ38_qlogis f_JSE76_qlogis 14.8408 15.4734 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): cyan_free_0 log_k_cyan_free log_k_cyan_free_bound cyan_free_0 4.589 0.0000 0.00 log_k_cyan_free 0.000 0.4849 0.00 log_k_cyan_free_bound 0.000 0.0000 1.62 log_k_cyan_bound_free 0.000 0.0000 0.00 log_k_JCZ38 0.000 0.0000 0.00 log_k_J9Z38 0.000 0.0000 0.00 log_k_JSE76 0.000 0.0000 0.00 f_cyan_ilr_1 0.000 0.0000 0.00 f_cyan_ilr_2 0.000 0.0000 0.00 f_JCZ38_qlogis 0.000 0.0000 0.00 f_JSE76_qlogis 0.000 0.0000 0.00 log_k_cyan_bound_free log_k_JCZ38 log_k_J9Z38 log_k_JSE76 cyan_free_0 0.000 0.0000 0.000 0.0 log_k_cyan_free 0.000 0.0000 0.000 0.0 log_k_cyan_free_bound 0.000 0.0000 0.000 0.0 log_k_cyan_bound_free 1.197 0.0000 0.000 0.0 log_k_JCZ38 0.000 0.7966 0.000 0.0 log_k_J9Z38 0.000 0.0000 1.561 0.0 log_k_JSE76 0.000 0.0000 0.000 0.8 f_cyan_ilr_1 0.000 0.0000 0.000 0.0 f_cyan_ilr_2 0.000 0.0000 0.000 0.0 f_JCZ38_qlogis 0.000 0.0000 0.000 0.0 f_JSE76_qlogis 0.000 0.0000 0.000 0.0 f_cyan_ilr_1 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis cyan_free_0 0.0000 0.000 0.0 0.00 log_k_cyan_free 0.0000 0.000 0.0 0.00 log_k_cyan_free_bound 0.0000 0.000 0.0 0.00 log_k_cyan_bound_free 0.0000 0.000 0.0 0.00 log_k_JCZ38 0.0000 0.000 0.0 0.00 log_k_J9Z38 0.0000 0.000 0.0 0.00 log_k_JSE76 0.0000 0.000 0.0 0.00 f_cyan_ilr_1 0.6349 0.000 0.0 0.00 f_cyan_ilr_2 0.0000 1.797 0.0 0.00 f_JCZ38_qlogis 0.0000 0.000 15.6 0.00 f_JSE76_qlogis 0.0000 0.000 0.0 17.52 Starting values for error model parameters: a.1 1 Results: Likelihood computed by importance sampling AIC BIC logLik 2283 2275 -1120 Optimised parameters: est. lower upper cyan_free_0 102.6517 101.40815 103.8952 log_k_cyan_free -2.8729 -3.18649 -2.5593 log_k_cyan_free_bound -2.7803 -3.60525 -1.9552 log_k_cyan_bound_free -3.5845 -4.16644 -3.0026 log_k_JCZ38 -2.3411 -2.89698 -1.7852 log_k_J9Z38 -5.2487 -6.01271 -4.4847 log_k_JSE76 -3.0259 -4.28274 -1.7690 f_cyan_ilr_1 0.7289 0.38214 1.0756 f_cyan_ilr_2 0.6891 0.18277 1.1954 f_JCZ38_qlogis 4.2162 0.47015 7.9622 f_JSE76_qlogis 5.8911 -20.19088 31.9730 a.1 2.7159 2.52587 2.9060 SD.log_k_cyan_free 0.3354 0.10979 0.5610 SD.log_k_cyan_free_bound 0.9061 0.30969 1.5025 SD.log_k_cyan_bound_free 0.6376 0.21229 1.0628 SD.log_k_JCZ38 0.5499 0.14533 0.9545 SD.log_k_J9Z38 0.7457 0.15106 1.3404 SD.log_k_JSE76 1.3822 0.47329 2.2912 SD.f_cyan_ilr_1 0.3820 0.13280 0.6313 SD.f_cyan_ilr_2 0.4317 0.06803 0.7953 SD.f_JCZ38_qlogis 1.8258 -0.25423 3.9059 SD.f_JSE76_qlogis 2.2348 -83.33679 87.8065 Correlation: cyn_f_0 lg_k_c_ lg_k_cyn_f_ lg_k_cyn_b_ l__JCZ3 l__J9Z3 log_k_cyan_free 0.1944 log_k_cyan_free_bound 0.0815 0.0814 log_k_cyan_bound_free 0.0106 0.0426 0.0585 log_k_JCZ38 -0.0231 -0.0106 -0.0089 -0.0051 log_k_J9Z38 -0.0457 -0.0108 0.0019 0.0129 0.0032 log_k_JSE76 -0.0054 -0.0024 -0.0017 -0.0005 0.1108 0.0009 f_cyan_ilr_1 0.0051 -0.0005 -0.0035 -0.0056 0.0131 -0.0967 f_cyan_ilr_2 -0.3182 -0.0771 -0.0309 -0.0038 0.0680 0.1643 f_JCZ38_qlogis 0.0834 0.0369 0.0302 0.0172 -0.1145 -0.0204 f_JSE76_qlogis -0.0553 -0.0365 -0.0441 -0.0414 0.1579 0.0175 l__JSE7 f_cy__1 f_cy__2 f_JCZ38 log_k_cyan_free log_k_cyan_free_bound log_k_cyan_bound_free log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 -0.0002 f_cyan_ilr_2 0.0020 -0.0415 f_JCZ38_qlogis 0.0052 -0.0665 -0.3437 f_JSE76_qlogis 0.0066 0.0635 0.3491 -0.7487 Random effects: est. lower upper SD.log_k_cyan_free 0.3354 0.10979 0.5610 SD.log_k_cyan_free_bound 0.9061 0.30969 1.5025 SD.log_k_cyan_bound_free 0.6376 0.21229 1.0628 SD.log_k_JCZ38 0.5499 0.14533 0.9545 SD.log_k_J9Z38 0.7457 0.15106 1.3404 SD.log_k_JSE76 1.3822 0.47329 2.2912 SD.f_cyan_ilr_1 0.3820 0.13280 0.6313 SD.f_cyan_ilr_2 0.4317 0.06803 0.7953 SD.f_JCZ38_qlogis 1.8258 -0.25423 3.9059 SD.f_JSE76_qlogis 2.2348 -83.33679 87.8065 Variance model: est. lower upper a.1 2.716 2.526 2.906 Backtransformed parameters: est. lower upper cyan_free_0 1.027e+02 1.014e+02 103.89517 k_cyan_free 5.654e-02 4.132e-02 0.07736 k_cyan_free_bound 6.202e-02 2.718e-02 0.14153 k_cyan_bound_free 2.775e-02 1.551e-02 0.04966 k_JCZ38 9.622e-02 5.519e-02 0.16777 k_J9Z38 5.254e-03 2.447e-03 0.01128 k_JSE76 4.852e-02 1.380e-02 0.17051 f_cyan_free_to_JCZ38 6.197e-01 5.643e-01 0.84429 f_cyan_free_to_J9Z38 2.211e-01 5.643e-01 0.84429 f_JCZ38_to_JSE76 9.855e-01 6.154e-01 0.99965 f_JSE76_to_JCZ38 9.972e-01 1.703e-09 1.00000 Estimated Eigenvalues of SFORB model(s): cyan_b1 cyan_b2 cyan_g 0.13466 0.01165 0.36490 Resulting formation fractions: ff cyan_free_JCZ38 0.619745 cyan_free_J9Z38 0.221083 cyan_free_sink 0.159172 cyan_free 1.000000 JCZ38_JSE76 0.985460 JCZ38_sink 0.014540 JSE76_JCZ38 0.997244 JSE76_sink 0.002756 Estimated disappearance times: DT50 DT90 DT50back DT50_cyan_b1 DT50_cyan_b2 cyan 23.293 158.67 47.77 5.147 59.5 JCZ38 7.203 23.93 NA NA NA J9Z38 131.918 438.22 NA NA NA JSE76 14.287 47.46 NA NA NA saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 R version used for fitting: 4.3.2 Date of fit: Thu Nov 16 04:44:02 2023 Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * cyan_free + k_cyan_bound_free * cyan_bound d_cyan_bound/dt = + k_cyan_free_bound * cyan_free - k_cyan_bound_free * cyan_bound d_JCZ38/dt = + f_cyan_free_to_JCZ38 * k_cyan_free * cyan_free - k_JCZ38 * JCZ38 + f_JSE76_to_JCZ38 * k_JSE76 * JSE76 d_J9Z38/dt = + f_cyan_free_to_J9Z38 * k_cyan_free * cyan_free - k_J9Z38 * J9Z38 d_JSE76/dt = + f_JCZ38_to_JSE76 * k_JCZ38 * JCZ38 - k_JSE76 * JSE76 Data: 433 observations of 4 variable(s) grouped in 5 datasets Model predictions using solution type deSolve Fitted in 713.14 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function Starting values for degradation parameters: cyan_free_0 log_k_cyan_free log_k_cyan_free_bound 101.7511 -2.8370 -3.0162 log_k_cyan_bound_free log_k_JCZ38 log_k_J9Z38 -3.6600 -2.2988 -5.3129 log_k_JSE76 f_cyan_ilr_1 f_cyan_ilr_2 -3.6991 0.6722 4.8596 f_JCZ38_qlogis f_JSE76_qlogis 13.4678 14.2149 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): cyan_free_0 log_k_cyan_free log_k_cyan_free_bound cyan_free_0 5.629 0.000 0.000 log_k_cyan_free 0.000 0.446 0.000 log_k_cyan_free_bound 0.000 0.000 1.449 log_k_cyan_bound_free 0.000 0.000 0.000 log_k_JCZ38 0.000 0.000 0.000 log_k_J9Z38 0.000 0.000 0.000 log_k_JSE76 0.000 0.000 0.000 f_cyan_ilr_1 0.000 0.000 0.000 f_cyan_ilr_2 0.000 0.000 0.000 f_JCZ38_qlogis 0.000 0.000 0.000 f_JSE76_qlogis 0.000 0.000 0.000 log_k_cyan_bound_free log_k_JCZ38 log_k_J9Z38 log_k_JSE76 cyan_free_0 0.000 0.0000 0.000 0.0000 log_k_cyan_free 0.000 0.0000 0.000 0.0000 log_k_cyan_free_bound 0.000 0.0000 0.000 0.0000 log_k_cyan_bound_free 1.213 0.0000 0.000 0.0000 log_k_JCZ38 0.000 0.7801 0.000 0.0000 log_k_J9Z38 0.000 0.0000 1.575 0.0000 log_k_JSE76 0.000 0.0000 0.000 0.8078 f_cyan_ilr_1 0.000 0.0000 0.000 0.0000 f_cyan_ilr_2 0.000 0.0000 0.000 0.0000 f_JCZ38_qlogis 0.000 0.0000 0.000 0.0000 f_JSE76_qlogis 0.000 0.0000 0.000 0.0000 f_cyan_ilr_1 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis cyan_free_0 0.0000 0.000 0.00 0.00 log_k_cyan_free 0.0000 0.000 0.00 0.00 log_k_cyan_free_bound 0.0000 0.000 0.00 0.00 log_k_cyan_bound_free 0.0000 0.000 0.00 0.00 log_k_JCZ38 0.0000 0.000 0.00 0.00 log_k_J9Z38 0.0000 0.000 0.00 0.00 log_k_JSE76 0.0000 0.000 0.00 0.00 f_cyan_ilr_1 0.6518 0.000 0.00 0.00 f_cyan_ilr_2 0.0000 9.981 0.00 0.00 f_JCZ38_qlogis 0.0000 0.000 14.26 0.00 f_JSE76_qlogis 0.0000 0.000 0.00 16.17 Starting values for error model parameters: a.1 b.1 1 1 Results: Likelihood computed by importance sampling AIC BIC logLik 2240 2231 -1098 Optimised parameters: est. lower upper cyan_free_0 100.73014 9.873e+01 1.027e+02 log_k_cyan_free -3.19634 -3.641e+00 -2.752e+00 log_k_cyan_free_bound -3.43533 -3.674e+00 -3.197e+00 log_k_cyan_bound_free -3.83282 -4.163e+00 -3.503e+00 log_k_JCZ38 -2.51065 -3.225e+00 -1.796e+00 log_k_J9Z38 -5.02539 -5.825e+00 -4.226e+00 log_k_JSE76 -3.24777 -4.163e+00 -2.333e+00 f_cyan_ilr_1 0.70640 3.562e-01 1.057e+00 f_cyan_ilr_2 1.42704 3.170e-01 2.537e+00 f_JCZ38_qlogis 2.84779 1.042e+00 4.654e+00 f_JSE76_qlogis 8.63674 -6.407e+02 6.580e+02 a.1 2.07082 1.846e+00 2.296e+00 b.1 0.06227 5.120e-02 7.334e-02 SD.log_k_cyan_free 0.49674 1.865e-01 8.069e-01 SD.log_k_cyan_bound_free 0.28537 6.808e-02 5.027e-01 SD.log_k_JCZ38 0.74846 2.305e-01 1.266e+00 SD.log_k_J9Z38 0.86077 2.713e-01 1.450e+00 SD.log_k_JSE76 0.97613 3.030e-01 1.649e+00 SD.f_cyan_ilr_1 0.38994 1.382e-01 6.417e-01 SD.f_cyan_ilr_2 0.82869 3.917e-02 1.618e+00 SD.f_JCZ38_qlogis 1.05000 -2.809e-02 2.128e+00 SD.f_JSE76_qlogis 0.44681 -3.986e+05 3.986e+05 Correlation: cyn_f_0 lg_k_c_ lg_k_cyn_f_ lg_k_cyn_b_ l__JCZ3 l__J9Z3 log_k_cyan_free 0.0936 log_k_cyan_free_bound 0.1302 0.1627 log_k_cyan_bound_free 0.0029 0.0525 0.5181 log_k_JCZ38 -0.0116 -0.0077 -0.0430 -0.0236 log_k_J9Z38 -0.0192 -0.0077 -0.0048 0.0229 -0.0005 log_k_JSE76 0.0007 -0.0020 -0.0134 -0.0072 0.1225 -0.0016 f_cyan_ilr_1 -0.0118 -0.0027 -0.0132 -0.0118 0.0127 -0.0505 f_cyan_ilr_2 -0.4643 -0.0762 -0.1245 0.0137 0.0497 0.1003 f_JCZ38_qlogis 0.0710 0.0371 0.1826 0.0925 -0.0869 -0.0130 f_JSE76_qlogis -0.0367 -0.0270 -0.2274 -0.1865 0.1244 0.0098 l__JSE7 f_cy__1 f_cy__2 f_JCZ38 log_k_cyan_free log_k_cyan_free_bound log_k_cyan_bound_free log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 0.0036 f_cyan_ilr_2 0.0050 -0.0201 f_JCZ38_qlogis 0.0142 -0.0529 -0.2698 f_JSE76_qlogis 0.0064 0.0345 0.2015 -0.7058 Random effects: est. lower upper SD.log_k_cyan_free 0.4967 1.865e-01 8.069e-01 SD.log_k_cyan_bound_free 0.2854 6.808e-02 5.027e-01 SD.log_k_JCZ38 0.7485 2.305e-01 1.266e+00 SD.log_k_J9Z38 0.8608 2.713e-01 1.450e+00 SD.log_k_JSE76 0.9761 3.030e-01 1.649e+00 SD.f_cyan_ilr_1 0.3899 1.382e-01 6.417e-01 SD.f_cyan_ilr_2 0.8287 3.917e-02 1.618e+00 SD.f_JCZ38_qlogis 1.0500 -2.809e-02 2.128e+00 SD.f_JSE76_qlogis 0.4468 -3.986e+05 3.986e+05 Variance model: est. lower upper a.1 2.07082 1.8458 2.29588 b.1 0.06227 0.0512 0.07334 Backtransformed parameters: est. lower upper cyan_free_0 1.007e+02 9.873e+01 102.72898 k_cyan_free 4.091e-02 2.623e-02 0.06382 k_cyan_free_bound 3.221e-02 2.537e-02 0.04090 k_cyan_bound_free 2.165e-02 1.557e-02 0.03011 k_JCZ38 8.122e-02 3.975e-02 0.16594 k_J9Z38 6.569e-03 2.954e-03 0.01461 k_JSE76 3.886e-02 1.556e-02 0.09703 f_cyan_free_to_JCZ38 6.785e-01 6.102e-01 0.97309 f_cyan_free_to_J9Z38 2.498e-01 6.102e-01 0.97309 f_JCZ38_to_JSE76 9.452e-01 7.392e-01 0.99056 f_JSE76_to_JCZ38 9.998e-01 5.580e-279 1.00000 Estimated Eigenvalues of SFORB model(s): cyan_b1 cyan_b2 cyan_g 0.08426 0.01051 0.41220 Resulting formation fractions: ff cyan_free_JCZ38 0.6784541 cyan_free_J9Z38 0.2498405 cyan_free_sink 0.0717054 cyan_free 1.0000000 JCZ38_JSE76 0.9452043 JCZ38_sink 0.0547957 JSE76_JCZ38 0.9998226 JSE76_sink 0.0001774 Estimated disappearance times: DT50 DT90 DT50back DT50_cyan_b1 DT50_cyan_b2 cyan 25.237 168.51 50.73 8.226 65.95 JCZ38 8.535 28.35 NA NA NA J9Z38 105.517 350.52 NA NA NA JSE76 17.837 59.25 NA NA NA"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_cyan_pathway.html","id":"pathway-2-refined-fits","dir":"Articles > Prebuilt","previous_headings":"Appendix > Hierarchical fit listings","what":"Pathway 2, refined fits","title":"Testing hierarchical pathway kinetics with residue data on cyantraniliprole","text":"Hierarchical FOMC path 2 fit reduced random effects, two-component error Hierarchical DFOP path 2 fit reduced random effects, constant variance Hierarchical DFOP path 2 fit reduced random effects, two-component error Hierarchical SFORB path 2 fit reduced random effects, constant variance Hierarchical SFORB path 2 fit reduced random effects, two-component error","code":"saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 R version used for fitting: 4.3.2 Date of fit: Thu Nov 16 04:57:07 2023 Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - (alpha/beta) * 1/((time/beta) + 1) * cyan d_JCZ38/dt = + f_cyan_to_JCZ38 * (alpha/beta) * 1/((time/beta) + 1) * cyan - k_JCZ38 * JCZ38 + f_JSE76_to_JCZ38 * k_JSE76 * JSE76 d_J9Z38/dt = + f_cyan_to_J9Z38 * (alpha/beta) * 1/((time/beta) + 1) * cyan - k_J9Z38 * J9Z38 d_JSE76/dt = + f_JCZ38_to_JSE76 * k_JCZ38 * JCZ38 - k_JSE76 * JSE76 Data: 433 observations of 4 variable(s) grouped in 5 datasets Model predictions using solution type deSolve Fitted in 776.732 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function Starting values for degradation parameters: cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 102.4477 -1.8631 -5.1087 -2.5114 0.6826 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_alpha log_beta 4.7944 15.9616 13.1566 -0.1564 2.9781 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 cyan_0 7.701 0.000 0.000 0.000 0.0000 log_k_JCZ38 0.000 1.448 0.000 0.000 0.0000 log_k_J9Z38 0.000 0.000 1.724 0.000 0.0000 log_k_JSE76 0.000 0.000 0.000 3.659 0.0000 f_cyan_ilr_1 0.000 0.000 0.000 0.000 0.6356 f_cyan_ilr_2 0.000 0.000 0.000 0.000 0.0000 f_JCZ38_qlogis 0.000 0.000 0.000 0.000 0.0000 f_JSE76_qlogis 0.000 0.000 0.000 0.000 0.0000 log_alpha 0.000 0.000 0.000 0.000 0.0000 log_beta 0.000 0.000 0.000 0.000 0.0000 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_alpha log_beta cyan_0 0.00 0.00 0.00 0.0000 0.0000 log_k_JCZ38 0.00 0.00 0.00 0.0000 0.0000 log_k_J9Z38 0.00 0.00 0.00 0.0000 0.0000 log_k_JSE76 0.00 0.00 0.00 0.0000 0.0000 f_cyan_ilr_1 0.00 0.00 0.00 0.0000 0.0000 f_cyan_ilr_2 10.32 0.00 0.00 0.0000 0.0000 f_JCZ38_qlogis 0.00 12.23 0.00 0.0000 0.0000 f_JSE76_qlogis 0.00 0.00 14.99 0.0000 0.0000 log_alpha 0.00 0.00 0.00 0.3924 0.0000 log_beta 0.00 0.00 0.00 0.0000 0.5639 Starting values for error model parameters: a.1 b.1 1 1 Results: Likelihood computed by importance sampling AIC BIC logLik 2249 2242 -1106 Optimised parameters: est. lower upper cyan_0 101.24524 NA NA log_k_JCZ38 -2.85375 NA NA log_k_J9Z38 -5.07729 NA NA log_k_JSE76 -3.53511 NA NA f_cyan_ilr_1 0.67478 NA NA f_cyan_ilr_2 0.97152 NA NA f_JCZ38_qlogis 213.48001 NA NA f_JSE76_qlogis 2.02040 NA NA log_alpha -0.11041 NA NA log_beta 3.06575 NA NA a.1 2.05279 1.82393 2.28166 b.1 0.07116 0.05910 0.08322 SD.log_k_JCZ38 1.21713 0.44160 1.99266 SD.log_k_J9Z38 0.88268 0.27541 1.48995 SD.log_k_JSE76 0.59452 0.15005 1.03898 SD.f_cyan_ilr_1 0.35370 0.12409 0.58331 SD.f_cyan_ilr_2 0.78186 0.18547 1.37824 SD.log_alpha 0.27781 0.08168 0.47394 SD.log_beta 0.32608 0.06490 0.58726 Correlation is not available Random effects: est. lower upper SD.log_k_JCZ38 1.2171 0.44160 1.9927 SD.log_k_J9Z38 0.8827 0.27541 1.4900 SD.log_k_JSE76 0.5945 0.15005 1.0390 SD.f_cyan_ilr_1 0.3537 0.12409 0.5833 SD.f_cyan_ilr_2 0.7819 0.18547 1.3782 SD.log_alpha 0.2778 0.08168 0.4739 SD.log_beta 0.3261 0.06490 0.5873 Variance model: est. lower upper a.1 2.05279 1.8239 2.28166 b.1 0.07116 0.0591 0.08322 Backtransformed parameters: est. lower upper cyan_0 1.012e+02 NA NA k_JCZ38 5.763e-02 NA NA k_J9Z38 6.237e-03 NA NA k_JSE76 2.916e-02 NA NA f_cyan_to_JCZ38 6.354e-01 NA NA f_cyan_to_J9Z38 2.447e-01 NA NA f_JCZ38_to_JSE76 1.000e+00 NA NA f_JSE76_to_JCZ38 8.829e-01 NA NA alpha 8.955e-01 NA NA beta 2.145e+01 NA NA Resulting formation fractions: ff cyan_JCZ38 0.6354 cyan_J9Z38 0.2447 cyan_sink 0.1200 JCZ38_JSE76 1.0000 JCZ38_sink 0.0000 JSE76_JCZ38 0.8829 JSE76_sink 0.1171 Estimated disappearance times: DT50 DT90 DT50back cyan 25.07 259.21 78.03 JCZ38 12.03 39.96 NA J9Z38 111.14 369.19 NA JSE76 23.77 78.98 NA saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 R version used for fitting: 4.3.2 Date of fit: Thu Nov 16 04:58:51 2023 Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * cyan d_JCZ38/dt = + f_cyan_to_JCZ38 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * cyan - k_JCZ38 * JCZ38 + f_JSE76_to_JCZ38 * k_JSE76 * JSE76 d_J9Z38/dt = + f_cyan_to_J9Z38 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * cyan - k_J9Z38 * J9Z38 d_JSE76/dt = + f_JCZ38_to_JSE76 * k_JCZ38 * JCZ38 - k_JSE76 * JSE76 Data: 433 observations of 4 variable(s) grouped in 5 datasets Model predictions using solution type deSolve Fitted in 880.94 s Using 300, 100 iterations and 10 chains Variance model: Constant variance Starting values for degradation parameters: cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 102.4380 -2.3107 -5.3123 -3.7120 0.6757 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_k1 log_k2 1.1439 13.1194 12.3492 -1.9317 -4.4557 g_qlogis -0.5644 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 cyan_0 4.591 0.0000 0.000 0.0 0.0000 log_k_JCZ38 0.000 0.7966 0.000 0.0 0.0000 log_k_J9Z38 0.000 0.0000 1.561 0.0 0.0000 log_k_JSE76 0.000 0.0000 0.000 0.8 0.0000 f_cyan_ilr_1 0.000 0.0000 0.000 0.0 0.6349 f_cyan_ilr_2 0.000 0.0000 0.000 0.0 0.0000 f_JCZ38_qlogis 0.000 0.0000 0.000 0.0 0.0000 f_JSE76_qlogis 0.000 0.0000 0.000 0.0 0.0000 log_k1 0.000 0.0000 0.000 0.0 0.0000 log_k2 0.000 0.0000 0.000 0.0 0.0000 g_qlogis 0.000 0.0000 0.000 0.0 0.0000 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_k1 log_k2 cyan_0 0.000 0.00 0.00 0.000 0.0000 log_k_JCZ38 0.000 0.00 0.00 0.000 0.0000 log_k_J9Z38 0.000 0.00 0.00 0.000 0.0000 log_k_JSE76 0.000 0.00 0.00 0.000 0.0000 f_cyan_ilr_1 0.000 0.00 0.00 0.000 0.0000 f_cyan_ilr_2 1.797 0.00 0.00 0.000 0.0000 f_JCZ38_qlogis 0.000 13.86 0.00 0.000 0.0000 f_JSE76_qlogis 0.000 0.00 13.91 0.000 0.0000 log_k1 0.000 0.00 0.00 1.106 0.0000 log_k2 0.000 0.00 0.00 0.000 0.6141 g_qlogis 0.000 0.00 0.00 0.000 0.0000 g_qlogis cyan_0 0.000 log_k_JCZ38 0.000 log_k_J9Z38 0.000 log_k_JSE76 0.000 f_cyan_ilr_1 0.000 f_cyan_ilr_2 0.000 f_JCZ38_qlogis 0.000 f_JSE76_qlogis 0.000 log_k1 0.000 log_k2 0.000 g_qlogis 1.595 Starting values for error model parameters: a.1 1 Results: Likelihood computed by importance sampling AIC BIC logLik 2282 2274 -1121 Optimised parameters: est. lower upper cyan_0 102.6036 NA NA log_k_JCZ38 -2.9348 NA NA log_k_J9Z38 -5.1617 NA NA log_k_JSE76 -3.6396 NA NA f_cyan_ilr_1 0.6991 NA NA f_cyan_ilr_2 0.6341 NA NA f_JCZ38_qlogis 4232.3011 NA NA f_JSE76_qlogis 1.9658 NA NA log_k1 -1.9503 NA NA log_k2 -4.4745 NA NA g_qlogis -0.4967 NA NA a.1 2.7461 2.59274 2.8994 SD.log_k_JCZ38 1.3178 0.47602 2.1596 SD.log_k_J9Z38 0.7022 0.15061 1.2538 SD.log_k_JSE76 0.6566 0.15613 1.1570 SD.f_cyan_ilr_1 0.3409 0.11666 0.5652 SD.f_cyan_ilr_2 0.4385 0.09482 0.7821 SD.log_k1 0.7381 0.25599 1.2202 SD.log_k2 0.5133 0.18152 0.8450 SD.g_qlogis 0.9866 0.35681 1.6164 Correlation is not available Random effects: est. lower upper SD.log_k_JCZ38 1.3178 0.47602 2.1596 SD.log_k_J9Z38 0.7022 0.15061 1.2538 SD.log_k_JSE76 0.6566 0.15613 1.1570 SD.f_cyan_ilr_1 0.3409 0.11666 0.5652 SD.f_cyan_ilr_2 0.4385 0.09482 0.7821 SD.log_k1 0.7381 0.25599 1.2202 SD.log_k2 0.5133 0.18152 0.8450 SD.g_qlogis 0.9866 0.35681 1.6164 Variance model: est. lower upper a.1 2.746 2.593 2.899 Backtransformed parameters: est. lower upper cyan_0 1.026e+02 NA NA k_JCZ38 5.314e-02 NA NA k_J9Z38 5.732e-03 NA NA k_JSE76 2.626e-02 NA NA f_cyan_to_JCZ38 6.051e-01 NA NA f_cyan_to_J9Z38 2.251e-01 NA NA f_JCZ38_to_JSE76 1.000e+00 NA NA f_JSE76_to_JCZ38 8.772e-01 NA NA k1 1.422e-01 NA NA k2 1.140e-02 NA NA g 3.783e-01 NA NA Resulting formation fractions: ff cyan_JCZ38 0.6051 cyan_J9Z38 0.2251 cyan_sink 0.1698 JCZ38_JSE76 1.0000 JCZ38_sink 0.0000 JSE76_JCZ38 0.8772 JSE76_sink 0.1228 Estimated disappearance times: DT50 DT90 DT50back DT50_k1 DT50_k2 cyan 22.05 160.35 48.27 4.873 60.83 JCZ38 13.04 43.33 NA NA NA J9Z38 120.93 401.73 NA NA NA JSE76 26.39 87.68 NA NA NA saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 R version used for fitting: 4.3.2 Date of fit: Thu Nov 16 04:58:58 2023 Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * cyan d_JCZ38/dt = + f_cyan_to_JCZ38 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * cyan - k_JCZ38 * JCZ38 + f_JSE76_to_JCZ38 * k_JSE76 * JSE76 d_J9Z38/dt = + f_cyan_to_J9Z38 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * cyan - k_J9Z38 * J9Z38 d_JSE76/dt = + f_JCZ38_to_JSE76 * k_JCZ38 * JCZ38 - k_JSE76 * JSE76 Data: 433 observations of 4 variable(s) grouped in 5 datasets Model predictions using solution type deSolve Fitted in 887.853 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function Starting values for degradation parameters: cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 101.7393 -1.4493 -5.0118 -2.1269 0.6720 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_k1 log_k2 7.3362 13.4423 13.2659 -2.0061 -4.5527 g_qlogis -0.5806 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): cyan_0 log_k_JCZ38 log_k_J9Z38 log_k_JSE76 f_cyan_ilr_1 cyan_0 5.604 0.00 0.000 0.000 0.0000 log_k_JCZ38 0.000 2.77 0.000 0.000 0.0000 log_k_J9Z38 0.000 0.00 1.662 0.000 0.0000 log_k_JSE76 0.000 0.00 0.000 5.021 0.0000 f_cyan_ilr_1 0.000 0.00 0.000 0.000 0.6519 f_cyan_ilr_2 0.000 0.00 0.000 0.000 0.0000 f_JCZ38_qlogis 0.000 0.00 0.000 0.000 0.0000 f_JSE76_qlogis 0.000 0.00 0.000 0.000 0.0000 log_k1 0.000 0.00 0.000 0.000 0.0000 log_k2 0.000 0.00 0.000 0.000 0.0000 g_qlogis 0.000 0.00 0.000 0.000 0.0000 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis log_k1 log_k2 cyan_0 0.00 0.00 0.00 0.0000 0.0000 log_k_JCZ38 0.00 0.00 0.00 0.0000 0.0000 log_k_J9Z38 0.00 0.00 0.00 0.0000 0.0000 log_k_JSE76 0.00 0.00 0.00 0.0000 0.0000 f_cyan_ilr_1 0.00 0.00 0.00 0.0000 0.0000 f_cyan_ilr_2 13.37 0.00 0.00 0.0000 0.0000 f_JCZ38_qlogis 0.00 14.21 0.00 0.0000 0.0000 f_JSE76_qlogis 0.00 0.00 14.58 0.0000 0.0000 log_k1 0.00 0.00 0.00 0.8453 0.0000 log_k2 0.00 0.00 0.00 0.0000 0.5969 g_qlogis 0.00 0.00 0.00 0.0000 0.0000 g_qlogis cyan_0 0.00 log_k_JCZ38 0.00 log_k_J9Z38 0.00 log_k_JSE76 0.00 f_cyan_ilr_1 0.00 f_cyan_ilr_2 0.00 f_JCZ38_qlogis 0.00 f_JSE76_qlogis 0.00 log_k1 0.00 log_k2 0.00 g_qlogis 1.69 Starting values for error model parameters: a.1 b.1 1 1 Results: Likelihood computed by importance sampling AIC BIC logLik 2237 2229 -1099 Optimised parameters: est. lower upper cyan_0 101.00243 NA NA log_k_JCZ38 -2.80828 NA NA log_k_J9Z38 -5.04449 NA NA log_k_JSE76 -3.66981 NA NA f_cyan_ilr_1 0.72564 NA NA f_cyan_ilr_2 1.37978 NA NA f_JCZ38_qlogis 1.98726 NA NA f_JSE76_qlogis 414.80884 NA NA log_k1 -2.38601 NA NA log_k2 -4.63632 NA NA g_qlogis -0.33920 NA NA a.1 2.10837 1.88051 2.33623 b.1 0.06223 0.05108 0.07338 SD.log_k_JCZ38 1.30902 0.48128 2.13675 SD.log_k_J9Z38 0.83882 0.25790 1.41974 SD.log_k_JSE76 0.58104 0.14201 1.02008 SD.f_cyan_ilr_1 0.35421 0.12398 0.58443 SD.f_cyan_ilr_2 0.79373 0.12007 1.46740 SD.log_k2 0.27476 0.08557 0.46394 SD.g_qlogis 0.96170 0.35463 1.56878 Correlation is not available Random effects: est. lower upper SD.log_k_JCZ38 1.3090 0.48128 2.1367 SD.log_k_J9Z38 0.8388 0.25790 1.4197 SD.log_k_JSE76 0.5810 0.14201 1.0201 SD.f_cyan_ilr_1 0.3542 0.12398 0.5844 SD.f_cyan_ilr_2 0.7937 0.12007 1.4674 SD.log_k2 0.2748 0.08557 0.4639 SD.g_qlogis 0.9617 0.35463 1.5688 Variance model: est. lower upper a.1 2.10837 1.88051 2.33623 b.1 0.06223 0.05108 0.07338 Backtransformed parameters: est. lower upper cyan_0 1.010e+02 NA NA k_JCZ38 6.031e-02 NA NA k_J9Z38 6.445e-03 NA NA k_JSE76 2.548e-02 NA NA f_cyan_to_JCZ38 6.808e-01 NA NA f_cyan_to_J9Z38 2.440e-01 NA NA f_JCZ38_to_JSE76 8.795e-01 NA NA f_JSE76_to_JCZ38 1.000e+00 NA NA k1 9.200e-02 NA NA k2 9.693e-03 NA NA g 4.160e-01 NA NA Resulting formation fractions: ff cyan_JCZ38 0.68081 cyan_J9Z38 0.24398 cyan_sink 0.07521 JCZ38_JSE76 0.87945 JCZ38_sink 0.12055 JSE76_JCZ38 1.00000 JSE76_sink 0.00000 Estimated disappearance times: DT50 DT90 DT50back DT50_k1 DT50_k2 cyan 25.00 182.05 54.8 7.535 71.51 JCZ38 11.49 38.18 NA NA NA J9Z38 107.55 357.28 NA NA NA JSE76 27.20 90.36 NA NA NA saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 R version used for fitting: 4.3.2 Date of fit: Thu Nov 16 04:58:49 2023 Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * cyan_free + k_cyan_bound_free * cyan_bound d_cyan_bound/dt = + k_cyan_free_bound * cyan_free - k_cyan_bound_free * cyan_bound d_JCZ38/dt = + f_cyan_free_to_JCZ38 * k_cyan_free * cyan_free - k_JCZ38 * JCZ38 + f_JSE76_to_JCZ38 * k_JSE76 * JSE76 d_J9Z38/dt = + f_cyan_free_to_J9Z38 * k_cyan_free * cyan_free - k_J9Z38 * J9Z38 d_JSE76/dt = + f_JCZ38_to_JSE76 * k_JCZ38 * JCZ38 - k_JSE76 * JSE76 Data: 433 observations of 4 variable(s) grouped in 5 datasets Model predictions using solution type deSolve Fitted in 878.878 s Using 300, 100 iterations and 10 chains Variance model: Constant variance Starting values for degradation parameters: cyan_free_0 log_k_cyan_free log_k_cyan_free_bound 102.4395 -2.7673 -2.8942 log_k_cyan_bound_free log_k_JCZ38 log_k_J9Z38 -3.6201 -2.3107 -5.3123 log_k_JSE76 f_cyan_ilr_1 f_cyan_ilr_2 -3.7120 0.6754 1.1448 f_JCZ38_qlogis f_JSE76_qlogis 14.8408 15.4734 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): cyan_free_0 log_k_cyan_free log_k_cyan_free_bound cyan_free_0 4.589 0.0000 0.00 log_k_cyan_free 0.000 0.4849 0.00 log_k_cyan_free_bound 0.000 0.0000 1.62 log_k_cyan_bound_free 0.000 0.0000 0.00 log_k_JCZ38 0.000 0.0000 0.00 log_k_J9Z38 0.000 0.0000 0.00 log_k_JSE76 0.000 0.0000 0.00 f_cyan_ilr_1 0.000 0.0000 0.00 f_cyan_ilr_2 0.000 0.0000 0.00 f_JCZ38_qlogis 0.000 0.0000 0.00 f_JSE76_qlogis 0.000 0.0000 0.00 log_k_cyan_bound_free log_k_JCZ38 log_k_J9Z38 log_k_JSE76 cyan_free_0 0.000 0.0000 0.000 0.0 log_k_cyan_free 0.000 0.0000 0.000 0.0 log_k_cyan_free_bound 0.000 0.0000 0.000 0.0 log_k_cyan_bound_free 1.197 0.0000 0.000 0.0 log_k_JCZ38 0.000 0.7966 0.000 0.0 log_k_J9Z38 0.000 0.0000 1.561 0.0 log_k_JSE76 0.000 0.0000 0.000 0.8 f_cyan_ilr_1 0.000 0.0000 0.000 0.0 f_cyan_ilr_2 0.000 0.0000 0.000 0.0 f_JCZ38_qlogis 0.000 0.0000 0.000 0.0 f_JSE76_qlogis 0.000 0.0000 0.000 0.0 f_cyan_ilr_1 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis cyan_free_0 0.0000 0.000 0.0 0.00 log_k_cyan_free 0.0000 0.000 0.0 0.00 log_k_cyan_free_bound 0.0000 0.000 0.0 0.00 log_k_cyan_bound_free 0.0000 0.000 0.0 0.00 log_k_JCZ38 0.0000 0.000 0.0 0.00 log_k_J9Z38 0.0000 0.000 0.0 0.00 log_k_JSE76 0.0000 0.000 0.0 0.00 f_cyan_ilr_1 0.6349 0.000 0.0 0.00 f_cyan_ilr_2 0.0000 1.797 0.0 0.00 f_JCZ38_qlogis 0.0000 0.000 15.6 0.00 f_JSE76_qlogis 0.0000 0.000 0.0 17.52 Starting values for error model parameters: a.1 1 Results: Likelihood computed by importance sampling AIC BIC logLik 2280 2272 -1120 Optimised parameters: est. lower upper cyan_free_0 102.6532 NA NA log_k_cyan_free -2.8547 NA NA log_k_cyan_free_bound -2.7004 NA NA log_k_cyan_bound_free -3.5078 NA NA log_k_JCZ38 -2.9255 NA NA log_k_J9Z38 -5.1089 NA NA log_k_JSE76 -3.6263 NA NA f_cyan_ilr_1 0.6873 NA NA f_cyan_ilr_2 0.6498 NA NA f_JCZ38_qlogis 3624.2149 NA NA f_JSE76_qlogis 1.9991 NA NA a.1 2.7472 2.55559 2.9388 SD.log_k_cyan_free 0.3227 0.10296 0.5423 SD.log_k_cyan_free_bound 0.8757 0.29525 1.4562 SD.log_k_cyan_bound_free 0.6128 0.20220 1.0233 SD.log_k_JCZ38 1.3431 0.48474 2.2014 SD.log_k_J9Z38 0.6881 0.14714 1.2291 SD.log_k_JSE76 0.6461 0.15321 1.1390 SD.f_cyan_ilr_1 0.3361 0.11376 0.5585 SD.f_cyan_ilr_2 0.4286 0.08419 0.7730 Correlation is not available Random effects: est. lower upper SD.log_k_cyan_free 0.3227 0.10296 0.5423 SD.log_k_cyan_free_bound 0.8757 0.29525 1.4562 SD.log_k_cyan_bound_free 0.6128 0.20220 1.0233 SD.log_k_JCZ38 1.3431 0.48474 2.2014 SD.log_k_J9Z38 0.6881 0.14714 1.2291 SD.log_k_JSE76 0.6461 0.15321 1.1390 SD.f_cyan_ilr_1 0.3361 0.11376 0.5585 SD.f_cyan_ilr_2 0.4286 0.08419 0.7730 Variance model: est. lower upper a.1 2.747 2.556 2.939 Backtransformed parameters: est. lower upper cyan_free_0 1.027e+02 NA NA k_cyan_free 5.758e-02 NA NA k_cyan_free_bound 6.718e-02 NA NA k_cyan_bound_free 2.996e-02 NA NA k_JCZ38 5.364e-02 NA NA k_J9Z38 6.042e-03 NA NA k_JSE76 2.662e-02 NA NA f_cyan_free_to_JCZ38 6.039e-01 NA NA f_cyan_free_to_J9Z38 2.285e-01 NA NA f_JCZ38_to_JSE76 1.000e+00 NA NA f_JSE76_to_JCZ38 8.807e-01 NA NA Estimated Eigenvalues of SFORB model(s): cyan_b1 cyan_b2 cyan_g 0.1426 0.0121 0.3484 Resulting formation fractions: ff cyan_free_JCZ38 0.6039 cyan_free_J9Z38 0.2285 cyan_free_sink 0.1676 cyan_free 1.0000 JCZ38_JSE76 1.0000 JCZ38_sink 0.0000 JSE76_JCZ38 0.8807 JSE76_sink 0.1193 Estimated disappearance times: DT50 DT90 DT50back DT50_cyan_b1 DT50_cyan_b2 cyan 23.84 154.95 46.65 4.86 57.31 JCZ38 12.92 42.93 NA NA NA J9Z38 114.71 381.07 NA NA NA JSE76 26.04 86.51 NA NA NA saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 R version used for fitting: 4.3.2 Date of fit: Thu Nov 16 04:59:10 2023 Date of summary: Thu Nov 16 04:59:11 2023 Equations: d_cyan_free/dt = - k_cyan_free * cyan_free - k_cyan_free_bound * cyan_free + k_cyan_bound_free * cyan_bound d_cyan_bound/dt = + k_cyan_free_bound * cyan_free - k_cyan_bound_free * cyan_bound d_JCZ38/dt = + f_cyan_free_to_JCZ38 * k_cyan_free * cyan_free - k_JCZ38 * JCZ38 + f_JSE76_to_JCZ38 * k_JSE76 * JSE76 d_J9Z38/dt = + f_cyan_free_to_J9Z38 * k_cyan_free * cyan_free - k_J9Z38 * J9Z38 d_JSE76/dt = + f_JCZ38_to_JSE76 * k_JCZ38 * JCZ38 - k_JSE76 * JSE76 Data: 433 observations of 4 variable(s) grouped in 5 datasets Model predictions using solution type deSolve Fitted in 899.539 s Using 300, 100 iterations and 10 chains Variance model: Two-component variance function Starting values for degradation parameters: cyan_free_0 log_k_cyan_free log_k_cyan_free_bound 101.7511 -2.8370 -3.0162 log_k_cyan_bound_free log_k_JCZ38 log_k_J9Z38 -3.6600 -2.2988 -5.3129 log_k_JSE76 f_cyan_ilr_1 f_cyan_ilr_2 -3.6991 0.6722 4.8596 f_JCZ38_qlogis f_JSE76_qlogis 13.4678 14.2149 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): cyan_free_0 log_k_cyan_free log_k_cyan_free_bound cyan_free_0 5.629 0.000 0.000 log_k_cyan_free 0.000 0.446 0.000 log_k_cyan_free_bound 0.000 0.000 1.449 log_k_cyan_bound_free 0.000 0.000 0.000 log_k_JCZ38 0.000 0.000 0.000 log_k_J9Z38 0.000 0.000 0.000 log_k_JSE76 0.000 0.000 0.000 f_cyan_ilr_1 0.000 0.000 0.000 f_cyan_ilr_2 0.000 0.000 0.000 f_JCZ38_qlogis 0.000 0.000 0.000 f_JSE76_qlogis 0.000 0.000 0.000 log_k_cyan_bound_free log_k_JCZ38 log_k_J9Z38 log_k_JSE76 cyan_free_0 0.000 0.0000 0.000 0.0000 log_k_cyan_free 0.000 0.0000 0.000 0.0000 log_k_cyan_free_bound 0.000 0.0000 0.000 0.0000 log_k_cyan_bound_free 1.213 0.0000 0.000 0.0000 log_k_JCZ38 0.000 0.7801 0.000 0.0000 log_k_J9Z38 0.000 0.0000 1.575 0.0000 log_k_JSE76 0.000 0.0000 0.000 0.8078 f_cyan_ilr_1 0.000 0.0000 0.000 0.0000 f_cyan_ilr_2 0.000 0.0000 0.000 0.0000 f_JCZ38_qlogis 0.000 0.0000 0.000 0.0000 f_JSE76_qlogis 0.000 0.0000 0.000 0.0000 f_cyan_ilr_1 f_cyan_ilr_2 f_JCZ38_qlogis f_JSE76_qlogis cyan_free_0 0.0000 0.000 0.00 0.00 log_k_cyan_free 0.0000 0.000 0.00 0.00 log_k_cyan_free_bound 0.0000 0.000 0.00 0.00 log_k_cyan_bound_free 0.0000 0.000 0.00 0.00 log_k_JCZ38 0.0000 0.000 0.00 0.00 log_k_J9Z38 0.0000 0.000 0.00 0.00 log_k_JSE76 0.0000 0.000 0.00 0.00 f_cyan_ilr_1 0.6518 0.000 0.00 0.00 f_cyan_ilr_2 0.0000 9.981 0.00 0.00 f_JCZ38_qlogis 0.0000 0.000 14.26 0.00 f_JSE76_qlogis 0.0000 0.000 0.00 16.17 Starting values for error model parameters: a.1 b.1 1 1 Results: Likelihood computed by importance sampling AIC BIC logLik 2241 2233 -1101 Optimised parameters: est. lower upper cyan_free_0 100.95469 NA NA log_k_cyan_free -3.18706 NA NA log_k_cyan_free_bound -3.38455 NA NA log_k_cyan_bound_free -3.75788 NA NA log_k_JCZ38 -2.77024 NA NA log_k_J9Z38 -5.03665 NA NA log_k_JSE76 -3.60289 NA NA f_cyan_ilr_1 0.72263 NA NA f_cyan_ilr_2 1.45352 NA NA f_JCZ38_qlogis 2.00778 NA NA f_JSE76_qlogis 941.58570 NA NA a.1 2.11130 1.88299 2.33960 b.1 0.06299 0.05176 0.07421 SD.log_k_cyan_free 0.50098 0.18805 0.81390 SD.log_k_cyan_bound_free 0.31671 0.08467 0.54875 SD.log_k_JCZ38 1.25865 0.45932 2.05798 SD.log_k_J9Z38 0.86833 0.27222 1.46444 SD.log_k_JSE76 0.59325 0.14711 1.03940 SD.f_cyan_ilr_1 0.35705 0.12521 0.58890 SD.f_cyan_ilr_2 0.88541 0.13797 1.63286 Correlation is not available Random effects: est. lower upper SD.log_k_cyan_free 0.5010 0.18805 0.8139 SD.log_k_cyan_bound_free 0.3167 0.08467 0.5488 SD.log_k_JCZ38 1.2587 0.45932 2.0580 SD.log_k_J9Z38 0.8683 0.27222 1.4644 SD.log_k_JSE76 0.5933 0.14711 1.0394 SD.f_cyan_ilr_1 0.3571 0.12521 0.5889 SD.f_cyan_ilr_2 0.8854 0.13797 1.6329 Variance model: est. lower upper a.1 2.11130 1.88299 2.33960 b.1 0.06299 0.05176 0.07421 Backtransformed parameters: est. lower upper cyan_free_0 1.010e+02 NA NA k_cyan_free 4.129e-02 NA NA k_cyan_free_bound 3.389e-02 NA NA k_cyan_bound_free 2.333e-02 NA NA k_JCZ38 6.265e-02 NA NA k_J9Z38 6.495e-03 NA NA k_JSE76 2.724e-02 NA NA f_cyan_free_to_JCZ38 6.844e-01 NA NA f_cyan_free_to_J9Z38 2.463e-01 NA NA f_JCZ38_to_JSE76 8.816e-01 NA NA f_JSE76_to_JCZ38 1.000e+00 NA NA Estimated Eigenvalues of SFORB model(s): cyan_b1 cyan_b2 cyan_g 0.08751 0.01101 0.39586 Resulting formation fractions: ff cyan_free_JCZ38 0.68444 cyan_free_J9Z38 0.24633 cyan_free_sink 0.06923 cyan_free 1.00000 JCZ38_JSE76 0.88161 JCZ38_sink 0.11839 JSE76_JCZ38 1.00000 JSE76_sink 0.00000 Estimated disappearance times: DT50 DT90 DT50back DT50_cyan_b1 DT50_cyan_b2 cyan 25.36 163.36 49.18 7.921 62.95 JCZ38 11.06 36.75 NA NA NA J9Z38 106.71 354.49 NA NA NA JSE76 25.44 84.51 NA NA NA"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_cyan_pathway.html","id":"session-info","dir":"Articles > Prebuilt","previous_headings":"Appendix","what":"Session info","title":"Testing hierarchical pathway kinetics with residue data on cyantraniliprole","text":"","code":"R version 4.3.2 (2023-10-31) 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_1.42 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_0.21-8 digest_0.6.31 magrittr_2.0.3 evaluate_0.21 [9] grid_4.3.2 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_4.3.2 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] MASS_7.3-60 ragg_1.2.5 callr_3.7.3 pkgconfig_2.0.3 [49] desc_1.4.2 pkgdown_2.0.7 bslib_0.4.2 pillar_1.9.0 [53] gtable_0.3.3 glue_1.6.2 systemfonts_1.0.4 highr_0.10 [57] xfun_0.39 tibble_3.2.1 lmtest_0.9-40 tidyselect_1.2.0 [61] htmltools_0.5.5 nlme_3.1-163 rmarkdown_2.21 compiler_4.3.2 [65] prettyunits_1.1.1 readxl_1.4.2"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_cyan_pathway.html","id":"hardware-info","dir":"Articles > Prebuilt","previous_headings":"Appendix","what":"Hardware info","title":"Testing hierarchical pathway kinetics with residue data on cyantraniliprole","text":"","code":"CPU model: AMD Ryzen 9 7950X 16-Core Processor MemTotal: 64927712 kB"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_dmta_parent.html","id":"introduction","dir":"Articles > Prebuilt","previous_headings":"","what":"Introduction","title":"Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P","text":"purpose document demonstrate nonlinear hierarchical models (NLHM) based parent degradation models SFO, FOMC, DFOP HS can fitted mkin package. assembled course work package 1.1 Project Number 173340 (Application nonlinear hierarchical models kinetic evaluation chemical degradation data) German Environment Agency carried 2022 2023. mkin package used version 1.2.6. contains test data functions used evaluations. saemix package used backend fitting NLHM, also loaded make convergence plot function available. document processed knitr package, also provides kable function used improve display tabular data R markdown documents. parallel processing, parallel package used.","code":"library(mkin) library(knitr) library(saemix) library(parallel) n_cores <- detectCores() if (Sys.info()[\"sysname\"] == \"Windows\") { cl <- makePSOCKcluster(n_cores) } else { cl <- makeForkCluster(n_cores) }"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_dmta_parent.html","id":"data","dir":"Articles > Prebuilt","previous_headings":"","what":"Data","title":"Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P","text":"test data available mkin package object class mkindsg (mkin dataset group) identifier dimethenamid_2018. following preprocessing steps still necessary: data available enantiomer dimethenamid-P (DMTAP) renamed substance name data racemic mixture dimethenamid (DMTA). reason difference degradation behaviour identified EU risk assessment. data transformation products unnecessary columns discarded observation times dataset multiplied corresponding normalisation factor also available dataset, order make possible describe datasets single set parameters independent temperature Finally, datasets observed soil (Elliot 1 Elliot 2) combined, resulting dimethenamid (DMTA) data six soils. following commented R code performs preprocessing. following tables show 6 datasets. Dataset Calke Dataset Borstel Dataset Flaach Dataset BBA 2.2 Dataset BBA 2.3 Dataset Elliot","code":"# Apply a function to each of the seven datasets in the mkindsg object to create a list dmta_ds <- lapply(1:7, function(i) { ds_i <- dimethenamid_2018$ds[[i]]$data # Get a dataset ds_i[ds_i$name == \"DMTAP\", \"name\"] <- \"DMTA\" # Rename DMTAP to DMTA ds_i <- subset(ds_i, name == \"DMTA\", c(\"name\", \"time\", \"value\")) # Select data ds_i$time <- ds_i$time * dimethenamid_2018$f_time_norm[i] # Normalise time ds_i # Return the dataset }) # Use dataset titles as names for the list elements names(dmta_ds) <- sapply(dimethenamid_2018$ds, function(ds) ds$title) # Combine data for Elliot soil to obtain a named list with six elements dmta_ds[[\"Elliot\"]] <- rbind(dmta_ds[[\"Elliot 1\"]], dmta_ds[[\"Elliot 2\"]]) # dmta_ds[[\"Elliot 1\"]] <- NULL dmta_ds[[\"Elliot 2\"]] <- NULL for (ds_name in names(dmta_ds)) { print(kable(mkin_long_to_wide(dmta_ds[[ds_name]]), caption = paste(\"Dataset\", ds_name), label = paste0(\"tab:\", ds_name), booktabs = TRUE)) cat(\"\\n\\\\clearpage\\n\") }"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_dmta_parent.html","id":"separate-evaluations","dir":"Articles > Prebuilt","previous_headings":"","what":"Separate evaluations","title":"Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P","text":"order obtain suitable starting parameters NLHM fits, separate fits four models data soil generated using mmkin function mkin package. first step, constant variance assumed. Convergence checked status function. table , OK indicates convergence, C indicates failure converge. separate fits constant variance converged, sole exception HS fit BBA 2.2 data. prepare fitting NLHM using two-component error model, separate fits updated assuming two-component error. Using two-component error model, one fit converge constant variance converge, non-SFO fits failed converge.","code":"deg_mods <- c(\"SFO\", \"FOMC\", \"DFOP\", \"HS\") f_sep_const <- mmkin( deg_mods, dmta_ds, error_model = \"const\", quiet = TRUE) status(f_sep_const) |> kable() f_sep_tc <- update(f_sep_const, error_model = \"tc\") status(f_sep_tc) |> kable()"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_dmta_parent.html","id":"hierarchichal-model-fits","dir":"Articles > Prebuilt","previous_headings":"","what":"Hierarchichal model fits","title":"Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P","text":"following code fits eight versions hierarchical models data, using SFO, FOMC, DFOP HS parent compound, using either constant variance two-component error error model. default parameter distribution model mkin allows variation degradation parameters across assumed population soils. words, degradation parameter associated random effect first step. mhmkin function makes possible fit eight versions parallel (given sufficient number computing cores available) save execution time. Convergence plots summaries fits shown appendix. output status function shows fits terminated successfully. AIC BIC values show biphasic models DFOP HS give best fits. DFOP model preferred , better mechanistic basis batch experiments constant incubation conditions. Also, shows lowest AIC BIC values first set fits combined two-component error model. Therefore, DFOP model selected refinements fits aim make model fully identifiable.","code":"f_saem <- mhmkin(list(f_sep_const, f_sep_tc), transformations = \"saemix\") status(f_saem) |> kable() anova(f_saem) |> kable(digits = 1)"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_dmta_parent.html","id":"parameter-identifiability-based-on-the-fisher-information-matrix","dir":"Articles > Prebuilt","previous_headings":"Hierarchichal model fits","what":"Parameter identifiability based on the Fisher Information Matrix","title":"Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P","text":"Using illparms function, ill-defined statistical model parameters standard deviations degradation parameters population error model parameters can found. According illparms function, fitted standard deviation second kinetic rate constant k2 ill-defined DFOP fits. suggests different values obtained standard deviation using different starting values. thus identified overparameterisation addressed removing random effect k2 parameter model. resulting fit, checked whether still ill-defined parameters, case. , refined model compared previous best model. model without random effect k2 reduced version previous model. Therefore, models nested can compared using likelihood ratio test. achieved argument test = TRUE anova function. AIC BIC criteria lower removal ill-defined random effect k2. p value likelihood ratio test much greater 0.05, indicating model higher likelihood (model random effects degradation parameters f_saem[[\"DFOP\", \"tc\"]]) fit significantly better model lower likelihood (reduced model f_saem_dfop_tc_no_ranef_k2). Therefore, AIC, BIC likelihood ratio test suggest use reduced model. convergence fit checked visually. Convergence plot NLHM DFOP fit two-component error without random effect ‘k2’ parameters appear converged satisfactory degree. final fit plotted using plot method mkin package. Plot final NLHM DFOP fit Finally, summary report fit produced.","code":"illparms(f_saem) |> kable() f_saem_dfop_tc_no_ranef_k2 <- update(f_saem[[\"DFOP\", \"tc\"]], no_random_effect = \"k2\") illparms(f_saem_dfop_tc_no_ranef_k2) anova(f_saem[[\"DFOP\", \"tc\"]], f_saem_dfop_tc_no_ranef_k2, test = TRUE) |> kable(format.args = list(digits = 4)) plot(f_saem_dfop_tc_no_ranef_k2) summary(f_saem_dfop_tc_no_ranef_k2) saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 R version used for fitting: 4.3.2 Date of fit: Thu Nov 16 04:59:35 2023 Date of summary: Thu Nov 16 04:59:35 2023 Equations: d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * DMTA Data: 155 observations of 1 variable(s) grouped in 6 datasets Model predictions using solution type analytical Fitted in 4.4 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function Starting values for degradation parameters: DMTA_0 k1 k2 g 98.71186 0.08675 0.01374 0.93491 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): DMTA_0 k1 k2 g DMTA_0 98.71 0 0 0 k1 0.00 1 0 0 k2 0.00 0 1 0 g 0.00 0 0 1 Starting values for error model parameters: a.1 b.1 1 1 Results: Likelihood computed by importance sampling AIC BIC logLik 663.7 661.8 -322.9 Optimised parameters: est. lower upper DMTA_0 98.256267 96.286112 100.22642 k1 0.064037 0.033281 0.09479 k2 0.008469 0.006002 0.01094 g 0.954167 0.914460 0.99387 a.1 1.061795 0.863943 1.25965 b.1 0.029550 0.022529 0.03657 SD.DMTA_0 2.068581 0.427706 3.70946 SD.k1 0.598285 0.258235 0.93833 SD.g 1.016689 0.360057 1.67332 Correlation: DMTA_0 k1 k2 k1 0.0213 k2 0.0541 0.0344 g -0.0521 -0.0286 -0.2744 Random effects: est. lower upper SD.DMTA_0 2.0686 0.4277 3.7095 SD.k1 0.5983 0.2582 0.9383 SD.g 1.0167 0.3601 1.6733 Variance model: est. lower upper a.1 1.06180 0.86394 1.25965 b.1 0.02955 0.02253 0.03657 Estimated disappearance times: DT50 DT90 DT50back DT50_k1 DT50_k2 DMTA 11.45 41.32 12.44 10.82 81.85"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_dmta_parent.html","id":"alternative-check-of-parameter-identifiability","dir":"Articles > Prebuilt","previous_headings":"Hierarchichal model fits","what":"Alternative check of parameter identifiability","title":"Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P","text":"parameter check used illparms function based quadratic approximation likelihood surface near optimum, calculated using Fisher Information Matrix (FIM). alternative way check parameter identifiability (Duchesne et al. 2021) based multistart approach recently implemented mkin. graph shows boxplots parameters obtained 50 runs saem algorithm different parameter combinations, sampled range parameters obtained individual datasets fitted separately using nonlinear regression. Scaled parameters multistart runs, full model graph clearly confirms lack identifiability variance k2 full model. overparameterisation model also indicates lack identifiability variance parameter g. parameter boxplots multistart runs reduced model shown indicate runs give similar results, regardless starting parameters. Scaled parameters multistart runs, reduced model parameters top 25% fits shown (based feature introduced mkin 1.2.2 currently development), scatter even less shown . Scaled parameters multistart runs, reduced model, fits top 25% likelihood values","code":"f_saem_dfop_tc_multi <- multistart(f_saem[[\"DFOP\", \"tc\"]], n = 50, cores = 15) par(mar = c(6.1, 4.1, 2.1, 2.1)) parplot(f_saem_dfop_tc_multi, lpos = \"bottomright\", ylim = c(0.3, 10), las = 2) f_saem_dfop_tc_no_ranef_k2_multi <- multistart(f_saem_dfop_tc_no_ranef_k2, n = 50, cores = 15) par(mar = c(6.1, 4.1, 2.1, 2.1)) parplot(f_saem_dfop_tc_no_ranef_k2_multi, ylim = c(0.5, 2), las = 2, lpos = \"bottomright\") par(mar = c(6.1, 4.1, 2.1, 2.1)) parplot(f_saem_dfop_tc_no_ranef_k2_multi, ylim = c(0.5, 2), las = 2, llquant = 0.25, lpos = \"bottomright\")"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_dmta_parent.html","id":"conclusions","dir":"Articles > Prebuilt","previous_headings":"","what":"Conclusions","title":"Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P","text":"Fitting four parent degradation models SFO, FOMC, DFOP HS part hierarchical model fits two different error models normal distributions transformed degradation parameters works without technical problems. biphasic models DFOP HS gave best fit data, default parameter distribution model fully identifiable. Removing random effect second kinetic rate constant DFOP model resulted reduced model fully identifiable showed lowest values model selection criteria AIC BIC. reliability identification model parameters confirmed using multiple starting values.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_dmta_parent.html","id":"acknowledgements","dir":"Articles > Prebuilt","previous_headings":"","what":"Acknowledgements","title":"Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P","text":"helpful comments Janina Wöltjen German Environment Agency gratefully acknowledged.","code":""},{"path":[]},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_dmta_parent.html","id":"hierarchical-model-fit-listings","dir":"Articles > Prebuilt","previous_headings":"Appendix","what":"Hierarchical model fit listings","title":"Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P","text":"Hierarchical mkin fit SFO model error model const Hierarchical mkin fit SFO model error model tc Hierarchical mkin fit FOMC model error model const Hierarchical mkin fit FOMC model error model tc Hierarchical mkin fit DFOP model error model const Hierarchical mkin fit DFOP model error model tc Hierarchical mkin fit HS model error model const Hierarchical mkin fit HS model error model tc","code":"saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 R version used for fitting: 4.3.2 Date of fit: Thu Nov 16 04:59:26 2023 Date of summary: Thu Nov 16 05:00:43 2023 Equations: d_DMTA/dt = - k_DMTA * DMTA Data: 155 observations of 1 variable(s) grouped in 6 datasets Model predictions using solution type analytical Fitted in 0.788 s Using 300, 100 iterations and 9 chains Variance model: Constant variance Starting values for degradation parameters: DMTA_0 k_DMTA 97.2953 0.0566 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): DMTA_0 k_DMTA DMTA_0 97.3 0 k_DMTA 0.0 1 Starting values for error model parameters: a.1 1 Results: Likelihood computed by importance sampling AIC BIC logLik 796.3 795.3 -393.2 Optimised parameters: est. lower upper DMTA_0 97.28130 95.71113 98.8515 k_DMTA 0.05665 0.02909 0.0842 a.1 2.66442 2.35579 2.9731 SD.DMTA_0 1.54776 0.15447 2.9411 SD.k_DMTA 0.60690 0.26248 0.9513 Correlation: DMTA_0 k_DMTA 0.0168 Random effects: est. lower upper SD.DMTA_0 1.5478 0.1545 2.9411 SD.k_DMTA 0.6069 0.2625 0.9513 Variance model: est. lower upper a.1 2.664 2.356 2.973 Estimated disappearance times: DT50 DT90 DMTA 12.24 40.65 saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 R version used for fitting: 4.3.2 Date of fit: Thu Nov 16 04:59:28 2023 Date of summary: Thu Nov 16 05:00:43 2023 Equations: d_DMTA/dt = - k_DMTA * DMTA Data: 155 observations of 1 variable(s) grouped in 6 datasets Model predictions using solution type analytical Fitted in 2.428 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function Starting values for degradation parameters: DMTA_0 k_DMTA 96.99175 0.05603 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): DMTA_0 k_DMTA DMTA_0 96.99 0 k_DMTA 0.00 1 Starting values for error model parameters: a.1 b.1 1 1 Results: Likelihood computed by importance sampling AIC BIC logLik 798.3 797.1 -393.2 Optimised parameters: est. lower upper DMTA_0 97.271822 95.703157 98.84049 k_DMTA 0.056638 0.029110 0.08417 a.1 2.660081 2.230398 3.08976 b.1 0.001665 -0.006911 0.01024 SD.DMTA_0 1.545520 0.145035 2.94601 SD.k_DMTA 0.606422 0.262274 0.95057 Correlation: DMTA_0 k_DMTA 0.0169 Random effects: est. lower upper SD.DMTA_0 1.5455 0.1450 2.9460 SD.k_DMTA 0.6064 0.2623 0.9506 Variance model: est. lower upper a.1 2.660081 2.230398 3.08976 b.1 0.001665 -0.006911 0.01024 Estimated disappearance times: DT50 DT90 DMTA 12.24 40.65 saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 R version used for fitting: 4.3.2 Date of fit: Thu Nov 16 04:59:27 2023 Date of summary: Thu Nov 16 05:00:43 2023 Equations: d_DMTA/dt = - (alpha/beta) * 1/((time/beta) + 1) * DMTA Data: 155 observations of 1 variable(s) grouped in 6 datasets Model predictions using solution type analytical Fitted in 1.28 s Using 300, 100 iterations and 9 chains Variance model: Constant variance Starting values for degradation parameters: DMTA_0 alpha beta 98.292 9.909 156.341 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): DMTA_0 alpha beta DMTA_0 98.29 0 0 alpha 0.00 1 0 beta 0.00 0 1 Starting values for error model parameters: a.1 1 Results: Likelihood computed by importance sampling AIC BIC logLik 734.2 732.7 -360.1 Optimised parameters: est. lower upper DMTA_0 98.3435 96.9033 99.784 alpha 7.2007 2.5889 11.812 beta 112.8745 34.8816 190.867 a.1 2.0459 1.8054 2.286 SD.DMTA_0 1.4795 0.2717 2.687 SD.alpha 0.6396 0.1509 1.128 SD.beta 0.6874 0.1587 1.216 Correlation: DMTA_0 alpha alpha -0.1125 beta -0.1227 0.3632 Random effects: est. lower upper SD.DMTA_0 1.4795 0.2717 2.687 SD.alpha 0.6396 0.1509 1.128 SD.beta 0.6874 0.1587 1.216 Variance model: est. lower upper a.1 2.046 1.805 2.286 Estimated disappearance times: DT50 DT90 DT50back DMTA 11.41 42.53 12.8 saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 R version used for fitting: 4.3.2 Date of fit: Thu Nov 16 04:59:28 2023 Date of summary: Thu Nov 16 05:00:43 2023 Equations: d_DMTA/dt = - (alpha/beta) * 1/((time/beta) + 1) * DMTA Data: 155 observations of 1 variable(s) grouped in 6 datasets Model predictions using solution type analytical Fitted in 2.793 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function Starting values for degradation parameters: DMTA_0 alpha beta 98.772 4.663 92.597 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): DMTA_0 alpha beta DMTA_0 98.77 0 0 alpha 0.00 1 0 beta 0.00 0 1 Starting values for error model parameters: a.1 b.1 1 1 Results: Likelihood computed by importance sampling AIC BIC logLik 720.7 719.1 -352.4 Optimised parameters: est. lower upper DMTA_0 99.10577 97.33296 100.87859 alpha 5.46260 2.52199 8.40321 beta 81.66080 30.46664 132.85497 a.1 1.50219 1.23601 1.76836 b.1 0.02893 0.02099 0.03687 SD.DMTA_0 1.61887 -0.03636 3.27411 SD.alpha 0.58145 0.17364 0.98925 SD.beta 0.68205 0.21108 1.15303 Correlation: DMTA_0 alpha alpha -0.1321 beta -0.1430 0.2467 Random effects: est. lower upper SD.DMTA_0 1.6189 -0.03636 3.2741 SD.alpha 0.5814 0.17364 0.9892 SD.beta 0.6821 0.21108 1.1530 Variance model: est. lower upper a.1 1.50219 1.23601 1.76836 b.1 0.02893 0.02099 0.03687 Estimated disappearance times: DT50 DT90 DT50back DMTA 11.05 42.81 12.89 saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 R version used for fitting: 4.3.2 Date of fit: Thu Nov 16 04:59:27 2023 Date of summary: Thu Nov 16 05:00:43 2023 Equations: d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * DMTA Data: 155 observations of 1 variable(s) grouped in 6 datasets Model predictions using solution type analytical Fitted in 1.752 s Using 300, 100 iterations and 9 chains Variance model: Constant variance Starting values for degradation parameters: DMTA_0 k1 k2 g 98.64383 0.09211 0.02999 0.76814 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): DMTA_0 k1 k2 g DMTA_0 98.64 0 0 0 k1 0.00 1 0 0 k2 0.00 0 1 0 g 0.00 0 0 1 Starting values for error model parameters: a.1 1 Results: Likelihood computed by importance sampling AIC BIC logLik 711.8 710 -346.9 Optimised parameters: est. lower upper DMTA_0 98.092481 96.573899 99.61106 k1 0.062499 0.030336 0.09466 k2 0.009065 -0.005133 0.02326 g 0.948967 0.862080 1.03586 a.1 1.821671 1.604774 2.03857 SD.DMTA_0 1.677785 0.472066 2.88350 SD.k1 0.634962 0.270788 0.99914 SD.k2 1.033498 -0.205994 2.27299 SD.g 1.710046 0.428642 2.99145 Correlation: DMTA_0 k1 k2 k1 0.0246 k2 0.0491 0.0953 g -0.0552 -0.0889 -0.4795 Random effects: est. lower upper SD.DMTA_0 1.678 0.4721 2.8835 SD.k1 0.635 0.2708 0.9991 SD.k2 1.033 -0.2060 2.2730 SD.g 1.710 0.4286 2.9914 Variance model: est. lower upper a.1 1.822 1.605 2.039 Estimated disappearance times: DT50 DT90 DT50back DT50_k1 DT50_k2 DMTA 11.79 42.8 12.88 11.09 76.46 saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 R version used for fitting: 4.3.2 Date of fit: Thu Nov 16 04:59:29 2023 Date of summary: Thu Nov 16 05:00:43 2023 Equations: d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * DMTA Data: 155 observations of 1 variable(s) grouped in 6 datasets Model predictions using solution type analytical Fitted in 3.186 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function Starting values for degradation parameters: DMTA_0 k1 k2 g 98.71186 0.08675 0.01374 0.93491 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): DMTA_0 k1 k2 g DMTA_0 98.71 0 0 0 k1 0.00 1 0 0 k2 0.00 0 1 0 g 0.00 0 0 1 Starting values for error model parameters: a.1 b.1 1 1 Results: Likelihood computed by importance sampling AIC BIC logLik 665.7 663.6 -322.9 Optimised parameters: est. lower upper DMTA_0 98.347470 96.380815 100.31413 k1 0.064524 0.034279 0.09477 k2 0.008304 0.005843 0.01076 g 0.952128 0.909578 0.99468 a.1 1.068907 0.868694 1.26912 b.1 0.029265 0.022262 0.03627 SD.DMTA_0 2.065796 0.428485 3.70311 SD.k1 0.583703 0.251796 0.91561 SD.k2 0.004167 -7.832168 7.84050 SD.g 1.064450 0.397476 1.73142 Correlation: DMTA_0 k1 k2 k1 0.0223 k2 0.0568 0.0394 g -0.0464 -0.0269 -0.2713 Random effects: est. lower upper SD.DMTA_0 2.065796 0.4285 3.7031 SD.k1 0.583703 0.2518 0.9156 SD.k2 0.004167 -7.8322 7.8405 SD.g 1.064450 0.3975 1.7314 Variance model: est. lower upper a.1 1.06891 0.86869 1.26912 b.1 0.02927 0.02226 0.03627 Estimated disappearance times: DT50 DT90 DT50back DT50_k1 DT50_k2 DMTA 11.39 41.36 12.45 10.74 83.48 saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 R version used for fitting: 4.3.2 Date of fit: Thu Nov 16 04:59:28 2023 Date of summary: Thu Nov 16 05:00:43 2023 Equations: d_DMTA/dt = - ifelse(time <= tb, k1, k2) * DMTA Data: 155 observations of 1 variable(s) grouped in 6 datasets Model predictions using solution type analytical Fitted in 2.28 s Using 300, 100 iterations and 9 chains Variance model: Constant variance Starting values for degradation parameters: DMTA_0 k1 k2 tb 97.82176 0.06931 0.02997 11.13945 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): DMTA_0 k1 k2 tb DMTA_0 97.82 0 0 0 k1 0.00 1 0 0 k2 0.00 0 1 0 tb 0.00 0 0 1 Starting values for error model parameters: a.1 1 Results: Likelihood computed by importance sampling AIC BIC logLik 714 712.1 -348 Optimised parameters: est. lower upper DMTA_0 98.16102 96.47747 99.84456 k1 0.07876 0.05261 0.10491 k2 0.02227 0.01706 0.02747 tb 13.99089 -7.40049 35.38228 a.1 1.82305 1.60700 2.03910 SD.DMTA_0 1.88413 0.56204 3.20622 SD.k1 0.34292 0.10482 0.58102 SD.k2 0.19851 0.01718 0.37985 SD.tb 1.68168 0.58064 2.78272 Correlation: DMTA_0 k1 k2 k1 0.0142 k2 0.0001 -0.0025 tb 0.0165 -0.1256 -0.0301 Random effects: est. lower upper SD.DMTA_0 1.8841 0.56204 3.2062 SD.k1 0.3429 0.10482 0.5810 SD.k2 0.1985 0.01718 0.3798 SD.tb 1.6817 0.58064 2.7827 Variance model: est. lower upper a.1 1.823 1.607 2.039 Estimated disappearance times: DT50 DT90 DT50back DT50_k1 DT50_k2 DMTA 8.801 67.91 20.44 8.801 31.13 saemix version used for fitting: 3.2 mkin version used for pre-fitting: 1.2.6 R version used for fitting: 4.3.2 Date of fit: Thu Nov 16 04:59:29 2023 Date of summary: Thu Nov 16 05:00:43 2023 Equations: d_DMTA/dt = - ifelse(time <= tb, k1, k2) * DMTA Data: 155 observations of 1 variable(s) grouped in 6 datasets Model predictions using solution type analytical Fitted in 3.658 s Using 300, 100 iterations and 9 chains Variance model: Two-component variance function Starting values for degradation parameters: DMTA_0 k1 k2 tb 98.45190 0.07525 0.02576 19.19375 Fixed degradation parameter values: None Starting values for random effects (square root of initial entries in omega): DMTA_0 k1 k2 tb DMTA_0 98.45 0 0 0 k1 0.00 1 0 0 k2 0.00 0 1 0 tb 0.00 0 0 1 Starting values for error model parameters: a.1 b.1 1 1 Results: Likelihood computed by importance sampling AIC BIC logLik 667.1 665 -323.6 Optimised parameters: est. lower upper DMTA_0 97.76571 95.81350 99.71791 k1 0.05855 0.03080 0.08630 k2 0.02337 0.01664 0.03010 tb 31.09638 29.38289 32.80987 a.1 1.08835 0.88590 1.29080 b.1 0.02964 0.02257 0.03671 SD.DMTA_0 2.04877 0.42607 3.67147 SD.k1 0.59166 0.25621 0.92711 SD.k2 0.30698 0.09561 0.51835 SD.tb 0.01274 -0.10914 0.13462 Correlation: DMTA_0 k1 k2 k1 0.0160 k2 -0.0070 -0.0024 tb -0.0668 -0.0103 -0.2013 Random effects: est. lower upper SD.DMTA_0 2.04877 0.42607 3.6715 SD.k1 0.59166 0.25621 0.9271 SD.k2 0.30698 0.09561 0.5183 SD.tb 0.01274 -0.10914 0.1346 Variance model: est. lower upper a.1 1.08835 0.88590 1.29080 b.1 0.02964 0.02257 0.03671 Estimated disappearance times: DT50 DT90 DT50back DT50_k1 DT50_k2 DMTA 11.84 51.71 15.57 11.84 29.66"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_dmta_parent.html","id":"hierarchical-model-convergence-plots","dir":"Articles > Prebuilt","previous_headings":"Appendix","what":"Hierarchical model convergence plots","title":"Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P","text":"Convergence plot NLHM SFO fit constant variance Convergence plot NLHM SFO fit two-component error Convergence plot NLHM FOMC fit constant variance Convergence plot NLHM FOMC fit two-component error Convergence plot NLHM DFOP fit constant variance Convergence plot NLHM DFOP fit two-component error Convergence plot NLHM HS fit constant variance Convergence plot NLHM HS fit two-component error","code":""},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_dmta_parent.html","id":"session-info","dir":"Articles > Prebuilt","previous_headings":"Appendix","what":"Session info","title":"Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P","text":"","code":"R version 4.3.2 (2023-10-31) 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_1.42 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_0.21-8 digest_0.6.31 magrittr_2.0.3 evaluate_0.21 [9] grid_4.3.2 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_4.3.2 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 MASS_7.3-60 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 nlme_3.1-163 rmarkdown_2.21 compiler_4.3.2"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_dmta_parent.html","id":"hardware-info","dir":"Articles > Prebuilt","previous_headings":"Appendix","what":"Hardware info","title":"Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P","text":"","code":"CPU model: AMD Ryzen 9 7950X 16-Core Processor MemTotal: 64927712 kB"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_dmta_pathway.html","id":"introduction","dir":"Articles > Prebuilt","previous_headings":"","what":"Introduction","title":"Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P","text":"purpose document test demonstrate nonlinear hierarchical models (NLHM) based parent degradation models SFO, FOMC, DFOP HS, parallel formation two metabolites can fitted mkin package. assembled course work package 1.2 Project Number 173340 (Application nonlinear hierarchical models kinetic evaluation chemical degradation data) German Environment Agency carried 2022 2023. mkin package used version 1.2.6, currently development. contains test data, functions used evaluations. saemix package used backend fitting NLHM, also loaded make convergence plot function available. document processed knitr package, also provides kable function used improve display tabular data R markdown documents. parallel processing, parallel package used.","code":"library(mkin) library(knitr) library(saemix) library(parallel) n_cores <- detectCores() # We need to start a new cluster after defining a compiled model that is # saved as a DLL to the user directory, therefore we define a function # This is used again after defining the pathway model start_cluster <- function(n_cores) { if (Sys.info()[\"sysname\"] == \"Windows\") { ret <- makePSOCKcluster(n_cores) } else { ret <- makeForkCluster(n_cores) } return(ret) }"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_dmta_pathway.html","id":"data","dir":"Articles > Prebuilt","previous_headings":"","what":"Data","title":"Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P","text":"test data available mkin package object class mkindsg (mkin dataset group) identifier dimethenamid_2018. following preprocessing steps done document. data available enantiomer dimethenamid-P (DMTAP) renamed substance name data racemic mixture dimethenamid (DMTA). reason difference degradation behaviour identified EU risk assessment. Unnecessary columns discarded observation times dataset multiplied corresponding normalisation factor also available dataset, order make possible describe datasets single set parameters independent temperature Finally, datasets observed soil (Elliot 1 Elliot 2) combined, resulting dimethenamid (DMTA) data six soils. following commented R code performs preprocessing. following tables show 6 datasets. Dataset Calke Dataset Borstel Dataset Flaach Dataset BBA 2.2 Dataset BBA 2.3 Dataset Elliot","code":"# Apply a function to each of the seven datasets in the mkindsg object to create a list dmta_ds <- lapply(1:7, function(i) { ds_i <- dimethenamid_2018$ds[[i]]$data # Get a dataset ds_i[ds_i$name == \"DMTAP\", \"name\"] <- \"DMTA\" # Rename DMTAP to DMTA ds_i <- subset(ds_i, select = c(\"name\", \"time\", \"value\")) # Select data ds_i$time <- ds_i$time * dimethenamid_2018$f_time_norm[i] # Normalise time ds_i # Return the dataset }) # Use dataset titles as names for the list elements names(dmta_ds) <- sapply(dimethenamid_2018$ds, function(ds) ds$title) # Combine data for Elliot soil to obtain a named list with six elements dmta_ds[[\"Elliot\"]] <- rbind(dmta_ds[[\"Elliot 1\"]], dmta_ds[[\"Elliot 2\"]]) # dmta_ds[[\"Elliot 1\"]] <- NULL dmta_ds[[\"Elliot 2\"]] <- NULL for (ds_name in names(dmta_ds)) { print( kable(mkin_long_to_wide(dmta_ds[[ds_name]]), caption = paste(\"Dataset\", ds_name), booktabs = TRUE, row.names = FALSE)) cat(\"\\n\\\\clearpage\\n\") }"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_dmta_pathway.html","id":"separate-evaluations","dir":"Articles > Prebuilt","previous_headings":"","what":"Separate evaluations","title":"Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P","text":"first step obtain suitable starting parameters NLHM fits, separate fits several variants pathway model used previously (Ranke et al. 2021), varying kinetic model parent compound. SFORB model often provides faster convergence DFOP model, can sometimes fitted DFOP model results errors, included set parent models tested . separate pathway fits SFO FOMC parent constant variance converged (status OK). fits DFOP SFORB parent converged well. fits HS parent converge default settings. two-component error model, set fits convergence problems slightly different, convergence problems appearing different data sets applying DFOP SFORB model additional convergence problems using FOMC model parent.","code":"if (!dir.exists(\"dmta_dlls\")) dir.create(\"dmta_dlls\") m_sfo_path_1 <- mkinmod( DMTA = mkinsub(\"SFO\", c(\"M23\", \"M27\", \"M31\")), M23 = mkinsub(\"SFO\"), M27 = mkinsub(\"SFO\"), M31 = mkinsub(\"SFO\", \"M27\", sink = FALSE), name = \"m_sfo_path\", dll_dir = \"dmta_dlls\", unload = TRUE, overwrite = TRUE, quiet = TRUE ) m_fomc_path_1 <- mkinmod( DMTA = mkinsub(\"FOMC\", c(\"M23\", \"M27\", \"M31\")), M23 = mkinsub(\"SFO\"), M27 = mkinsub(\"SFO\"), M31 = mkinsub(\"SFO\", \"M27\", sink = FALSE), name = \"m_fomc_path\", dll_dir = \"dmta_dlls\", unload = TRUE, overwrite = TRUE, quiet = TRUE ) m_dfop_path_1 <- mkinmod( DMTA = mkinsub(\"DFOP\", c(\"M23\", \"M27\", \"M31\")), M23 = mkinsub(\"SFO\"), M27 = mkinsub(\"SFO\"), M31 = mkinsub(\"SFO\", \"M27\", sink = FALSE), name = \"m_dfop_path\", dll_dir = \"dmta_dlls\", unload = TRUE, overwrite = TRUE, quiet = TRUE ) m_sforb_path_1 <- mkinmod( DMTA = mkinsub(\"SFORB\", c(\"M23\", \"M27\", \"M31\")), M23 = mkinsub(\"SFO\"), M27 = mkinsub(\"SFO\"), M31 = mkinsub(\"SFO\", \"M27\", sink = FALSE), name = \"m_sforb_path\", dll_dir = \"dmta_dlls\", unload = TRUE, overwrite = TRUE, quiet = TRUE ) m_hs_path_1 <- mkinmod( DMTA = mkinsub(\"HS\", c(\"M23\", \"M27\", \"M31\")), M23 = mkinsub(\"SFO\"), M27 = mkinsub(\"SFO\"), M31 = mkinsub(\"SFO\", \"M27\", sink = FALSE), name = \"m_hs_path\", dll_dir = \"dmta_dlls\", unload = TRUE, overwrite = TRUE, quiet = TRUE ) cl <- start_cluster(n_cores) deg_mods_1 <- list( sfo_path_1 = m_sfo_path_1, fomc_path_1 = m_fomc_path_1, dfop_path_1 = m_dfop_path_1, sforb_path_1 = m_sforb_path_1, hs_path_1 = m_hs_path_1) sep_1_const <- mmkin( deg_mods_1, dmta_ds, error_model = \"const\", quiet = TRUE) status(sep_1_const) |> kable() sep_1_tc <- update(sep_1_const, error_model = \"tc\") status(sep_1_tc) |> kable()"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_dmta_pathway.html","id":"hierarchichal-model-fits","dir":"Articles > Prebuilt","previous_headings":"","what":"Hierarchichal model fits","title":"Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P","text":"following code fits two sets corresponding hierarchical models data, one assuming constant variance, one assuming two-component error. run time fits around two hours five year old hardware. recent hardware upgrade fits complete less twenty minutes. According status function, fits terminated successfully. goodness--fit models compared, warning obtained, indicating likelihood pathway fit SFORB parent compound constant variance calculated importance sampling (method ‘’). default method AIC BIC comparisons based, variant included model comparison table. Comparing goodness--fit remaining models, HS model model two-component error provides best fit. However, batch experiments performed constant conditions experiments evaluated , reason assume discontinuity, SFORB model preferable mechanistic viewpoint. addition, information criteria AIC BIC similar HS SFORB. Therefore, SFORB model selected refinements.","code":"saem_1 <- mhmkin(list(sep_1_const, sep_1_tc)) status(saem_1) |> kable() anova(saem_1) |> kable(digits = 1)"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_dmta_pathway.html","id":"parameter-identifiability-based-on-the-fisher-information-matrix","dir":"Articles > Prebuilt","previous_headings":"Hierarchichal model fits","what":"Parameter identifiability based on the Fisher Information Matrix","title":"Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P","text":"Using illparms function, ill-defined statistical model parameters standard deviations degradation parameters population error model parameters can found. using constant variance, ill-defined variance parameters identified illparms function degradation models. using two-component error model, one ill-defined variance parameter variants except variant using DFOP parent compound. selected combination SFORB pathway model two-component error, random effect rate constant reversibly bound DMTA free DMTA (k_DMTA_bound_free) well-defined. Therefore, fit updated without assuming random effect parameter. expected, ill-defined parameters remain. model comparison shows reduced model preferable. convergence plot refined fit shown . parameters, example f_DMTA_ilr_1 f_DMTA_ilr_2, .e. two parameters determining formation fractions parallel formation three metabolites, movement parameters still visible second phase algorithm. However, amplitude movement range amplitude towards end first phase. Therefore, likely increase iterations improve parameter estimates much, proposed fit acceptable. numeric convergence criterion implemented saemix.","code":"illparms(saem_1) |> kable() saem_sforb_path_1_tc_reduced <- update(saem_1[[\"sforb_path_1\", \"tc\"]], no_random_effect = \"log_k_DMTA_bound_free\") illparms(saem_sforb_path_1_tc_reduced) anova(saem_1[[\"sforb_path_1\", \"tc\"]], saem_sforb_path_1_tc_reduced) |> kable(digits = 1) plot(saem_sforb_path_1_tc_reduced$so, plot.type = \"convergence\")"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_dmta_pathway.html","id":"alternative-check-of-parameter-identifiability","dir":"Articles > Prebuilt","previous_headings":"Hierarchichal model fits","what":"Alternative check of parameter identifiability","title":"Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P","text":"alternative check parameter identifiability (Duchesne et al. 2021), multistart runs performed basis refined fit shown . 32 fits initiated, 17 terminated without error. reason wide variation starting parameters combination parameter variation used SAEM algorithm leads parameter combinations degradation model numerical integration routine cope . variation initial parameters, model fits take two times time original fit. Parameter boxplots multistart runs succeeded However, visual analysis boxplot parameters obtained successful fits confirms results sufficiently independent starting parameters, remaining ill-defined parameters.","code":"saem_sforb_path_1_tc_reduced_multi <- multistart(saem_sforb_path_1_tc_reduced, n = 32, cores = 10) print(saem_sforb_path_1_tc_reduced_multi) <multistart> object with 32 fits: E OK 7 25 OK: Fit terminated successfully E: Error par(mar = c(12.1, 4.1, 2.1, 2.1)) parplot(saem_sforb_path_1_tc_reduced_multi, ylim = c(0.5, 2), las = 2)"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_dmta_pathway.html","id":"plots-of-selected-fits","dir":"Articles > Prebuilt","previous_headings":"","what":"Plots of selected fits","title":"Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P","text":"SFORB pathway fits full reduced parameter distribution model shown . SFORB pathway fit two-component error SFORB pathway fit two-component error, reduced parameter model Plots remaining fits listings successful fits shown Appendix.","code":"plot(saem_1[[\"sforb_path_1\", \"tc\"]]) plot(saem_sforb_path_1_tc_reduced) stopCluster(cl)"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_dmta_pathway.html","id":"conclusions","dir":"Articles > Prebuilt","previous_headings":"","what":"Conclusions","title":"Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P","text":"Pathway fits SFO, FOMC, DFOP, SFORB HS models parent compound successfully performed.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_dmta_pathway.html","id":"acknowledgements","dir":"Articles > Prebuilt","previous_headings":"","what":"Acknowledgements","title":"Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P","text":"helpful comments Janina Wöltjen German Environment Agency earlier versions document gratefully acknowledged.","code":""},{"path":[]},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_dmta_pathway.html","id":"plots-of-hierarchical-fits-not-selected-for-refinement","dir":"Articles > Prebuilt","previous_headings":"Appendix","what":"Plots of hierarchical fits not selected for refinement","title":"Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P","text":"SFO pathway fit two-component error FOMC pathway fit two-component error HS pathway fit two-component error","code":"plot(saem_1[[\"sfo_path_1\", \"tc\"]]) plot(saem_1[[\"fomc_path_1\", \"tc\"]]) plot(saem_1[[\"sforb_path_1\", \"tc\"]])"},{"path":[]},{"path":[]},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_dmta_pathway.html","id":"session-info","dir":"Articles > Prebuilt","previous_headings":"Appendix","what":"Session info","title":"Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P","text":"","code":"R version 4.3.2 (2023-10-31) 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_1.42 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_0.21-8 digest_0.6.31 magrittr_2.0.3 evaluate_0.21 [9] grid_4.3.2 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_4.3.2 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 MASS_7.3-60 [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_3.1-163 rmarkdown_2.21 compiler_4.3.2 prettyunits_1.1.1"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2022_dmta_pathway.html","id":"hardware-info","dir":"Articles > Prebuilt","previous_headings":"Appendix","what":"Hardware info","title":"Testing hierarchical pathway kinetics with residue data on dimethenamid and dimethenamid-P","text":"","code":"CPU model: AMD Ryzen 9 7950X 16-Core Processor MemTotal: 64927712 kB"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2023_mesotrione_parent.html","id":"introduction","dir":"Articles > Prebuilt","previous_headings":"","what":"Introduction","title":"Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione","text":"purpose document test demonstrate nonlinear hierarchical models (NLHM) based parent degradation models SFO, FOMC, DFOP HS can fitted mkin package, also considering influence covariates like soil pH different degradation parameters. case studies, SFORB parameterisation biexponential decline shown advantages DFOP parameterisation, SFORB included list tested models well. mkin package used version 1.2.6, contains functions used evaluations. saemix package used backend fitting NLHM, also loaded make convergence plot function available. document processed knitr package, also provides kable function used improve display tabular data R markdown documents. parallel processing, parallel package used.","code":"library(mkin) library(knitr) library(saemix) library(parallel) n_cores <- detectCores() if (Sys.info()[\"sysname\"] == \"Windows\") { cl <- makePSOCKcluster(n_cores) } else { cl <- makeForkCluster(n_cores) }"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2023_mesotrione_parent.html","id":"test-data","dir":"Articles > Prebuilt","previous_headings":"Introduction","what":"Test data","title":"Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione","text":"following tables show covariate data 18 datasets read spreadsheet file. Covariate data Dataset Richmond Dataset Richmond 2 Dataset ERTC Dataset Toulouse Dataset Picket Piece Dataset 721 Dataset 722 Dataset 723 Dataset 724 Dataset 725 Dataset 727 Dataset 728 Dataset 729 Dataset 730 Dataset 731 Dataset 732 Dataset 741 Dataset 742","code":"data_file <- system.file( \"testdata\", \"mesotrione_soil_efsa_2016.xlsx\", package = \"mkin\") meso_ds <- read_spreadsheet(data_file, parent_only = TRUE) pH <- attr(meso_ds, \"covariates\") kable(pH, caption = \"Covariate data\") for (ds_name in names(meso_ds)) { print( kable(mkin_long_to_wide(meso_ds[[ds_name]]), caption = paste(\"Dataset\", ds_name), booktabs = TRUE, row.names = FALSE)) }"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2023_mesotrione_parent.html","id":"separate-evaluations","dir":"Articles > Prebuilt","previous_headings":"","what":"Separate evaluations","title":"Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione","text":"order obtain suitable starting parameters NLHM fits, separate fits five models data soil generated using mmkin function mkin package. first step, constant variance assumed. Convergence checked status function. tables , OK indicates convergence C indicates failure converge. separate fits constant variance converged, exception two FOMC fits, one SFORB fit one HS fit. two-component error model, set fits converge larger, convergence problems appearing number non-SFO fits.","code":"deg_mods <- c(\"SFO\", \"FOMC\", \"DFOP\", \"SFORB\", \"HS\") f_sep_const <- mmkin( deg_mods, meso_ds, error_model = \"const\", cluster = cl, quiet = TRUE) status(f_sep_const[, 1:5]) |> kable() status(f_sep_const[, 6:18]) |> kable() f_sep_tc <- update(f_sep_const, error_model = \"tc\") status(f_sep_tc[, 1:5]) |> kable() status(f_sep_tc[, 6:18]) |> kable()"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2023_mesotrione_parent.html","id":"hierarchical-model-fits-without-covariate-effect","dir":"Articles > Prebuilt","previous_headings":"","what":"Hierarchical model fits without covariate effect","title":"Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione","text":"following code fits hierarchical kinetic models ten combinations five different degradation models two different error models parallel. fits terminate without errors (status OK). model comparisons show fits constant variance consistently preferable corresponding fits two-component error data. confirmed fact parameter b.1 (relative standard deviation fits obtained saemix package), ill-defined fits. obtaining fits well-defined random effects, update set fits, excluding random effects ill-defined according illparms function. updated fits terminate without errors. ill-defined errors remain fits constant variance.","code":"f_saem_1 <- mhmkin(list(f_sep_const, f_sep_tc), cluster = cl) status(f_saem_1) |> kable() anova(f_saem_1) |> kable(digits = 1) illparms(f_saem_1) |> kable() f_saem_2 <- update(f_saem_1, no_random_effect = illparms(f_saem_1)) status(f_saem_2) |> kable() illparms(f_saem_2) |> kable()"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2023_mesotrione_parent.html","id":"hierarchical-model-fits-with-covariate-effect","dir":"Articles > Prebuilt","previous_headings":"","what":"Hierarchical model fits with covariate effect","title":"Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione","text":"following sections, hierarchical fits including model influence pH selected degradation parameters shown parent models. Constant variance selected error model based fits without covariate effects. Random effects ill-defined fits without pH influence excluded. potential influence soil pH included parameters well-defined random effect, experience shown parameters significant pH effect found.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2023_mesotrione_parent.html","id":"sfo","dir":"Articles > Prebuilt","previous_headings":"Hierarchical model fits with covariate effect","what":"SFO","title":"Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione","text":"parameter showing pH influence table beta_pH(log_k_meso). confidence interval include zero, indicating influence soil pH log degradation rate constant significantly greater zero. comparison SFO fit without covariate effect confirms considering soil pH improves model, comparison AIC BIC likelihood ratio test. Endpoints model covariates default calculated median covariate values. quantile can adapted, specific covariate value can given shown .","code":"sfo_pH <- saem(f_sep_const[\"SFO\", ], no_random_effect = \"meso_0\", covariates = pH, covariate_models = list(log_k_meso ~ pH)) summary(sfo_pH)$confint_trans |> kable(digits = 2) anova(f_saem_2[[\"SFO\", \"const\"]], sfo_pH, test = TRUE) 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 plot(sfo_pH) endpoints(sfo_pH) $covariates pH 50% 5.75 $distimes DT50 DT90 meso 18.52069 61.52441 endpoints(sfo_pH, covariate_quantile = 0.9) $covariates pH 90% 7.13 $distimes DT50 DT90 meso 8.237019 27.36278 endpoints(sfo_pH, covariates = c(pH = 7.0)) $covariates pH User 7 $distimes DT50 DT90 meso 8.89035 29.5331"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2023_mesotrione_parent.html","id":"fomc","dir":"Articles > Prebuilt","previous_headings":"Hierarchical model fits with covariate effect","what":"FOMC","title":"Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione","text":"case SFO, confidence interval slope parameter (beta_pH(log_alpha)) quantifying influence soil pH include zero, model comparison clearly indicates model covariate influence preferable. However, random effect alpha well-defined inclusion covariate effect (confidence interval SD.log_alpha includes zero). Therefore, model updated without random effect, ill-defined parameters remain. Model comparison indicates including pH dependence significantly improves fit, reduced model covariate influence results preferable FOMC fit.","code":"fomc_pH <- saem(f_sep_const[\"FOMC\", ], no_random_effect = \"meso_0\", covariates = pH, covariate_models = list(log_alpha ~ pH)) summary(fomc_pH)$confint_trans |> kable(digits = 2) illparms(fomc_pH) [1] \"sd(log_alpha)\" fomc_pH_2 <- update(fomc_pH, no_random_effect = c(\"meso_0\", \"log_alpha\")) illparms(fomc_pH_2) anova(f_saem_2[[\"FOMC\", \"const\"]], fomc_pH, fomc_pH_2, test = TRUE) 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 summary(fomc_pH_2)$confint_trans |> kable(digits = 2) plot(fomc_pH_2) endpoints(fomc_pH_2) $covariates pH 50% 5.75 $distimes DT50 DT90 DT50back meso 17.30248 82.91343 24.95943 endpoints(fomc_pH_2, covariates = c(pH = 7)) $covariates pH User 7 $distimes DT50 DT90 DT50back meso 6.986239 27.02927 8.136621"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2023_mesotrione_parent.html","id":"dfop","dir":"Articles > Prebuilt","previous_headings":"Hierarchical model fits with covariate effect","what":"DFOP","title":"Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione","text":"DFOP fits without covariate effects, random effects two degradation parameters (k2 g) identifiable. fit pH dependent degradation parameters obtained excluding random effects refined DFOP fit without covariate influence, including covariate models two identifiable parameters k2 g. corresponding parameters influence soil pH beta_pH(log_k2) influence soil pH k2, beta_pH(g_qlogis) influence g. Confidence intervals neither include zero, indicating significant difference zero. However, random effect g now ill-defined. fit updated without ill-defined random effect. Now, slope parameter pH effect g ill-defined. Therefore, another attempt made without corresponding covariate model. random effect g ill-defined, fit repeated without . ill-defined parameters remain, model comparison suggests previous model dfop_pH_2 two pH dependent parameters preferable, based information criteria well based likelihood ratio test. focussing parameter identifiability using test confidence interval includes zero, dfop_pH_4 still preferred model. However, kept mind parameter confidence intervals constructed using simple linearisation likelihood. confidence interval random effect g marginally includes zero, suggested acceptable, dfop_pH_2 can considered preferable model.","code":"summary(f_saem_2[[\"DFOP\", \"const\"]])$confint_trans |> kable(digits = 2) dfop_pH <- saem(f_sep_const[\"DFOP\", ], no_random_effect = c(\"meso_0\", \"log_k1\"), covariates = pH, covariate_models = list(log_k2 ~ pH, g_qlogis ~ pH)) summary(dfop_pH)$confint_trans |> kable(digits = 2) illparms(dfop_pH) [1] \"sd(g_qlogis)\" dfop_pH_2 <- update(dfop_pH, no_random_effect = c(\"meso_0\", \"log_k1\", \"g_qlogis\")) illparms(dfop_pH_2) [1] \"beta_pH(g_qlogis)\" dfop_pH_3 <- saem(f_sep_const[\"DFOP\", ], no_random_effect = c(\"meso_0\", \"log_k1\"), covariates = pH, covariate_models = list(log_k2 ~ pH)) illparms(dfop_pH_3) [1] \"sd(g_qlogis)\" dfop_pH_4 <- update(dfop_pH_3, no_random_effect = c(\"meso_0\", \"log_k1\", \"g_qlogis\")) illparms(dfop_pH_4) anova(f_saem_2[[\"DFOP\", \"const\"]], dfop_pH, dfop_pH_2, dfop_pH_3, dfop_pH_4) 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 anova(dfop_pH_2, dfop_pH_4, test = TRUE) 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 plot(dfop_pH_2) endpoints(dfop_pH_2) $covariates pH 50% 5.75 $distimes DT50 DT90 DT50back DT50_k1 DT50_k2 meso 18.36876 73.51841 22.13125 4.191901 23.98672 endpoints(dfop_pH_2, covariates = c(pH = 7)) $covariates pH User 7 $distimes DT50 DT90 DT50back DT50_k1 DT50_k2 meso 8.346428 28.34437 8.532507 4.191901 8.753618"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2023_mesotrione_parent.html","id":"sforb","dir":"Articles > Prebuilt","previous_headings":"Hierarchical model fits with covariate effect","what":"SFORB","title":"Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione","text":"confidence interval beta_pH(log_k_meso_bound_free) includes zero, indicating influence soil pH k_meso_bound_free reliably quantified. Also, confidence interval random effect parameter (SD.log_k_meso_bound_free) includes zero. Using illparms function, ill-defined parameters can found conveniently. remove ill-defined parameters, second variant SFORB model pH influence fitted. ill-defined parameters remain. model comparison SFORB fits includes refined model without covariate effect, versions SFORB fit covariate effect. first model including pH influence preferable based information criteria likelihood ratio test. However, fully identifiable, second model selected.","code":"sforb_pH <- saem(f_sep_const[\"SFORB\", ], no_random_effect = c(\"meso_free_0\", \"log_k_meso_free_bound\"), covariates = pH, covariate_models = list(log_k_meso_free ~ pH, log_k_meso_bound_free ~ pH)) summary(sforb_pH)$confint_trans |> kable(digits = 2) illparms(sforb_pH) [1] \"sd(log_k_meso_bound_free)\" \"beta_pH(log_k_meso_bound_free)\" sforb_pH_2 <- update(sforb_pH, no_random_effect = c(\"meso_free_0\", \"log_k_meso_free_bound\", \"log_k_meso_bound_free\"), covariate_models = list(log_k_meso_free ~ pH)) illparms(sforb_pH_2) anova(f_saem_2[[\"SFORB\", \"const\"]], sforb_pH, sforb_pH_2, test = TRUE) 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 summary(sforb_pH_2)$confint_trans |> kable(digits = 2) plot(sforb_pH_2) endpoints(sforb_pH_2) $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 endpoints(sforb_pH_2, covariates = c(pH = 7)) $covariates pH User 7 $ff meso_free 1 $SFORB meso_b1 meso_b2 meso_g 0.13315233 0.03795988 0.61186191 $distimes DT50 DT90 DT50back DT50_meso_b1 DT50_meso_b2 meso 7.932495 36.93311 11.11797 5.205671 18.26"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2023_mesotrione_parent.html","id":"hs","dir":"Articles > Prebuilt","previous_headings":"Hierarchical model fits with covariate effect","what":"HS","title":"Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione","text":"According output illparms function, random effect break time tb reliably quantified, neither can influence soil pH tb. fit repeated without corresponding covariate model, ill-defined parameters remain. Model comparison confirms model preferable fit without covariate influence, also first version covariate influence.","code":"hs_pH <- saem(f_sep_const[\"HS\", ], no_random_effect = c(\"meso_0\"), covariates = pH, covariate_models = list(log_k1 ~ pH, log_k2 ~ pH, log_tb ~ pH)) summary(hs_pH)$confint_trans |> kable(digits = 2) illparms(hs_pH) [1] \"sd(log_tb)\" \"beta_pH(log_tb)\" hs_pH_2 <- update(hs_pH, covariate_models = list(log_k1 ~ pH, log_k2 ~ pH)) illparms(hs_pH_2) anova(f_saem_2[[\"HS\", \"const\"]], hs_pH, hs_pH_2, test = TRUE) 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 summary(hs_pH_2)$confint_trans |> kable(digits = 2) plot(hs_pH_2) endpoints(hs_pH_2) $covariates pH 50% 5.75 $distimes DT50 DT90 DT50back DT50_k1 DT50_k2 meso 14.68725 82.45287 24.82079 14.68725 29.29299 endpoints(hs_pH_2, covariates = c(pH = 7)) $covariates pH User 7 $distimes DT50 DT90 DT50back DT50_k1 DT50_k2 meso 8.298536 38.85371 11.69613 8.298536 15.71561"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2023_mesotrione_parent.html","id":"comparison-across-parent-models","dir":"Articles > Prebuilt","previous_headings":"Hierarchical model fits with covariate effect","what":"Comparison across parent models","title":"Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione","text":"model reduction models pH influence, compared . DFOP model pH influence k2 g random effect k2 finally selected best fit. endpoints resulting model listed . Please refer Appendix detailed listing.","code":"anova(sfo_pH, fomc_pH_2, dfop_pH_2, dfop_pH_4, sforb_pH_2, hs_pH_2) 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 endpoints(dfop_pH_2) $covariates pH 50% 5.75 $distimes DT50 DT90 DT50back DT50_k1 DT50_k2 meso 18.36876 73.51841 22.13125 4.191901 23.98672 endpoints(dfop_pH_2, covariates = c(pH = 7)) $covariates pH User 7 $distimes DT50 DT90 DT50back DT50_k1 DT50_k2 meso 8.346428 28.34437 8.532507 4.191901 8.753618"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2023_mesotrione_parent.html","id":"conclusions","dir":"Articles > Prebuilt","previous_headings":"","what":"Conclusions","title":"Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione","text":"evaluations demonstrate covariate effects can included types parent degradation models. models can refined make fully identifiable.","code":""},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2023_mesotrione_parent.html","id":"session-info","dir":"Articles > Prebuilt","previous_headings":"Appendix","what":"Session info","title":"Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione","text":"","code":"R version 4.3.2 (2023-10-31) 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_1.42 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_0.21-8 digest_0.6.31 magrittr_2.0.3 evaluate_0.21 [9] grid_4.3.2 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 textshaping_0.3.6 jquerylib_0.1.4 [21] cli_3.6.1 rlang_1.1.1 munsell_0.5.0 cachem_1.0.8 [25] yaml_2.3.7 tools_4.3.2 memoise_2.0.1 dplyr_1.1.2 [29] colorspace_2.1-0 ggplot2_3.4.2 vctrs_0.6.2 R6_2.5.1 [33] zoo_1.8-12 lifecycle_1.0.3 stringr_1.5.0 fs_1.6.2 [37] MASS_7.3-60 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 xfun_0.39 tibble_3.2.1 [49] lmtest_0.9-40 tidyselect_1.2.0 htmltools_0.5.5 nlme_3.1-163 [53] rmarkdown_2.21 compiler_4.3.2"},{"path":"https://pkgdown.jrwb.de/mkin/articles/prebuilt/2023_mesotrione_parent.html","id":"hardware-info","dir":"Articles > Prebuilt","previous_headings":"Appendix","what":"Hardware info","title":"Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione","text":"","code":"CPU model: AMD Ryzen 9 7950X 16-Core Processor MemTotal: 64928100 kB"},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/FOCUS_Z.html","id":"the-data","dir":"Articles > Web_only","previous_headings":"","what":"The data","title":"Example evaluation of FOCUS dataset Z","text":"following code defines example dataset Appendix 7 FOCUS kinetics report (FOCUS Work Group Degradation Kinetics 2014, 354).","code":"library(mkin, quietly = TRUE) LOD = 0.5 FOCUS_2006_Z = data.frame( t = c(0, 0.04, 0.125, 0.29, 0.54, 1, 2, 3, 4, 7, 10, 14, 21, 42, 61, 96, 124), Z0 = c(100, 81.7, 70.4, 51.1, 41.2, 6.6, 4.6, 3.9, 4.6, 4.3, 6.8, 2.9, 3.5, 5.3, 4.4, 1.2, 0.7), Z1 = c(0, 18.3, 29.6, 46.3, 55.1, 65.7, 39.1, 36, 15.3, 5.6, 1.1, 1.6, 0.6, 0.5 * LOD, NA, NA, NA), Z2 = c(0, NA, 0.5 * LOD, 2.6, 3.8, 15.3, 37.2, 31.7, 35.6, 14.5, 0.8, 2.1, 1.9, 0.5 * LOD, NA, NA, NA), Z3 = c(0, NA, NA, NA, NA, 0.5 * LOD, 9.2, 13.1, 22.3, 28.4, 32.5, 25.2, 17.2, 4.8, 4.5, 2.8, 4.4)) FOCUS_2006_Z_mkin <- mkin_wide_to_long(FOCUS_2006_Z)"},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/FOCUS_Z.html","id":"parent-and-one-metabolite","dir":"Articles > Web_only","previous_headings":"","what":"Parent and one metabolite","title":"Example evaluation of FOCUS dataset Z","text":"next step set models used kinetic analysis. simultaneous fit parent first metabolite usually straightforward, Step 1 (SFO parent ) skipped . start model 2a, formation decline metabolite Z1 pathway parent directly sink included (default mkin). obvious parameter summary (component summary), kinetic rate constant parent compound Z sink small t-test parameter suggests significantly different zero. suggests, agreement analysis FOCUS kinetics report, simplify model removing pathway sink. similar result can obtained formation fractions used model formulation: , ilr transformed formation fraction fitted model takes large value, backtransformed formation fraction parent Z Z1 practically unity. , covariance matrix used calculation confidence intervals returned model overparameterised. simplified model obtained removing pathway sink. following, use parameterisation formation fractions order able compare results FOCUS guidance, makes easier use parameters obtained previous fit adding metabolite. one transformation product Z0 pathway sink, formation fraction internally fixed unity.","code":"Z.2a <- mkinmod(Z0 = mkinsub(\"SFO\", \"Z1\"), Z1 = mkinsub(\"SFO\")) ## Temporary DLL for differentials generated and loaded m.Z.2a <- mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE) ## Warning in mkinfit(Z.2a, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with ## value of zero were removed from the data plot_sep(m.Z.2a) summary(m.Z.2a, data = FALSE)$bpar ## Estimate se_notrans t value Pr(>t) Lower Upper ## Z0_0 97.01488 3.301084 29.3888 3.2971e-21 91.66556 102.3642 ## k_Z0 2.23601 0.207078 10.7979 3.3309e-11 1.95303 2.5600 ## k_Z1 0.48212 0.063265 7.6207 2.8154e-08 0.40341 0.5762 ## f_Z0_to_Z1 1.00000 0.094764 10.5525 5.3560e-11 0.00000 1.0000 ## sigma 4.80411 0.635638 7.5579 3.2592e-08 3.52677 6.0815 Z.2a.ff <- mkinmod(Z0 = mkinsub(\"SFO\", \"Z1\"), Z1 = mkinsub(\"SFO\"), use_of_ff = \"max\") ## Temporary DLL for differentials generated and loaded m.Z.2a.ff <- mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE) ## Warning in mkinfit(Z.2a.ff, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with ## value of zero were removed from the data plot_sep(m.Z.2a.ff) summary(m.Z.2a.ff, data = FALSE)$bpar ## Estimate se_notrans t value Pr(>t) Lower Upper ## Z0_0 97.01488 3.301084 29.3888 3.2971e-21 91.66556 102.3642 ## k_Z0 2.23601 0.207078 10.7979 3.3309e-11 1.95303 2.5600 ## k_Z1 0.48212 0.063265 7.6207 2.8154e-08 0.40341 0.5762 ## f_Z0_to_Z1 1.00000 0.094764 10.5525 5.3560e-11 0.00000 1.0000 ## sigma 4.80411 0.635638 7.5579 3.2592e-08 3.52677 6.0815 Z.3 <- mkinmod(Z0 = mkinsub(\"SFO\", \"Z1\", sink = FALSE), Z1 = mkinsub(\"SFO\"), use_of_ff = \"max\") ## Temporary DLL for differentials generated and loaded m.Z.3 <- mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE) ## Warning in mkinfit(Z.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with ## value of zero were removed from the data plot_sep(m.Z.3) summary(m.Z.3, data = FALSE)$bpar ## Estimate se_notrans t value Pr(>t) Lower Upper ## Z0_0 97.01488 2.597342 37.352 2.0106e-24 91.67597 102.3538 ## k_Z0 2.23601 0.146904 15.221 9.1477e-15 1.95354 2.5593 ## k_Z1 0.48212 0.041727 11.554 4.8268e-12 0.40355 0.5760 ## sigma 4.80411 0.620208 7.746 1.6110e-08 3.52925 6.0790"},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/FOCUS_Z.html","id":"metabolites-z2-and-z3","dir":"Articles > Web_only","previous_headings":"","what":"Metabolites Z2 and Z3","title":"Example evaluation of FOCUS dataset Z","text":"suggested FOCUS report, pathway sink removed metabolite Z1 well next step. step appears questionable basis results, followed purpose comparison. Also, FOCUS report, assumed additional empirical evidence Z1 quickly exclusively hydrolyses Z2. Finally, metabolite Z3 added model. use optimised differential equation parameter values previous fit order accelerate optimization. fit corresponds final result chosen Appendix 7 FOCUS report. Confidence intervals returned mkin based internally transformed parameters, however.","code":"Z.5 <- mkinmod(Z0 = mkinsub(\"SFO\", \"Z1\", sink = FALSE), Z1 = mkinsub(\"SFO\", \"Z2\", sink = FALSE), Z2 = mkinsub(\"SFO\"), use_of_ff = \"max\") ## Temporary DLL for differentials generated and loaded m.Z.5 <- mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE) ## Warning in mkinfit(Z.5, FOCUS_2006_Z_mkin, quiet = TRUE): Observations with ## value of zero were removed from the data plot_sep(m.Z.5) Z.FOCUS <- mkinmod(Z0 = mkinsub(\"SFO\", \"Z1\", sink = FALSE), Z1 = mkinsub(\"SFO\", \"Z2\", sink = FALSE), Z2 = mkinsub(\"SFO\", \"Z3\"), Z3 = mkinsub(\"SFO\"), use_of_ff = \"max\") ## Temporary DLL for differentials generated and loaded m.Z.FOCUS <- mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, quiet = TRUE) ## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, : ## Observations with value of zero were removed from the data ## Warning in mkinfit(Z.FOCUS, FOCUS_2006_Z_mkin, parms.ini = m.Z.5$bparms.ode, : Optimisation did not converge: ## false convergence (8) plot_sep(m.Z.FOCUS) summary(m.Z.FOCUS, data = FALSE)$bpar ## Estimate se_notrans t value Pr(>t) Lower Upper ## Z0_0 96.842440 1.994291 48.5598 4.0226e-42 92.830421 100.854459 ## k_Z0 2.215425 0.118457 18.7023 1.0404e-23 1.989490 2.467019 ## k_Z1 0.478307 0.028257 16.9272 6.2332e-22 0.424709 0.538669 ## k_Z2 0.451642 0.042139 10.7178 1.6304e-14 0.374348 0.544894 ## k_Z3 0.058692 0.015245 3.8499 1.7803e-04 0.034804 0.098975 ## f_Z2_to_Z3 0.471483 0.058348 8.0806 9.6585e-11 0.357720 0.588287 ## sigma 3.984431 0.383402 10.3923 4.5576e-14 3.213126 4.755737 endpoints(m.Z.FOCUS) ## $ff ## Z2_Z3 Z2_sink ## 0.47148 0.52852 ## ## $distimes ## DT50 DT90 ## Z0 0.31287 1.0393 ## Z1 1.44917 4.8140 ## Z2 1.53473 5.0983 ## Z3 11.80991 39.2317"},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/FOCUS_Z.html","id":"using-the-sforb-model","dir":"Articles > Web_only","previous_headings":"","what":"Using the SFORB model","title":"Example evaluation of FOCUS dataset Z","text":"FOCUS report states, certain tailing time course metabolite Z3. Also, time course parent compound fitted well using SFO model, residues certain low level remain. Therefore, additional model offered , using single first-order reversible binding (SFORB) model metabolite Z3. expected, \\(\\chi^2\\) error level lower metabolite Z3 using model graphical fit Z3 improved. However, covariance matrix returned. Therefore, stepwise model building performed starting stage parent two metabolites, starting assumption model fit parent compound can improved using SFORB model. results much better representation behaviour parent compound Z0. Finally, Z3 added well. models appear overparameterised (covariance matrix returned) sink Z1 left models. error level fit, especially metabolite Z3, can improved SFORB model chosen metabolite, model capable representing tailing metabolite decline phase. summary view backtransformed parameters shows get confidence intervals due overparameterisation. optimized excessively small, seems reasonable fix zero. expected, residual plots Z0 Z3 random case SFO model shown . conclusion, model proposed best-fit model dataset Appendix 7 FOCUS report. graphical representation confidence intervals can finally obtained. endpoints obtained model clear degradation rate Z3 towards end experiment low DT50_Z3_b2 (second Eigenvalue system two differential equations representing SFORB system Z3, corresponding slower rate constant DFOP model) reported infinity. However, appears feature data.","code":"Z.mkin.1 <- mkinmod(Z0 = mkinsub(\"SFO\", \"Z1\", sink = FALSE), Z1 = mkinsub(\"SFO\", \"Z2\", sink = FALSE), Z2 = mkinsub(\"SFO\", \"Z3\"), Z3 = mkinsub(\"SFORB\")) ## Temporary DLL for differentials generated and loaded m.Z.mkin.1 <- mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE) ## Warning in mkinfit(Z.mkin.1, FOCUS_2006_Z_mkin, quiet = TRUE): Observations ## with value of zero were removed from the data plot_sep(m.Z.mkin.1) summary(m.Z.mkin.1, data = FALSE)$cov.unscaled ## NULL Z.mkin.3 <- mkinmod(Z0 = mkinsub(\"SFORB\", \"Z1\", sink = FALSE), Z1 = mkinsub(\"SFO\", \"Z2\", sink = FALSE), Z2 = mkinsub(\"SFO\")) ## Temporary DLL for differentials generated and loaded m.Z.mkin.3 <- mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE) ## Warning in mkinfit(Z.mkin.3, FOCUS_2006_Z_mkin, quiet = TRUE): Observations ## with value of zero were removed from the data plot_sep(m.Z.mkin.3) Z.mkin.4 <- mkinmod(Z0 = mkinsub(\"SFORB\", \"Z1\", sink = FALSE), Z1 = mkinsub(\"SFO\", \"Z2\", sink = FALSE), Z2 = mkinsub(\"SFO\", \"Z3\"), Z3 = mkinsub(\"SFO\")) ## Temporary DLL for differentials generated and loaded m.Z.mkin.4 <- mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin, parms.ini = m.Z.mkin.3$bparms.ode, quiet = TRUE) ## Warning in mkinfit(Z.mkin.4, FOCUS_2006_Z_mkin, parms.ini = ## m.Z.mkin.3$bparms.ode, : Observations with value of zero were removed from the ## data plot_sep(m.Z.mkin.4) Z.mkin.5 <- mkinmod(Z0 = mkinsub(\"SFORB\", \"Z1\", sink = FALSE), Z1 = mkinsub(\"SFO\", \"Z2\", sink = FALSE), Z2 = mkinsub(\"SFO\", \"Z3\"), Z3 = mkinsub(\"SFORB\")) ## Temporary DLL for differentials generated and loaded m.Z.mkin.5 <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini = m.Z.mkin.4$bparms.ode[1:4], quiet = TRUE) ## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini = ## m.Z.mkin.4$bparms.ode[1:4], : Observations with value of zero were removed from ## the data plot_sep(m.Z.mkin.5) m.Z.mkin.5a <- mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini = c(m.Z.mkin.5$bparms.ode[1:7], k_Z3_bound_free = 0), fixed_parms = \"k_Z3_bound_free\", quiet = TRUE) ## Warning in mkinfit(Z.mkin.5, FOCUS_2006_Z_mkin, parms.ini = ## c(m.Z.mkin.5$bparms.ode[1:7], : Observations with value of zero were removed ## from the data plot_sep(m.Z.mkin.5a) mkinparplot(m.Z.mkin.5a) endpoints(m.Z.mkin.5a) ## $ff ## Z0_free Z2_Z3 Z2_sink Z3_free ## 1.00000 0.53656 0.46344 1.00000 ## ## $SFORB ## Z0_b1 Z0_b2 Z0_g Z3_b1 Z3_b2 Z3_g ## 2.4471342 0.0075124 0.9519866 0.0800071 0.0000000 0.9347816 ## ## $distimes ## DT50 DT90 DT50back DT50_Z0_b1 DT50_Z0_b2 DT50_Z3_b1 DT50_Z3_b2 ## Z0 0.3043 1.1848 0.35666 0.28325 92.267 NA NA ## Z1 1.5148 5.0320 NA NA NA NA NA ## Z2 1.6414 5.4526 NA NA NA NA NA ## Z3 NA NA NA NA NA 8.6636 Inf"},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/NAFTA_examples.html","id":"introduction","dir":"Articles > Web_only","previous_headings":"","what":"Introduction","title":"Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance","text":"document, example evaluations provided Attachment 1 SOP US EPA using NAFTA guidance (US EPA 2015) repeated using mkin. original evaluations reported attachment performed using PestDF version 0.8.4. Note PestDF 0.8.13 version distributed US EPA website today (2019-02-26). datasets now distributed mkin package.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/NAFTA_examples.html","id":"examples-where-dfop-did-not-converge-with-pestdf-0-8-4","dir":"Articles > Web_only","previous_headings":"","what":"Examples where DFOP did not converge with PestDF 0.8.4","title":"Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance","text":"attachment 1, reported DFOP model converge datasets PestDF 0.8.4 used. four datasets, DFOP model can fitted mkin (see ). negative half-life given PestDF 0.8.4 fits appears result bug. results two models (SFO IORE) .","code":""},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/NAFTA_examples.html","id":"example-on-page-5-upper-panel","dir":"Articles > Web_only","previous_headings":"Examples where DFOP did not converge with PestDF 0.8.4","what":"Example on page 5, upper panel","title":"Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance","text":"","code":"p5a <- nafta(NAFTA_SOP_Attachment[[\"p5a\"]]) ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c ## The half-life obtained from the IORE model may be used plot(p5a) print(p5a) ## Sums of squares: ## SFO IORE DFOP ## 465.21753 56.27506 32.06401 ## ## Critical sum of squares for checking the SFO model: ## [1] 64.4304 ## ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper ## parent_0 95.8401 4.67e-21 92.245 99.4357 ## k_parent 0.0102 3.92e-12 0.009 0.0117 ## sigma 4.8230 3.81e-06 3.214 6.4318 ## ## $IORE ## Estimate Pr(>t) Lower Upper ## parent_0 1.01e+02 NA 9.91e+01 1.02e+02 ## k__iore_parent 1.54e-05 NA 4.08e-06 5.84e-05 ## N_parent 2.57e+00 NA 2.25e+00 2.89e+00 ## sigma 1.68e+00 NA 1.12e+00 2.24e+00 ## ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 9.99e+01 1.41e-26 98.8116 101.0810 ## k1 2.67e-02 5.05e-06 0.0243 0.0295 ## k2 3.41e-12 5.00e-01 0.0000 Inf ## g 6.47e-01 3.67e-06 0.6248 0.6677 ## sigma 1.27e+00 8.91e-06 0.8395 1.6929 ## ## ## DTx values: ## DT50 DT90 DT50_rep ## SFO 67.7 2.25e+02 6.77e+01 ## IORE 58.2 1.07e+03 3.22e+02 ## DFOP 55.5 3.70e+11 2.03e+11 ## ## Representative half-life: ## [1] 321.51"},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/NAFTA_examples.html","id":"example-on-page-5-lower-panel","dir":"Articles > Web_only","previous_headings":"Examples where DFOP did not converge with PestDF 0.8.4","what":"Example on page 5, lower panel","title":"Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance","text":"","code":"p5b <- nafta(NAFTA_SOP_Attachment[[\"p5b\"]]) ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c ## The half-life obtained from the IORE model may be used plot(p5b) print(p5b) ## Sums of squares: ## SFO IORE DFOP ## 94.81123 10.10936 7.55871 ## ## Critical sum of squares for checking the SFO model: ## [1] 11.77879 ## ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper ## parent_0 96.497 2.32e-24 94.85271 98.14155 ## k_parent 0.008 3.42e-14 0.00737 0.00869 ## sigma 2.295 1.22e-05 1.47976 3.11036 ## ## $IORE ## Estimate Pr(>t) Lower Upper ## parent_0 9.85e+01 1.17e-28 9.79e+01 9.92e+01 ## k__iore_parent 1.53e-04 6.50e-03 7.21e-05 3.26e-04 ## N_parent 1.94e+00 5.88e-13 1.76e+00 2.12e+00 ## sigma 7.49e-01 1.63e-05 4.82e-01 1.02e+00 ## ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 9.84e+01 1.24e-27 97.8078 98.9187 ## k1 1.55e-02 4.10e-04 0.0143 0.0167 ## k2 9.07e-12 5.00e-01 0.0000 Inf ## g 6.89e-01 2.92e-03 0.6626 0.7142 ## sigma 6.48e-01 2.38e-05 0.4147 0.8813 ## ## ## DTx values: ## DT50 DT90 DT50_rep ## SFO 86.6 2.88e+02 8.66e+01 ## IORE 85.5 7.17e+02 2.16e+02 ## DFOP 83.6 1.25e+11 7.64e+10 ## ## Representative half-life: ## [1] 215.87"},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/NAFTA_examples.html","id":"example-on-page-6","dir":"Articles > Web_only","previous_headings":"Examples where DFOP did not converge with PestDF 0.8.4","what":"Example on page 6","title":"Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance","text":"","code":"p6 <- nafta(NAFTA_SOP_Attachment[[\"p6\"]]) ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c ## The half-life obtained from the IORE model may be used plot(p6) print(p6) ## Sums of squares: ## SFO IORE DFOP ## 188.45361 51.00699 42.46931 ## ## Critical sum of squares for checking the SFO model: ## [1] 58.39888 ## ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper ## parent_0 94.7759 7.29e-24 92.3478 97.2039 ## k_parent 0.0179 8.02e-16 0.0166 0.0194 ## sigma 3.0696 3.81e-06 2.0456 4.0936 ## ## $IORE ## Estimate Pr(>t) Lower Upper ## parent_0 97.12446 2.63e-26 95.62461 98.62431 ## k__iore_parent 0.00252 1.95e-03 0.00134 0.00472 ## N_parent 1.49587 4.07e-13 1.33896 1.65279 ## sigma 1.59698 5.05e-06 1.06169 2.13227 ## ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 9.66e+01 1.57e-25 95.3476 97.8979 ## k1 2.55e-02 7.33e-06 0.0233 0.0278 ## k2 3.84e-11 5.00e-01 0.0000 Inf ## g 8.61e-01 7.55e-06 0.8314 0.8867 ## sigma 1.46e+00 6.93e-06 0.9661 1.9483 ## ## ## DTx values: ## DT50 DT90 DT50_rep ## SFO 38.6 1.28e+02 3.86e+01 ## IORE 34.0 1.77e+02 5.32e+01 ## DFOP 34.1 8.50e+09 1.80e+10 ## ## Representative half-life: ## [1] 53.17"},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/NAFTA_examples.html","id":"example-on-page-7","dir":"Articles > Web_only","previous_headings":"Examples where DFOP did not converge with PestDF 0.8.4","what":"Example on page 7","title":"Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance","text":"","code":"p7 <- nafta(NAFTA_SOP_Attachment[[\"p7\"]]) ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c ## The half-life obtained from the IORE model may be used plot(p7) print(p7) ## Sums of squares: ## SFO IORE DFOP ## 3661.661 3195.030 3174.145 ## ## Critical sum of squares for checking the SFO model: ## [1] 3334.194 ## ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper ## parent_0 96.41796 4.80e-53 93.32245 99.51347 ## k_parent 0.00735 7.64e-21 0.00641 0.00843 ## sigma 7.94557 1.83e-15 6.46713 9.42401 ## ## $IORE ## Estimate Pr(>t) Lower Upper ## parent_0 9.92e+01 NA 9.55e+01 1.03e+02 ## k__iore_parent 1.60e-05 NA 1.45e-07 1.77e-03 ## N_parent 2.45e+00 NA 1.35e+00 3.54e+00 ## sigma 7.42e+00 NA 6.04e+00 8.80e+00 ## ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 9.89e+01 9.44e-49 95.4640 102.2573 ## k1 1.81e-02 1.75e-01 0.0116 0.0281 ## k2 3.62e-10 5.00e-01 0.0000 Inf ## g 6.06e-01 2.19e-01 0.4826 0.7178 ## sigma 7.40e+00 2.97e-15 6.0201 8.7754 ## ## ## DTx values: ## DT50 DT90 DT50_rep ## SFO 94.3 3.13e+02 9.43e+01 ## IORE 96.7 1.51e+03 4.55e+02 ## DFOP 96.4 3.79e+09 1.92e+09 ## ## Representative half-life: ## [1] 454.55"},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/NAFTA_examples.html","id":"example-on-page-8","dir":"Articles > Web_only","previous_headings":"Examples where the representative half-life deviates from the observed DT50","what":"Example on page 8","title":"Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance","text":"dataset, IORE fit converge default starting values used mkin IORE model used. Therefore, lower value rate constant used .","code":"p8 <- nafta(NAFTA_SOP_Attachment[[\"p8\"]], parms.ini = c(k__iore_parent = 1e-3)) ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c ## The half-life obtained from the IORE model may be used plot(p8) print(p8) ## Sums of squares: ## SFO IORE DFOP ## 1996.9408 444.9237 547.5616 ## ## Critical sum of squares for checking the SFO model: ## [1] 477.4924 ## ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper ## parent_0 88.16549 6.53e-29 83.37344 92.95754 ## k_parent 0.00803 1.67e-13 0.00674 0.00957 ## sigma 7.44786 4.17e-10 5.66209 9.23363 ## ## $IORE ## Estimate Pr(>t) Lower Upper ## parent_0 9.77e+01 7.03e-35 9.44e+01 1.01e+02 ## k__iore_parent 6.14e-05 3.20e-02 2.12e-05 1.78e-04 ## N_parent 2.27e+00 4.23e-18 2.00e+00 2.54e+00 ## sigma 3.52e+00 5.36e-10 2.67e+00 4.36e+00 ## ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 95.70619 8.99e-32 91.87941 99.53298 ## k1 0.02500 5.25e-04 0.01422 0.04394 ## k2 0.00273 6.84e-03 0.00125 0.00597 ## g 0.58835 2.84e-06 0.36595 0.77970 ## sigma 3.90001 6.94e-10 2.96260 4.83741 ## ## ## DTx values: ## DT50 DT90 DT50_rep ## SFO 86.3 287 86.3 ## IORE 53.4 668 201.0 ## DFOP 55.6 517 253.0 ## ## Representative half-life: ## [1] 201.03"},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/NAFTA_examples.html","id":"example-on-page-9-upper-panel","dir":"Articles > Web_only","previous_headings":"Examples where SFO was not selected for an abiotic study","what":"Example on page 9, upper panel","title":"Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance","text":"example, residuals SFO indicate lack fit model, even abiotic experiment, data suggest simple exponential decline.","code":"p9a <- nafta(NAFTA_SOP_Attachment[[\"p9a\"]]) ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c ## The half-life obtained from the IORE model may be used plot(p9a) print(p9a) ## Sums of squares: ## SFO IORE DFOP ## 839.35238 88.57064 9.93363 ## ## Critical sum of squares for checking the SFO model: ## [1] 105.5678 ## ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper ## parent_0 88.1933 3.06e-12 79.9447 96.4419 ## k_parent 0.0409 2.07e-07 0.0324 0.0516 ## sigma 7.2429 3.92e-05 4.4768 10.0090 ## ## $IORE ## Estimate Pr(>t) Lower Upper ## parent_0 9.89e+01 1.12e-16 9.54e+01 1.02e+02 ## k__iore_parent 1.93e-05 1.13e-01 3.49e-06 1.06e-04 ## N_parent 2.91e+00 1.45e-09 2.50e+00 3.32e+00 ## sigma 2.35e+00 5.31e-05 1.45e+00 3.26e+00 ## ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 9.85e+01 2.54e-20 97.390 99.672 ## k1 1.38e-01 3.52e-05 0.131 0.146 ## k2 9.02e-13 5.00e-01 0.000 Inf ## g 6.52e-01 8.13e-06 0.642 0.661 ## sigma 7.88e-01 6.13e-02 0.481 1.095 ## ## ## DTx values: ## DT50 DT90 DT50_rep ## SFO 16.9 5.63e+01 1.69e+01 ## IORE 11.6 3.37e+02 1.01e+02 ## DFOP 10.5 1.38e+12 7.68e+11 ## ## Representative half-life: ## [1] 101.43"},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/NAFTA_examples.html","id":"example-on-page-9-lower-panel","dir":"Articles > Web_only","previous_headings":"Examples where SFO was not selected for an abiotic study","what":"Example on page 9, lower panel","title":"Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance","text":", mkin gives longer slow DT50 DFOP model (17.8 days) PestDF (13.5 days). Presumably, related fact PestDF gives negative value proportion fast degradation 0 1, inclusive. parameter called f PestDF g mkin. mkin, restricted interval 0 1.","code":"p9b <- nafta(NAFTA_SOP_Attachment[[\"p9b\"]]) ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c ## The half-life obtained from the IORE model may be used plot(p9b) print(p9b) ## Sums of squares: ## SFO IORE DFOP ## 35.64867 23.22334 35.64867 ## ## Critical sum of squares for checking the SFO model: ## [1] 28.54188 ## ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper ## parent_0 94.7123 2.15e-19 93.178 96.2464 ## k_parent 0.0389 4.47e-14 0.037 0.0408 ## sigma 1.5957 1.28e-04 0.932 2.2595 ## ## $IORE ## Estimate Pr(>t) Lower Upper ## parent_0 93.863 2.32e-18 92.4565 95.269 ## k__iore_parent 0.127 1.85e-02 0.0504 0.321 ## N_parent 0.711 1.88e-05 0.4843 0.937 ## sigma 1.288 1.76e-04 0.7456 1.830 ## ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 94.7123 1.61e-16 93.1355 96.2891 ## k1 0.0389 1.08e-04 0.0266 0.0569 ## k2 0.0389 2.24e-04 0.0255 0.0592 ## g 0.5256 5.00e-01 0.0000 1.0000 ## sigma 1.5957 2.50e-04 0.9135 2.2779 ## ## ## DTx values: ## DT50 DT90 DT50_rep ## SFO 17.8 59.2 17.8 ## IORE 18.4 49.2 14.8 ## DFOP 17.8 59.2 17.8 ## ## Representative half-life: ## [1] 14.8"},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/NAFTA_examples.html","id":"example-on-page-10","dir":"Articles > Web_only","previous_headings":"Examples where SFO was not selected for an abiotic study","what":"Example on page 10","title":"Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance","text":", value N given IORE model, data suggests faster decline towards end experiment, appears physically rather unlikely case photolysis study. seems PestDF constrain N values zero, thus slight difference IORE model parameters PestDF mkin.","code":"p10 <- nafta(NAFTA_SOP_Attachment[[\"p10\"]]) ## Warning in sqrt(diag(covar_notrans)): NaNs produced ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c ## The half-life obtained from the IORE model may be used plot(p10) print(p10) ## Sums of squares: ## SFO IORE DFOP ## 899.4089 336.4348 899.4089 ## ## Critical sum of squares for checking the SFO model: ## [1] 413.4841 ## ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper ## parent_0 101.7315 6.42e-11 91.9259 111.5371 ## k_parent 0.0495 1.70e-07 0.0404 0.0607 ## sigma 8.0152 1.28e-04 4.6813 11.3491 ## ## $IORE ## Estimate Pr(>t) Lower Upper ## parent_0 96.86 3.32e-12 90.848 102.863 ## k__iore_parent 2.96 7.91e-02 0.687 12.761 ## N_parent 0.00 5.00e-01 -0.372 0.372 ## sigma 4.90 1.77e-04 2.837 6.968 ## ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 101.7315 1.41e-09 91.6534 111.810 ## k1 0.0495 3.04e-03 0.0188 0.131 ## k2 0.0495 4.92e-04 0.0197 0.124 ## g 0.4487 NaN 0.0000 1.000 ## sigma 8.0152 2.50e-04 4.5886 11.442 ## ## ## DTx values: ## DT50 DT90 DT50_rep ## SFO 14.0 46.5 14.00 ## IORE 16.4 29.4 8.86 ## DFOP 14.0 46.5 14.00 ## ## Representative half-life: ## [1] 8.86"},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/NAFTA_examples.html","id":"example-on-page-11","dir":"Articles > Web_only","previous_headings":"The DT50 was not observed during the study","what":"Example on page 11","title":"Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance","text":"case, DFOP fit reported PestDF resulted negative value slower rate constant, possible mkin. results agreement.","code":"p11 <- nafta(NAFTA_SOP_Attachment[[\"p11\"]]) ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c ## The half-life obtained from the IORE model may be used plot(p11) print(p11) ## Sums of squares: ## SFO IORE DFOP ## 579.6805 204.7932 144.7783 ## ## Critical sum of squares for checking the SFO model: ## [1] 251.6944 ## ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper ## parent_0 96.15820 4.83e-13 90.24934 1.02e+02 ## k_parent 0.00321 4.71e-05 0.00222 4.64e-03 ## sigma 6.43473 1.28e-04 3.75822 9.11e+00 ## ## $IORE ## Estimate Pr(>t) Lower Upper ## parent_0 1.05e+02 NA 9.90e+01 1.10e+02 ## k__iore_parent 3.11e-17 NA 1.35e-20 7.18e-14 ## N_parent 8.36e+00 NA 6.62e+00 1.01e+01 ## sigma 3.82e+00 NA 2.21e+00 5.44e+00 ## ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 1.05e+02 9.47e-13 99.9990 109.1224 ## k1 4.41e-02 5.95e-03 0.0296 0.0658 ## k2 9.94e-13 5.00e-01 0.0000 Inf ## g 3.22e-01 1.45e-03 0.2814 0.3650 ## sigma 3.22e+00 3.52e-04 1.8410 4.5906 ## ## ## DTx values: ## DT50 DT90 DT50_rep ## SFO 2.16e+02 7.18e+02 2.16e+02 ## IORE 9.73e+02 1.37e+08 4.11e+07 ## DFOP 3.07e+11 1.93e+12 6.98e+11 ## ## Representative half-life: ## [1] 41148169"},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/NAFTA_examples.html","id":"n-is-less-than-1-and-the-dfop-rate-constants-are-like-the-sfo-rate-constant","dir":"Articles > Web_only","previous_headings":"","what":"N is less than 1 and the DFOP rate constants are like the SFO rate constant","title":"Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance","text":"following three examples, results obtained mkin reported PestDF. case page 10, N values 1 deemed unrealistic appear result overparameterisation.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/NAFTA_examples.html","id":"example-on-page-12-upper-panel","dir":"Articles > Web_only","previous_headings":"N is less than 1 and the DFOP rate constants are like the SFO rate constant","what":"Example on page 12, upper panel","title":"Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance","text":"","code":"p12a <- nafta(NAFTA_SOP_Attachment[[\"p12a\"]]) ## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance ## matrix ## Warning in sqrt(diag(covar_notrans)): NaNs produced ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c ## The half-life obtained from the IORE model may be used plot(p12a) print(p12a) ## Sums of squares: ## SFO IORE DFOP ## 695.4440 220.0685 695.4440 ## ## Critical sum of squares for checking the SFO model: ## [1] 270.4679 ## ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper ## parent_0 100.521 8.75e-12 92.461 108.581 ## k_parent 0.124 3.61e-08 0.104 0.148 ## sigma 7.048 1.28e-04 4.116 9.980 ## ## $IORE ## Estimate Pr(>t) Lower Upper ## parent_0 96.823 NA NA NA ## k__iore_parent 2.436 NA NA NA ## N_parent 0.263 NA NA NA ## sigma 3.965 NA NA NA ## ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 100.521 2.74e-10 92.2366 108.805 ## k1 0.124 2.53e-05 0.0908 0.170 ## k2 0.124 2.52e-02 0.0456 0.339 ## g 0.793 NaN 0.0000 1.000 ## sigma 7.048 2.50e-04 4.0349 10.061 ## ## ## DTx values: ## DT50 DT90 DT50_rep ## SFO 5.58 18.5 5.58 ## IORE 6.49 13.2 3.99 ## DFOP 5.58 18.5 5.58 ## ## Representative half-life: ## [1] 3.99"},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/NAFTA_examples.html","id":"example-on-page-12-lower-panel","dir":"Articles > Web_only","previous_headings":"N is less than 1 and the DFOP rate constants are like the SFO rate constant","what":"Example on page 12, lower panel","title":"Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance","text":"","code":"p12b <- nafta(NAFTA_SOP_Attachment[[\"p12b\"]]) ## Warning in sqrt(diag(covar)): NaNs produced ## Warning in qt(alpha/2, rdf): NaNs produced ## Warning in qt(1 - alpha/2, rdf): NaNs produced ## Warning in pt(abs(tval), rdf, lower.tail = FALSE): NaNs produced ## Warning in sqrt(1/diag(V)): NaNs produced ## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result ## is doubtful ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c ## The half-life obtained from the IORE model may be used plot(p12b) print(p12b) ## Sums of squares: ## SFO IORE DFOP ## 58.90242 19.06353 58.90242 ## ## Critical sum of squares for checking the SFO model: ## [1] 51.51756 ## ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper ## parent_0 97.6840 0.00039 85.9388 109.4292 ## k_parent 0.0589 0.00261 0.0431 0.0805 ## sigma 3.4323 0.04356 -1.2377 8.1023 ## ## $IORE ## Estimate Pr(>t) Lower Upper ## parent_0 95.523 0.0055 74.539157 116.51 ## k__iore_parent 0.333 0.1433 0.000717 154.57 ## N_parent 0.568 0.0677 -0.989464 2.13 ## sigma 1.953 0.0975 -5.893100 9.80 ## ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 97.6840 NaN NaN NaN ## k1 0.0589 NaN NA NA ## k2 0.0589 NaN NA NA ## g 0.6473 NaN NA NA ## sigma 3.4323 NaN NaN NaN ## ## ## DTx values: ## DT50 DT90 DT50_rep ## SFO 11.8 39.1 11.80 ## IORE 12.9 31.4 9.46 ## DFOP 11.8 39.1 11.80 ## ## Representative half-life: ## [1] 9.46"},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/NAFTA_examples.html","id":"example-on-page-13","dir":"Articles > Web_only","previous_headings":"N is less than 1 and the DFOP rate constants are like the SFO rate constant","what":"Example on page 13","title":"Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance","text":"","code":"p13 <- nafta(NAFTA_SOP_Attachment[[\"p13\"]]) ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c ## The half-life obtained from the IORE model may be used plot(p13) print(p13) ## Sums of squares: ## SFO IORE DFOP ## 174.5971 142.3951 174.5971 ## ## Critical sum of squares for checking the SFO model: ## [1] 172.131 ## ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper ## parent_0 92.73500 5.99e-17 89.61936 95.85065 ## k_parent 0.00258 2.42e-09 0.00223 0.00299 ## sigma 3.41172 7.07e-05 2.05455 4.76888 ## ## $IORE ## Estimate Pr(>t) Lower Upper ## parent_0 91.6016 6.34e-16 88.53086 94.672 ## k__iore_parent 0.0396 2.36e-01 0.00207 0.759 ## N_parent 0.3541 1.46e-01 -0.35153 1.060 ## sigma 3.0811 9.64e-05 1.84296 4.319 ## ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 92.73500 NA 8.95e+01 95.92118 ## k1 0.00258 NA 4.18e-04 0.01592 ## k2 0.00258 NA 1.75e-03 0.00381 ## g 0.16452 NA 0.00e+00 1.00000 ## sigma 3.41172 NA 2.02e+00 4.79960 ## ## ## DTx values: ## DT50 DT90 DT50_rep ## SFO 269 892 269 ## IORE 261 560 169 ## DFOP 269 892 269 ## ## Representative half-life: ## [1] 168.51"},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/NAFTA_examples.html","id":"dt50-not-observed-in-the-study-and-dfop-problems-in-pestdf","dir":"Articles > Web_only","previous_headings":"","what":"DT50 not observed in the study and DFOP problems in PestDF","title":"Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance","text":"slower rate constant reported PestDF negative, physically realistic, possible mkin. fits give results mkin PestDF.","code":"p14 <- nafta(NAFTA_SOP_Attachment[[\"p14\"]]) ## Warning in sqrt(diag(covar)): NaNs produced ## Warning in sqrt(1/diag(V)): NaNs produced ## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result ## is doubtful ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c ## The half-life obtained from the IORE model may be used plot(p14) print(p14) ## Sums of squares: ## SFO IORE DFOP ## 48.43249 28.67746 27.26248 ## ## Critical sum of squares for checking the SFO model: ## [1] 32.83337 ## ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper ## parent_0 99.47124 2.06e-30 98.42254 1.01e+02 ## k_parent 0.00279 3.75e-15 0.00256 3.04e-03 ## sigma 1.55616 3.81e-06 1.03704 2.08e+00 ## ## $IORE ## Estimate Pr(>t) Lower Upper ## parent_0 1.00e+02 NA NaN NaN ## k__iore_parent 9.44e-08 NA NaN NaN ## N_parent 3.31e+00 NA NaN NaN ## sigma 1.20e+00 NA 0.796 1.6 ## ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 1.00e+02 2.96e-28 99.40280 101.2768 ## k1 9.53e-03 1.20e-01 0.00638 0.0143 ## k2 5.21e-12 5.00e-01 0.00000 Inf ## g 3.98e-01 2.19e-01 0.30481 0.4998 ## sigma 1.17e+00 7.68e-06 0.77406 1.5610 ## ## ## DTx values: ## DT50 DT90 DT50_rep ## SFO 2.48e+02 8.25e+02 2.48e+02 ## IORE 4.34e+02 2.22e+04 6.70e+03 ## DFOP 3.55e+10 3.44e+11 1.33e+11 ## ## Representative half-life: ## [1] 6697.44"},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/NAFTA_examples.html","id":"n-is-less-than-1-and-dfop-fraction-parameter-is-below-zero","dir":"Articles > Web_only","previous_headings":"","what":"N is less than 1 and DFOP fraction parameter is below zero","title":"Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance","text":"mkin, IORE fit affected (deemed unrealistic), fraction parameter DFOP model restricted interval 0 1 mkin. SFO fits give results mkin PestDF.","code":"p15a <- nafta(NAFTA_SOP_Attachment[[\"p15a\"]]) ## Warning in sqrt(diag(covar)): NaNs produced ## Warning in sqrt(1/diag(V)): NaNs produced ## Warning in cov2cor(ans$covar): diag(.) had 0 or NA entries; non-finite result ## is doubtful ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c ## The half-life obtained from the IORE model may be used plot(p15a) print(p15a) ## Sums of squares: ## SFO IORE DFOP ## 245.5248 135.0132 245.5248 ## ## Critical sum of squares for checking the SFO model: ## [1] 165.9335 ## ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper ## parent_0 97.96751 2.00e-15 94.32049 101.615 ## k_parent 0.00952 4.93e-09 0.00824 0.011 ## sigma 4.18778 1.28e-04 2.44588 5.930 ## ## $IORE ## Estimate Pr(>t) Lower Upper ## parent_0 95.874 2.94e-15 92.937 98.811 ## k__iore_parent 0.629 2.11e-01 0.044 8.982 ## N_parent 0.000 5.00e-01 -0.642 0.642 ## sigma 3.105 1.78e-04 1.795 4.416 ## ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 97.96751 2.85e-13 94.21913 101.7159 ## k1 0.00952 6.28e-02 0.00260 0.0349 ## k2 0.00952 1.27e-04 0.00652 0.0139 ## g 0.21241 5.00e-01 NA NA ## sigma 4.18778 2.50e-04 2.39747 5.9781 ## ## ## DTx values: ## DT50 DT90 DT50_rep ## SFO 72.8 242 72.8 ## IORE 76.3 137 41.3 ## DFOP 72.8 242 72.8 ## ## Representative half-life: ## [1] 41.33 p15b <- nafta(NAFTA_SOP_Attachment[[\"p15b\"]]) ## Warning in summary.mkinfit(x): Could not calculate correlation; no covariance ## matrix ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c ## The half-life obtained from the IORE model may be used plot(p15b) print(p15b) ## Sums of squares: ## SFO IORE DFOP ## 106.91629 68.55574 106.91629 ## ## Critical sum of squares for checking the SFO model: ## [1] 84.25618 ## ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper ## parent_0 1.01e+02 3.06e-17 98.31594 1.03e+02 ## k_parent 4.86e-03 2.48e-10 0.00435 5.42e-03 ## sigma 2.76e+00 1.28e-04 1.61402 3.91e+00 ## ## $IORE ## Estimate Pr(>t) Lower Upper ## parent_0 99.83 1.81e-16 97.51348 102.14 ## k__iore_parent 0.38 3.22e-01 0.00352 41.05 ## N_parent 0.00 5.00e-01 -1.07696 1.08 ## sigma 2.21 2.57e-04 1.23245 3.19 ## ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 1.01e+02 NA NA NA ## k1 4.86e-03 NA NA NA ## k2 4.86e-03 NA NA NA ## g 1.88e-01 NA NA NA ## sigma 2.76e+00 NA NA NA ## ## ## DTx values: ## DT50 DT90 DT50_rep ## SFO 143 474 143.0 ## IORE 131 236 71.2 ## DFOP 143 474 143.0 ## ## Representative half-life: ## [1] 71.18"},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/NAFTA_examples.html","id":"the-dfop-fraction-parameter-is-greater-than-1","dir":"Articles > Web_only","previous_headings":"","what":"The DFOP fraction parameter is greater than 1","title":"Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance","text":"PestDF, DFOP fit seems stuck local minimum, mkin finds solution much lower \\(\\chi^2\\) error level. half-life slower rate constant DFOP model larger IORE derived half-life, NAFTA recommendation obtained mkin use DFOP representative half-life 8.9 days.","code":"p16 <- nafta(NAFTA_SOP_Attachment[[\"p16\"]]) ## The SFO model is rejected as S_SFO is equal or higher than the critical value S_c ## The representative half-life of the IORE model is longer than the one corresponding ## to the terminal degradation rate found with the DFOP model. ## The representative half-life obtained from the DFOP model may be used plot(p16) print(p16) ## Sums of squares: ## SFO IORE DFOP ## 3831.804 2062.008 1550.980 ## ## Critical sum of squares for checking the SFO model: ## [1] 2247.348 ## ## Parameters: ## $SFO ## Estimate Pr(>t) Lower Upper ## parent_0 71.953 2.33e-13 60.509 83.40 ## k_parent 0.159 4.86e-05 0.102 0.25 ## sigma 11.302 1.25e-08 8.308 14.30 ## ## $IORE ## Estimate Pr(>t) Lower Upper ## parent_0 8.74e+01 2.48e-16 7.72e+01 97.52972 ## k__iore_parent 4.55e-04 2.16e-01 3.48e-05 0.00595 ## N_parent 2.70e+00 1.21e-08 1.99e+00 3.40046 ## sigma 8.29e+00 1.61e-08 6.09e+00 10.49062 ## ## $DFOP ## Estimate Pr(>t) Lower Upper ## parent_0 88.5333 7.40e-18 79.9836 97.083 ## k1 18.8461 5.00e-01 0.0000 Inf ## k2 0.0776 1.41e-05 0.0518 0.116 ## g 0.4733 1.41e-09 0.3674 0.582 ## sigma 7.1902 2.11e-08 5.2785 9.102 ## ## ## DTx values: ## DT50 DT90 DT50_rep ## SFO 4.35 14.4 4.35 ## IORE 1.48 32.1 9.67 ## DFOP 0.67 21.4 8.93 ## ## Representative half-life: ## [1] 8.93"},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/NAFTA_examples.html","id":"conclusions","dir":"Articles > Web_only","previous_headings":"","what":"Conclusions","title":"Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance","text":"results obtained mkin deviate results obtained PestDF either cases one interpretive rules apply, .e. IORE parameter N less one DFOP k values obtained PestDF equal SFO k values, cases DFOP model converge, often lead negative rate constants returned PestDF. Therefore, mkin appears suitable kinetic evaluations according NAFTA guidance.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/benchmarks.html","id":"test-cases","dir":"Articles > Web_only","previous_headings":"","what":"Test cases","title":"Benchmark timings for mkin","text":"Parent : One metabolite: Two metabolites, synthetic data:","code":"FOCUS_C <- FOCUS_2006_C FOCUS_D <- subset(FOCUS_2006_D, value != 0) parent_datasets <- list(FOCUS_C, FOCUS_D) t1 <- system.time(mmkin_bench(c(\"SFO\", \"FOMC\", \"DFOP\", \"HS\"), parent_datasets))[[\"elapsed\"]] t2 <- system.time(mmkin_bench(c(\"SFO\", \"FOMC\", \"DFOP\", \"HS\"), parent_datasets, error_model = \"tc\"))[[\"elapsed\"]] SFO_SFO <- mkinmod( parent = mkinsub(\"SFO\", \"m1\"), m1 = mkinsub(\"SFO\")) FOMC_SFO <- mkinmod( parent = mkinsub(\"FOMC\", \"m1\"), m1 = mkinsub(\"SFO\")) DFOP_SFO <- mkinmod( parent = mkinsub(\"FOMC\", \"m1\"), # erroneously used FOMC twice, not fixed for consistency m1 = mkinsub(\"SFO\")) t3 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D)))[[\"elapsed\"]] t4 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D), error_model = \"tc\"))[[\"elapsed\"]] t5 <- system.time(mmkin_bench(list(SFO_SFO, FOMC_SFO, DFOP_SFO), list(FOCUS_D), error_model = \"obs\"))[[\"elapsed\"]] m_synth_SFO_lin <- mkinmod(parent = mkinsub(\"SFO\", \"M1\"), M1 = mkinsub(\"SFO\", \"M2\"), M2 = mkinsub(\"SFO\"), use_of_ff = \"max\", quiet = TRUE) m_synth_DFOP_par <- mkinmod(parent = mkinsub(\"DFOP\", c(\"M1\", \"M2\")), M1 = mkinsub(\"SFO\"), M2 = mkinsub(\"SFO\"), use_of_ff = \"max\", quiet = TRUE) SFO_lin_a <- synthetic_data_for_UBA_2014[[1]]$data DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data t6 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a)))[[\"elapsed\"]] t7 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c)))[[\"elapsed\"]] t8 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), error_model = \"tc\"))[[\"elapsed\"]] t9 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), error_model = \"tc\"))[[\"elapsed\"]] t10 <- system.time(mmkin_bench(list(m_synth_SFO_lin), list(SFO_lin_a), error_model = \"obs\"))[[\"elapsed\"]] t11 <- system.time(mmkin_bench(list(m_synth_DFOP_par), list(DFOP_par_c), error_model = \"obs\"))[[\"elapsed\"]]"},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/benchmarks.html","id":"results","dir":"Articles > Web_only","previous_headings":"","what":"Results","title":"Benchmark timings for mkin","text":"Benchmarks available error models shown. intended improving mkin, comparing CPUs operating systems. trademarks belong respective owners.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/benchmarks.html","id":"parent-only","dir":"Articles > Web_only","previous_headings":"Results","what":"Parent only","title":"Benchmark timings for mkin","text":"Constant variance (t1) two-component error model (t2) four models fitted two datasets, .e. eight fits test.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/benchmarks.html","id":"one-metabolite","dir":"Articles > Web_only","previous_headings":"Results","what":"One metabolite","title":"Benchmark timings for mkin","text":"Constant variance (t3), two-component error model (t4), variance variable (t5) three models fitted one dataset, .e. three fits test.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/benchmarks.html","id":"two-metabolites","dir":"Articles > Web_only","previous_headings":"Results","what":"Two metabolites","title":"Benchmark timings for mkin","text":"Constant variance (t6 t7), two-component error model (t8 t9), variance variable (t10 t11) one model fitted one dataset, .e. one fit test.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/compiled_models.html","id":"how-to-benefit-from-compiled-models","dir":"Articles > Web_only","previous_headings":"","what":"How to benefit from compiled models","title":"Performance benefit by using compiled model definitions in mkin","text":"using mkin version equal greater 0.9-36 C compiler available, see message model compiled autogenerated C code defining model using mkinmod. Starting version 0.9.49.9, mkinmod() function checks presence compiler using previous versions, used Sys.(\"gcc\") check. Linux, need essential build tools like make gcc clang installed. Debian based linux distributions, pulled installing build-essential package. MacOS, use personally, reports compiler available default. Windows, need install Rtools path bin directory PATH variable. need modify PATH variable installing Rtools. Instead, recommend put line .Rprofile startup file. just text file R code executed R session starts. named .Rprofile located home directory, generally Documents folder. can check location home directory used R issuing","code":"pkgbuild::has_compiler() Sys.setenv(PATH = paste(\"C:/Rtools/bin\", Sys.getenv(\"PATH\"), sep=\";\")) Sys.getenv(\"HOME\")"},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/compiled_models.html","id":"comparison-with-other-solution-methods","dir":"Articles > Web_only","previous_headings":"","what":"Comparison with other solution methods","title":"Performance benefit by using compiled model definitions in mkin","text":"First, build simple degradation model parent compound one metabolite, remove zero values dataset. can compare performance Eigenvalue based solution compiled version R implementation differential equations using benchmark package. output code, warnings zero removed FOCUS D dataset suppressed. Since mkin version 0.9.49.11, analytical solution also implemented, included tests . see using compiled model factor 10 faster using deSolve without compiled code.","code":"library(\"mkin\", quietly = TRUE) SFO_SFO <- mkinmod( parent = mkinsub(\"SFO\", \"m1\"), m1 = mkinsub(\"SFO\")) ## Temporary DLL for differentials generated and loaded FOCUS_D <- subset(FOCUS_2006_D, value != 0) if (require(rbenchmark)) { b.1 <- benchmark( \"deSolve, not compiled\" = mkinfit(SFO_SFO, FOCUS_D, solution_type = \"deSolve\", use_compiled = FALSE, quiet = TRUE), \"Eigenvalue based\" = mkinfit(SFO_SFO, FOCUS_D, solution_type = \"eigen\", quiet = TRUE), \"deSolve, compiled\" = mkinfit(SFO_SFO, FOCUS_D, solution_type = \"deSolve\", quiet = TRUE), \"analytical\" = mkinfit(SFO_SFO, FOCUS_D, solution_type = \"analytical\", use_compiled = FALSE, quiet = TRUE), replications = 1, order = \"relative\", columns = c(\"test\", \"replications\", \"relative\", \"elapsed\")) print(b.1) } else { print(\"R package rbenchmark is not available\") } ## test replications relative elapsed ## 4 analytical 1 1.000 0.109 ## 3 deSolve, compiled 1 1.284 0.140 ## 2 Eigenvalue based 1 1.670 0.182 ## 1 deSolve, not compiled 1 21.927 2.390"},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/compiled_models.html","id":"model-without-analytical-solution","dir":"Articles > Web_only","previous_headings":"","what":"Model without analytical solution","title":"Performance benefit by using compiled model definitions in mkin","text":"evaluation also taken example section mkinfit. analytical solution available system, now Eigenvalue based solution possible, deSolve using without compiled code available. get performance benefit factor 24 using version differential equation model compiled C code! vignette built mkin 1.2.6 ","code":"if (require(rbenchmark)) { FOMC_SFO <- mkinmod( parent = mkinsub(\"FOMC\", \"m1\"), m1 = mkinsub( \"SFO\")) b.2 <- benchmark( \"deSolve, not compiled\" = mkinfit(FOMC_SFO, FOCUS_D, use_compiled = FALSE, quiet = TRUE), \"deSolve, compiled\" = mkinfit(FOMC_SFO, FOCUS_D, quiet = TRUE), replications = 1, order = \"relative\", columns = c(\"test\", \"replications\", \"relative\", \"elapsed\")) print(b.2) factor_FOMC_SFO <- round(b.2[\"1\", \"relative\"]) } else { factor_FOMC_SFO <- NA print(\"R package benchmark is not available\") } ## Temporary DLL for differentials generated and loaded ## test replications relative elapsed ## 2 deSolve, compiled 1 1.000 0.181 ## 1 deSolve, not compiled 1 23.646 4.280 ## R version 4.3.2 (2023-10-31) ## Platform: x86_64-pc-linux-gnu (64-bit) ## Running under: Debian GNU/Linux 12 (bookworm) ## CPU model: AMD Ryzen 9 7950X 16-Core Processor"},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/dimethenamid_2018.html","id":"introduction","dir":"Articles > Web_only","previous_headings":"","what":"Introduction","title":"Example evaluations of the dimethenamid data from 2018","text":"first analysis data analysed presented recent journal article nonlinear mixed-effects models degradation kinetics (Ranke et al. 2021). analysis based nlme package development version saemix package unpublished time. Meanwhile, version 3.0 saemix package available CRAN repository. Also, turned error handling Borstel data mkin package time, leading duplication data points soil. dataset mkin package corrected, interface saemix mkin package updated use released version. vignette intended present date analysis data, using corrected dataset released versions mkin saemix.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/dimethenamid_2018.html","id":"data","dir":"Articles > Web_only","previous_headings":"","what":"Data","title":"Example evaluations of the dimethenamid data from 2018","text":"Residue data forming basis endpoints derived conclusion peer review pesticide risk assessment dimethenamid-P published European Food Safety Authority (EFSA) 2018 (EFSA 2018) transcribed risk assessment report (Rapporteur Member State Germany, Co-Rapporteur Member State Bulgaria 2018) can downloaded Open EFSA repository https://open.efsa.europa.eu/study-inventory/EFSA-Q-2014-00716. data available mkin package. following code (hidden default, please use button right show ) treats data available racemic mixture dimethenamid (DMTA) enantiomer dimethenamid-P (DMTAP) way, difference degradation behaviour identified EU risk assessment. observation times dataset multiplied corresponding normalisation factor also available dataset, order make possible describe datasets single set parameters. Also, datasets observed soil merged, resulting dimethenamid (DMTA) data six soils.","code":"library(mkin, quietly = TRUE) dmta_ds <- lapply(1:7, function(i) { ds_i <- dimethenamid_2018$ds[[i]]$data ds_i[ds_i$name == \"DMTAP\", \"name\"] <- \"DMTA\" ds_i$time <- ds_i$time * dimethenamid_2018$f_time_norm[i] ds_i }) names(dmta_ds) <- sapply(dimethenamid_2018$ds, function(ds) ds$title) dmta_ds[[\"Elliot\"]] <- rbind(dmta_ds[[\"Elliot 1\"]], dmta_ds[[\"Elliot 2\"]]) dmta_ds[[\"Elliot 1\"]] <- NULL dmta_ds[[\"Elliot 2\"]] <- NULL"},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/dimethenamid_2018.html","id":"parent-degradation","dir":"Articles > Web_only","previous_headings":"","what":"Parent degradation","title":"Example evaluations of the dimethenamid data from 2018","text":"evaluate observed degradation parent compound using simple exponential decline (SFO) biexponential decline (DFOP), using constant variance (const) two-component variance (tc) error models.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/dimethenamid_2018.html","id":"separate-evaluations","dir":"Articles > Web_only","previous_headings":"Parent degradation","what":"Separate evaluations","title":"Example evaluations of the dimethenamid data from 2018","text":"first step, get visual impression fit different models, separate evaluations soil using mmkin function mkin package: plot individual SFO fits shown suggests least datasets degradation slows towards later time points, scatter residuals error smaller smaller values (panel right): Using biexponential decline (DFOP) results slightly random scatter residuals: population curve (bold line) plot results taking mean individual transformed parameters, .e. log k1 log k2, well logit g parameter DFOP model). , procedure result parameters represent degradation well, datasets fitted value k2 extremely close zero, leading log k2 value dominates average. alleviated rate constants pass t-test significant difference zero (untransformed scale) considered averaging: visually much satisfactory, average procedure introduce bias, results individual fits enter population curve weight. nonlinear mixed-effects models can help treating datasets equally fitting parameter distribution model together degradation model error model (see ). remaining trend residuals higher higher predicted residues reduced using two-component error model: However, note case using error model, fits Flaach BBA 2.3 datasets appear ill-defined, indicated fact converge:","code":"f_parent_mkin_const <- mmkin(c(\"SFO\", \"DFOP\"), dmta_ds, error_model = \"const\", quiet = TRUE) f_parent_mkin_tc <- mmkin(c(\"SFO\", \"DFOP\"), dmta_ds, error_model = \"tc\", quiet = TRUE) plot(mixed(f_parent_mkin_const[\"SFO\", ])) plot(mixed(f_parent_mkin_const[\"DFOP\", ])) plot(mixed(f_parent_mkin_const[\"DFOP\", ]), test_log_parms = TRUE) plot(mixed(f_parent_mkin_tc[\"DFOP\", ]), test_log_parms = TRUE) print(f_parent_mkin_tc[\"DFOP\", ]) <mmkin> object Status of individual fits: dataset model Calke Borstel Flaach BBA 2.2 BBA 2.3 Elliot DFOP OK OK OK OK C OK C: Optimisation did not converge: iteration limit reached without convergence (10) OK: No warnings"},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/dimethenamid_2018.html","id":"nonlinear-mixed-effects-models","dir":"Articles > Web_only","previous_headings":"Parent degradation","what":"Nonlinear mixed-effects models","title":"Example evaluations of the dimethenamid data from 2018","text":"Instead taking model selection decision individual fits, fit nonlinear mixed-effects models (using different fitting algorithms implemented different packages) model selection using available data time. order make sure decisions unduly influenced type algorithm used, implementation details use wrong control parameters, compare model selection results obtained different R packages, different algorithms checking control parameters.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/dimethenamid_2018.html","id":"nlme","dir":"Articles > Web_only","previous_headings":"Parent degradation > Nonlinear mixed-effects models","what":"nlme","title":"Example evaluations of the dimethenamid data from 2018","text":"nlme package first R extension providing facilities fit nonlinear mixed-effects models. like model selection four combinations degradation models error models based AIC. However, fitting DFOP model constant variance using default control parameters results error, signalling maximum number 50 iterations reached, potentially indicating overparameterisation. Nevertheless, algorithm converges two-component error model used combination DFOP model. can explained fact smaller residues observed later sampling times get weight using two-component error model counteract tendency algorithm try parameter combinations unsuitable fitting data. Note certain degree overparameterisation also indicated warning obtained fitting DFOP two-component error model (‘false convergence’ ‘LME step’ iteration 3). However, warning occur later iterations, specifically last 5 iterations, can ignore warning. model comparison function nlme package can directly applied fits showing much lower AIC DFOP model fitted two-component error model. Also, likelihood ratio test indicates difference significant p-value 0.0001. addition fits, attempts also made include correlations random effects using log Cholesky parameterisation matrix specifying . code used attempts can made visible . SFO variants converge fast, additional parameters introduced lead convergence warnings DFOP model. model comparison clearly show adding correlations random effects improve fits. selected model (DFOP two-component error) fitted data assuming correlations random effects shown .","code":"library(nlme) f_parent_nlme_sfo_const <- nlme(f_parent_mkin_const[\"SFO\", ]) # f_parent_nlme_dfop_const <- nlme(f_parent_mkin_const[\"DFOP\", ]) f_parent_nlme_sfo_tc <- nlme(f_parent_mkin_tc[\"SFO\", ]) f_parent_nlme_dfop_tc <- nlme(f_parent_mkin_tc[\"DFOP\", ]) anova( f_parent_nlme_sfo_const, f_parent_nlme_sfo_tc, f_parent_nlme_dfop_tc ) Model df AIC BIC logLik Test L.Ratio p-value f_parent_nlme_sfo_const 1 5 796.60 811.82 -393.30 f_parent_nlme_sfo_tc 2 6 798.60 816.86 -393.30 1 vs 2 0.00 0.998 f_parent_nlme_dfop_tc 3 10 671.91 702.34 -325.95 2 vs 3 134.69 <.0001 f_parent_nlme_sfo_const_logchol <- nlme(f_parent_mkin_const[\"SFO\", ], random = nlme::pdLogChol(list(DMTA_0 ~ 1, log_k_DMTA ~ 1))) anova(f_parent_nlme_sfo_const, f_parent_nlme_sfo_const_logchol) f_parent_nlme_sfo_tc_logchol <- nlme(f_parent_mkin_tc[\"SFO\", ], random = nlme::pdLogChol(list(DMTA_0 ~ 1, log_k_DMTA ~ 1))) anova(f_parent_nlme_sfo_tc, f_parent_nlme_sfo_tc_logchol) f_parent_nlme_dfop_tc_logchol <- nlme(f_parent_mkin_const[\"DFOP\", ], random = nlme::pdLogChol(list(DMTA_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1))) anova(f_parent_nlme_dfop_tc, f_parent_nlme_dfop_tc_logchol) plot(f_parent_nlme_dfop_tc)"},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/dimethenamid_2018.html","id":"saemix","dir":"Articles > Web_only","previous_headings":"Parent degradation > Nonlinear mixed-effects models","what":"saemix","title":"Example evaluations of the dimethenamid data from 2018","text":"saemix package provided first Open Source implementation Stochastic Approximation Expectation Maximisation (SAEM) algorithm. SAEM fits degradation models can conveniently performed using interface saemix package available current development versions mkin package. corresponding SAEM fits four combinations degradation error models fitted . convergence criterion implemented saemix package, convergence plots need manually checked every fit. define control settings work well parent data fits shown vignette. convergence plot SFO model using constant variance shown . Obviously selected number iterations sufficient reach convergence. can also said SFO fit using two-component error model. fitting DFOP model constant variance (see ), parameter convergence unambiguous. parameters converge credible values, variance k2 (omega2.k2) converges small value. printout saem.mmkin model shows estimated standard deviation k2 across population soils (SD.k2) ill-defined, indicating overparameterisation model. DFOP model fitted two-component error model, also observe estimated variance k2 becomes small, ill-defined, illustrated excessive confidence interval SD.k2. Doubling number iterations first phase algorithm leads slightly lower likelihood, therefore slightly higher AIC BIC values. even iterations, algorithm stops error message. related variance k2 approximating zero submitted bug saemix package, algorithm converge case. alternative way fit DFOP combination two-component error model use model formulation transformed parameters used per default mkin. using option, convergence slower, eventually algorithm stops well error message. four combinations (SFO/const, SFO/tc, DFOP/const DFOP/tc) version increased iterations can compared using model comparison function saemix package: order check influence likelihood calculation algorithms implemented saemix, likelihood Gaussian quadrature added best fit, AIC values obtained three methods compared. AIC values based importance sampling Gaussian quadrature similar. Using linearisation known less accurate, still gives similar value. order illustrate comparison three method depends degree convergence obtained fit, comparison shown fit using defaults number iterations number MCMC chains. using OpenBlas linear algebra, large difference values obtained Gaussian quadrature, larger number iterations makes lot difference. using LAPACK version coming Debian Bullseye, AIC based Gaussian quadrature almost one obtained methods, also using defaults fit.","code":"library(saemix) saemix_control <- saemixControl(nbiter.saemix = c(800, 300), nb.chains = 15, print = FALSE, save = FALSE, save.graphs = FALSE, displayProgress = FALSE) saemix_control_moreiter <- saemixControl(nbiter.saemix = c(1600, 300), nb.chains = 15, print = FALSE, save = FALSE, save.graphs = FALSE, displayProgress = FALSE) saemix_control_10k <- saemixControl(nbiter.saemix = c(10000, 300), nb.chains = 15, print = FALSE, save = FALSE, save.graphs = FALSE, displayProgress = FALSE) f_parent_saemix_sfo_const <- mkin::saem(f_parent_mkin_const[\"SFO\", ], quiet = TRUE, control = saemix_control, transformations = \"saemix\") plot(f_parent_saemix_sfo_const$so, plot.type = \"convergence\") f_parent_saemix_sfo_tc <- mkin::saem(f_parent_mkin_tc[\"SFO\", ], quiet = TRUE, control = saemix_control, transformations = \"saemix\") plot(f_parent_saemix_sfo_tc$so, plot.type = \"convergence\") f_parent_saemix_dfop_const <- mkin::saem(f_parent_mkin_const[\"DFOP\", ], quiet = TRUE, control = saemix_control, transformations = \"saemix\") plot(f_parent_saemix_dfop_const$so, plot.type = \"convergence\") print(f_parent_saemix_dfop_const) Kinetic nonlinear mixed-effects model fit by SAEM Structural model: d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * DMTA Data: 155 observations of 1 variable(s) grouped in 6 datasets Likelihood computed by importance sampling AIC BIC logLik 706 704 -344 Fitted parameters: estimate lower upper DMTA_0 97.99583 96.50079 99.4909 k1 0.06377 0.03432 0.0932 k2 0.00848 0.00444 0.0125 g 0.95701 0.91313 1.0009 a.1 1.82141 1.60516 2.0377 SD.DMTA_0 1.64787 0.45729 2.8384 SD.k1 0.57439 0.24731 0.9015 SD.k2 0.03296 -2.50524 2.5712 SD.g 1.10266 0.32354 1.8818 f_parent_saemix_dfop_tc <- mkin::saem(f_parent_mkin_tc[\"DFOP\", ], quiet = TRUE, control = saemix_control, transformations = \"saemix\") f_parent_saemix_dfop_tc_moreiter <- mkin::saem(f_parent_mkin_tc[\"DFOP\", ], quiet = TRUE, control = saemix_control_moreiter, transformations = \"saemix\") plot(f_parent_saemix_dfop_tc$so, plot.type = \"convergence\") print(f_parent_saemix_dfop_tc) Kinetic nonlinear mixed-effects model fit by SAEM Structural model: d_DMTA/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) * DMTA Data: 155 observations of 1 variable(s) grouped in 6 datasets Likelihood computed by importance sampling AIC BIC logLik 666 664 -323 Fitted parameters: estimate lower upper DMTA_0 98.24165 96.29190 100.1914 k1 0.06421 0.03352 0.0949 k2 0.00866 0.00617 0.0111 g 0.95340 0.91218 0.9946 a.1 1.06463 0.86503 1.2642 b.1 0.02964 0.02259 0.0367 SD.DMTA_0 2.03611 0.40416 3.6681 SD.k1 0.59534 0.25692 0.9338 SD.k2 0.00042 -73.01372 73.0146 SD.g 1.04234 0.37189 1.7128 AIC_parent_saemix <- saemix::compare.saemix( f_parent_saemix_sfo_const$so, f_parent_saemix_sfo_tc$so, f_parent_saemix_dfop_const$so, f_parent_saemix_dfop_tc$so, f_parent_saemix_dfop_tc_moreiter$so) Likelihoods calculated by importance sampling rownames(AIC_parent_saemix) <- c( \"SFO const\", \"SFO tc\", \"DFOP const\", \"DFOP tc\", \"DFOP tc more iterations\") print(AIC_parent_saemix) AIC BIC SFO const 796.38 795.34 SFO tc 798.38 797.13 DFOP const 705.75 703.88 DFOP tc 665.67 663.59 DFOP tc more iterations 665.85 663.76 f_parent_saemix_dfop_tc$so <- saemix::llgq.saemix(f_parent_saemix_dfop_tc$so) AIC_parent_saemix_methods <- c( is = AIC(f_parent_saemix_dfop_tc$so, method = \"is\"), gq = AIC(f_parent_saemix_dfop_tc$so, method = \"gq\"), lin = AIC(f_parent_saemix_dfop_tc$so, method = \"lin\") ) print(AIC_parent_saemix_methods) is gq lin 665.67 665.74 665.13 f_parent_saemix_dfop_tc_defaults <- mkin::saem(f_parent_mkin_tc[\"DFOP\", ]) f_parent_saemix_dfop_tc_defaults$so <- saemix::llgq.saemix(f_parent_saemix_dfop_tc_defaults$so) AIC_parent_saemix_methods_defaults <- c( is = AIC(f_parent_saemix_dfop_tc_defaults$so, method = \"is\"), gq = AIC(f_parent_saemix_dfop_tc_defaults$so, method = \"gq\"), lin = AIC(f_parent_saemix_dfop_tc_defaults$so, method = \"lin\") ) print(AIC_parent_saemix_methods_defaults) is gq lin 670.09 669.37 671.29"},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/dimethenamid_2018.html","id":"comparison","dir":"Articles > Web_only","previous_headings":"Parent degradation","what":"Comparison","title":"Example evaluations of the dimethenamid data from 2018","text":"following table gives AIC values obtained backend packages using control parameters (800 iterations burn-, 300 iterations second phase, 15 chains).","code":"AIC_all <- data.frame( check.names = FALSE, \"Degradation model\" = c(\"SFO\", \"SFO\", \"DFOP\", \"DFOP\"), \"Error model\" = c(\"const\", \"tc\", \"const\", \"tc\"), nlme = c(AIC(f_parent_nlme_sfo_const), AIC(f_parent_nlme_sfo_tc), NA, AIC(f_parent_nlme_dfop_tc)), saemix_lin = sapply(list(f_parent_saemix_sfo_const$so, f_parent_saemix_sfo_tc$so, f_parent_saemix_dfop_const$so, f_parent_saemix_dfop_tc$so), AIC, method = \"lin\"), saemix_is = sapply(list(f_parent_saemix_sfo_const$so, f_parent_saemix_sfo_tc$so, f_parent_saemix_dfop_const$so, f_parent_saemix_dfop_tc$so), AIC, method = \"is\") ) kable(AIC_all)"},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/dimethenamid_2018.html","id":"conclusion","dir":"Articles > Web_only","previous_headings":"","what":"Conclusion","title":"Example evaluations of the dimethenamid data from 2018","text":"detailed analysis dimethenamid dataset confirmed DFOP model provides appropriate description decline parent compound data. hand, closer inspection results revealed variability k2 parameter across population soils ill-defined. coincides observation parameter robustly quantified soils. Regarding regulatory use data, claimed improved characterisation mean parameter values across population obtained using nonlinear mixed-effects models presented . However, attempts quantify variability slower rate constant biphasic decline dimethenamid indicate data sufficient characterise variability satisfactory precision.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/dimethenamid_2018.html","id":"session-info","dir":"Articles > Web_only","previous_headings":"","what":"Session Info","title":"Example evaluations of the dimethenamid data from 2018","text":"","code":"sessionInfo() R version 4.3.2 (2023-10-31) 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=C 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] stats graphics grDevices utils datasets methods base other attached packages: [1] saemix_3.2 npde_3.3 nlme_3.1-163 mkin_1.2.6 knitr_1.42 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_0.21-8 digest_0.6.31 magrittr_2.0.3 evaluate_0.21 [9] grid_4.3.2 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_4.3.2 parallel_4.3.2 [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 MASS_7.3-60 ragg_1.2.5 [41] pkgconfig_2.0.3 desc_1.4.2 pkgdown_2.0.7 bslib_0.4.2 [45] pillar_1.9.0 gtable_0.3.3 glue_1.6.2 systemfonts_1.0.4 [49] highr_0.10 xfun_0.39 tibble_3.2.1 lmtest_0.9-40 [53] tidyselect_1.2.0 htmltools_0.5.5 rmarkdown_2.21 compiler_4.3.2"},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/saem_benchmarks.html","id":"test-data","dir":"Articles > Web_only","previous_headings":"","what":"Test data","title":"Benchmark timings for saem.mmkin","text":"Please refer vignette dimethenamid_2018 explanation following preprocessing.","code":"dmta_ds <- lapply(1:7, function(i) { ds_i <- dimethenamid_2018$ds[[i]]$data ds_i[ds_i$name == \"DMTAP\", \"name\"] <- \"DMTA\" ds_i$time <- ds_i$time * dimethenamid_2018$f_time_norm[i] ds_i }) names(dmta_ds) <- sapply(dimethenamid_2018$ds, function(ds) ds$title) dmta_ds[[\"Elliot\"]] <- rbind(dmta_ds[[\"Elliot 1\"]], dmta_ds[[\"Elliot 2\"]]) dmta_ds[[\"Elliot 1\"]] <- NULL dmta_ds[[\"Elliot 2\"]] <- NULL"},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/saem_benchmarks.html","id":"parent-only","dir":"Articles > Web_only","previous_headings":"Test cases","what":"Parent only","title":"Benchmark timings for saem.mmkin","text":"model comparison suggests use SFORB model two-component error. comparison, keep DFOP model two-component error, competes SFORB biphasic curves. two models, random effects transformed parameters k2 k_DMTA_bound_free quantified.","code":"parent_mods <- c(\"SFO\", \"DFOP\", \"SFORB\", \"HS\") parent_sep_const <- mmkin(parent_mods, dmta_ds, quiet = TRUE, cores = n_cores) parent_sep_tc <- update(parent_sep_const, error_model = \"tc\") t1 <- system.time(sfo_const <- saem(parent_sep_const[\"SFO\", ]))[[\"elapsed\"]] t2 <- system.time(dfop_const <- saem(parent_sep_const[\"DFOP\", ]))[[\"elapsed\"]] t3 <- system.time(sforb_const <- saem(parent_sep_const[\"SFORB\", ]))[[\"elapsed\"]] t4 <- system.time(hs_const <- saem(parent_sep_const[\"HS\", ]))[[\"elapsed\"]] t5 <- system.time(sfo_tc <- saem(parent_sep_tc[\"SFO\", ]))[[\"elapsed\"]] t6 <- system.time(dfop_tc <- saem(parent_sep_tc[\"DFOP\", ]))[[\"elapsed\"]] t7 <- system.time(sforb_tc <- saem(parent_sep_tc[\"SFORB\", ]))[[\"elapsed\"]] t8 <- system.time(hs_tc <- saem(parent_sep_tc[\"HS\", ]))[[\"elapsed\"]] anova( sfo_const, dfop_const, sforb_const, hs_const, sfo_tc, dfop_tc, sforb_tc, hs_tc) |> kable(, digits = 1) illparms(dfop_tc) ## [1] \"sd(log_k2)\" illparms(sforb_tc) ## [1] \"sd(log_k_DMTA_bound_free)\""},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/saem_benchmarks.html","id":"one-metabolite","dir":"Articles > Web_only","previous_headings":"Test cases","what":"One metabolite","title":"Benchmark timings for saem.mmkin","text":"remove parameters found ill-defined parent fits.","code":"one_met_mods <- list( DFOP_SFO = mkinmod( DMTA = mkinsub(\"DFOP\", \"M23\"), M23 = mkinsub(\"SFO\")), SFORB_SFO = mkinmod( DMTA = mkinsub(\"SFORB\", \"M23\"), M23 = mkinsub(\"SFO\"))) one_met_sep_const <- mmkin(one_met_mods, dmta_ds, error_model = \"const\", cores = n_cores, quiet = TRUE) one_met_sep_tc <- mmkin(one_met_mods, dmta_ds, error_model = \"tc\", cores = n_cores, quiet = TRUE) t9 <- system.time(dfop_sfo_tc <- saem(one_met_sep_tc[\"DFOP_SFO\", ], no_random_effect = \"log_k2\"))[[\"elapsed\"]] t10 <- system.time(sforb_sfo_tc <- saem(one_met_sep_tc[\"SFORB_SFO\", ], no_random_effect = \"log_k_DMTA_bound_free\"))[[\"elapsed\"]]"},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/saem_benchmarks.html","id":"three-metabolites","dir":"Articles > Web_only","previous_headings":"Test cases","what":"Three metabolites","title":"Benchmark timings for saem.mmkin","text":"case three metabolites, keep SFORB model order limit time compiling vignette, fitting parallel may disturb benchmark. , include random effects ill-defined previous fits subsets degradation model.","code":"illparms(sforb_sfo_tc) three_met_mods <- list( SFORB_SFO3_plus = mkinmod( DMTA = mkinsub(\"SFORB\", c(\"M23\", \"M27\", \"M31\")), M23 = mkinsub(\"SFO\"), M27 = mkinsub(\"SFO\"), M31 = mkinsub(\"SFO\", \"M27\", sink = FALSE))) three_met_sep_tc <- mmkin(three_met_mods, dmta_ds, error_model = \"tc\", cores = n_cores, quiet = TRUE) t11 <- system.time(sforb_sfo3_plus_const <- saem(three_met_sep_tc[\"SFORB_SFO3_plus\", ], no_random_effect = \"log_k_DMTA_bound_free\"))[[\"elapsed\"]]"},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/saem_benchmarks.html","id":"results","dir":"Articles > Web_only","previous_headings":"","what":"Results","title":"Benchmark timings for saem.mmkin","text":"Benchmarks available error models shown. intended improving mkin, comparing CPUs operating systems. trademarks belong respective owners.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/saem_benchmarks.html","id":"parent-only-1","dir":"Articles > Web_only","previous_headings":"Results","what":"Parent only","title":"Benchmark timings for saem.mmkin","text":"Constant variance SFO, DFOP, SFORB HS. Two-component error fits SFO, DFOP, SFORB HS.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/saem_benchmarks.html","id":"one-metabolite-1","dir":"Articles > Web_only","previous_headings":"Results","what":"One metabolite","title":"Benchmark timings for saem.mmkin","text":"Two-component error DFOP-SFO SFORB-SFO.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/articles/web_only/saem_benchmarks.html","id":"three-metabolites-1","dir":"Articles > Web_only","previous_headings":"Results","what":"Three metabolites","title":"Benchmark timings for saem.mmkin","text":"Two-component error SFORB-SFO3-plus","code":""},{"path":"https://pkgdown.jrwb.de/mkin/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Johannes Ranke. Author, maintainer, copyright holder. Katrin Lindenberger. Contributor. contributed mkinresplot() René Lehmann. Contributor. ilr() invilr() Eurofins Regulatory AG. Copyright holder. copyright contributions JR 2012-2014","code":""},{"path":"https://pkgdown.jrwb.de/mkin/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Ranke J (2023). mkin: Kinetic Evaluation Chemical Degradation Data. R package version 1.2.6, https://pkgdown.jrwb.de/mkin/.","code":"@Manual{, title = {mkin: Kinetic Evaluation of Chemical Degradation Data}, author = {Johannes Ranke}, year = {2023}, note = {R package version 1.2.6}, url = {https://pkgdown.jrwb.de/mkin/}, }"},{"path":"https://pkgdown.jrwb.de/mkin/index.html","id":"mkin","dir":"","previous_headings":"","what":"Kinetic Evaluation of Chemical Degradation Data","title":"Kinetic Evaluation of Chemical Degradation Data","text":"R package mkin provides calculation routines analysis chemical degradation data, including multicompartment kinetics needed modelling formation decline transformation products, several degradation compartments involved. provides stable functionality kinetic evaluations according FOCUS guidance (see details). addition, provides functionality hierarchical kinetics based nonlinear mixed-effects models.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Kinetic Evaluation of Chemical Degradation Data","text":"can install latest released version CRAN within R:","code":"install.packages(\"mkin\")"},{"path":"https://pkgdown.jrwb.de/mkin/index.html","id":"background","dir":"","previous_headings":"","what":"Background","title":"Kinetic Evaluation of Chemical Degradation Data","text":"regulatory evaluation chemical substances like plant protection products (pesticides), biocides chemicals, degradation data play important role. evaluation pesticide degradation experiments, detailed guidance various helpful tools developed detailed ‘Credits historical remarks’ . package aims provide one stop solution degradation kinetics, addressing modellers willing , even prefer work R.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/index.html","id":"basic-usage","dir":"","previous_headings":"","what":"Basic usage","title":"Kinetic Evaluation of Chemical Degradation Data","text":"start, look code examples provided plot.mkinfit plot.mmkin, package vignettes FOCUS L FOCUS D.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/index.html","id":"documentation","dir":"","previous_headings":"","what":"Documentation","title":"Kinetic Evaluation of Chemical Degradation Data","text":"HTML documentation latest version released CRAN available jrwb.de github. Documentation development version found ‘dev’ subdirectory. articles section documentation, can also find demonstrations application nonlinear hierarchical models, also known nonlinear mixed-effects models, complex data, including transformation products covariates.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/index.html","id":"general","dir":"","previous_headings":"Features","what":"General","title":"Kinetic Evaluation of Chemical Degradation Data","text":"Highly flexible model specification using mkinmod, including equilibrium reactions using single first-order reversible binding (SFORB) model, automatically create two state variables observed variable. Model solution (forward modelling) function mkinpredict performed either using analytical solution case parent degradation simple models involving single transformation product, , eigenvalue based solution simple first-order (SFO) SFORB kinetics used model, using numeric solver deSolve package (default lsoda). usual one-sided t-test significant difference zero shown based estimators untransformed parameters. Summary plotting functions. summary mkinfit object fact full report give enough information able approximately reproduce fit tools. chi-squared error level defined FOCUS kinetics guidance (see ) calculated observed variable. ‘variance variable’ error model often fitted using Iteratively Reweighted Least Squares (IRLS) can specified error_model = \"obs\".","code":""},{"path":"https://pkgdown.jrwb.de/mkin/index.html","id":"unique-in-mkin","dir":"","previous_headings":"Features","what":"Unique in mkin","title":"Kinetic Evaluation of Chemical Degradation Data","text":"Three different error models can selected using argument error_model mkinfit function. two-component error model similar one proposed Rocke Lorenzato can selected using argument error_model = \"tc\". Model comparisons using Akaike Information Criterion (AIC) supported can also used non-constant variance. cases FOCUS chi-squared error level meaningful. default, kinetic rate constants kinetic formation fractions transformed internally using transform_odeparms estimators can reasonably expected follow normal distribution. parameter estimates backtransformed match model definition, confidence intervals calculated standard errors also backtransformed correct scale, include meaningless values like negative rate constants formation fractions adding 1, occur single experiment single defined radiolabel position. metabolite decline phase described well SFO kinetics, SFORB kinetics can used metabolite. Mathematically, SFORB model equivalent DFOP model. However, SFORB model advantage mechanistic interpretation model parameters. Nonlinear mixed-effects models (hierarchical models) can created fits degradation model different datasets compound using nlme.mmkin saem.mmkin methods. Note convergence nlme fits depends quality data. Convergence better simple models data many groups (e.g. soils). saem method uses saemix package backend. Analytical solutions suitable use package implemented parent models important models including one metabolite (SFO-SFO DFOP-SFO). Fitting models saem.mmkin, makes use compiled ODE models mkin provides, longer run times (couple minutes hour).","code":""},{"path":"https://pkgdown.jrwb.de/mkin/index.html","id":"performance","dir":"","previous_headings":"Features","what":"Performance","title":"Kinetic Evaluation of Chemical Degradation Data","text":"Parallel fitting several models several datasets supported, see example plot.mmkin. C compiler installed, kinetic models compiled automatically generated C code, see vignette compiled_models. autogeneration C code inspired ccSolve package. Thanks Karline Soetaert work . Even compiler installed, many degradation models still give good performance, current versions mkin also analytical solutions models one metabolite, SFO SFORB used parent compound, Eigenvalue based solutions degradation model available.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/index.html","id":"gui","dir":"","previous_headings":"","what":"GUI","title":"Kinetic Evaluation of Chemical Degradation Data","text":"graphical user interface may useful. Please refer documentation page installation instructions manual. supports evaluations using (generalised) nonlinear regression, simultaneous fits using nonlinear mixed-effects models.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/index.html","id":"news","dir":"","previous_headings":"","what":"News","title":"Kinetic Evaluation of Chemical Degradation Data","text":"list changes latest CRAN release one github branch, e.g. main branch.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/index.html","id":"credits-and-historical-remarks","dir":"","previous_headings":"","what":"Credits and historical remarks","title":"Kinetic Evaluation of Chemical Degradation Data","text":"mkin possible without underlying software stack consisting , among others, R package deSolve. previous version, mkin also using functionality FME package. Please refer package page CRAN full list imported suggested R packages. Also, Debian Linux, vim editor Nvim-R plugin invaluable development. mkin written without introduced regulatory fate modelling pesticides Adrian Gurney time Harlan Laboratories Ltd (formerly RCC Ltd). mkin greatly profits largely follows work done FOCUS Degradation Kinetics Workgroup, detailed guidance document 2006, slightly updated 2011 2014. Also, inspired first version KinGUI developed BayerCropScience, based MatLab runtime environment. companion package kinfit (now deprecated) started 2008 first published CRAN 01 May 2010. first mkin code published 11 May 2010 first CRAN version 18 May 2010. 2011, Bayer Crop Science started distribute R based successor KinGUI named KinGUII whose R code based mkin, added, among refinements, closed source graphical user interface (GUI), iteratively reweighted least squares (IRLS) optimisation variance observed variables, Markov Chain Monte Carlo (MCMC) simulation functionality, similar available e.g. FME package. Somewhat parallel, Syngenta sponsored development mkin KinGUII based GUI application called CAKE, also adds IRLS MCMC, limited model formulation, puts weight usability. CAKE available download CAKE website, can also find zip archive R scripts derived mkin, published GPL license. Finally, KineticEval, contains development scripts used KinGUII. Thanks René Lehmann, formerly working Umweltbundesamt, nice cooperation parameter transformations, especially isometric log-ratio transformation now used formation fractions case two transformation targets. Many inspirations improvements mkin resulted kinetic evaluations degradation data clients working Harlan Laboratories Eurofins Regulatory AG, now independent consultant. Funding received Umweltbundesamt course projects Project Number 27452 (Testing validation modelling software alternative ModelMaker 4.0, 2014-2015) Project Number 56703 (Optimization gmkin routine use Umweltbundesamt, 2015) Project Number 92570 (Update Project Number 27452, 2017-2018) Project Number 112407 (Testing feasibility using error model according Rocke Lorenzato realistic parameter estimates kinetic evaluation degradation data, 2018-2019) Project Number 120667 (Development objective criteria evaluation visual fit kinetic evaluation degradation data, 2019-2020) Project Number 146839 (Checking feasibility using mixed-effects models derivation kinetic modelling parameters degradation studies, 2020-2021) Project Number 173340 (Application nonlinear hierarchical models kinetic evaluation chemical degradation data) Thanks everyone involved collaboration support! Thanks due also Emmanuelle Comets, maintainer saemix package, interest support using SAEM algorithm implementation saemix evaluation chemical degradation data. Regarding application nonlinear mixed-effects models degradation data, von Götz et al (1999) already proposed use technique context environmental risk assessments pesticides. However, work apparently followed , independently arrive idea missed cite previous work topic first publications.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/index.html","id":"development","dir":"","previous_headings":"","what":"Development","title":"Kinetic Evaluation of Chemical Degradation Data","text":"Contributions welcome!","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/AIC.mmkin.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate the AIC for a column of an mmkin object — AIC.mmkin","title":"Calculate the AIC for a column of an mmkin object — AIC.mmkin","text":"Provides convenient way compare different kinetic models fitted dataset.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/AIC.mmkin.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate the AIC for a column of an mmkin object — AIC.mmkin","text":"","code":"# S3 method for mmkin AIC(object, ..., k = 2) # S3 method for mmkin BIC(object, ...)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/AIC.mmkin.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate the AIC for a column of an mmkin object — AIC.mmkin","text":"object object class mmkin, containing one column. ... compatibility generic method k generic method","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/AIC.mmkin.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate the AIC for a column of an mmkin object — AIC.mmkin","text":"generic method (numeric value single fits, dataframe several fits column).","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/AIC.mmkin.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate the AIC for a column of an mmkin object — AIC.mmkin","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/AIC.mmkin.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate the AIC for a column of an mmkin object — AIC.mmkin","text":"","code":"# skip, as it takes > 10 s on winbuilder f <- mmkin(c(\"SFO\", \"FOMC\", \"DFOP\"), list(\"FOCUS A\" = FOCUS_2006_A, \"FOCUS C\" = FOCUS_2006_C), cores = 1, quiet = TRUE) #> Warning: Optimisation did not converge: #> false convergence (8) # We get a warning because the FOMC model does not converge for the # FOCUS A dataset, as it is well described by SFO AIC(f[\"SFO\", \"FOCUS A\"]) # We get a single number for a single fit #> [1] 55.28197 AIC(f[[\"SFO\", \"FOCUS A\"]]) # or when extracting an mkinfit object #> [1] 55.28197 # For FOCUS A, the models fit almost equally well, so the higher the number # of parameters, the higher (worse) the AIC AIC(f[, \"FOCUS A\"]) #> df AIC #> SFO 3 55.28197 #> FOMC 4 57.28198 #> DFOP 5 59.28197 AIC(f[, \"FOCUS A\"], k = 0) # If we do not penalize additional parameters, we get nearly the same #> df AIC #> SFO 3 49.28197 #> FOMC 4 49.28198 #> DFOP 5 49.28197 BIC(f[, \"FOCUS A\"]) # Comparing the BIC gives a very similar picture #> df BIC #> SFO 3 55.52030 #> FOMC 4 57.59974 #> DFOP 5 59.67918 # For FOCUS C, the more complex models fit better AIC(f[, \"FOCUS C\"]) #> df AIC #> SFO 3 59.29336 #> FOMC 4 44.68652 #> DFOP 5 29.02372 BIC(f[, \"FOCUS C\"]) #> df BIC #> SFO 3 59.88504 #> FOMC 4 45.47542 #> DFOP 5 30.00984"},{"path":"https://pkgdown.jrwb.de/mkin/reference/CAKE_export.html","id":null,"dir":"Reference","previous_headings":"","what":"Export a list of datasets format to a CAKE study file — CAKE_export","title":"Export a list of datasets format to a CAKE study file — CAKE_export","text":"addition datasets, pathways degradation model can specified well.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/CAKE_export.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Export a list of datasets format to a CAKE study file — CAKE_export","text":"","code":"CAKE_export( ds, map = c(parent = \"Parent\"), links = NA, filename = \"CAKE_export.csf\", path = \".\", overwrite = FALSE, study = \"Degradinol aerobic soil degradation\", description = \"\", time_unit = \"days\", res_unit = \"% AR\", comment = \"\", date = Sys.Date(), optimiser = \"IRLS\" )"},{"path":"https://pkgdown.jrwb.de/mkin/reference/CAKE_export.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Export a list of datasets format to a CAKE study file — CAKE_export","text":"ds named list datasets long format compatible mkinfit. map character vector CAKE compartment names (Parent, A1, ...), named names used list datasets. links optional character vector target compartments, named names source compartments. order make easier, names used datasets supplied. filename write result. end .csf order compatible CAKE. path optional path output file. overwrite TRUE, existing files overwritten. study name study. description optional description. time_unit time unit residue data. res_unit unit used residues. comment optional comment. date date file creation. optimiser Can OLS IRLS.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/CAKE_export.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Export a list of datasets format to a CAKE study file — CAKE_export","text":"function called side effect.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/CAKE_export.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Export a list of datasets format to a CAKE study file — CAKE_export","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/D24_2014.html","id":null,"dir":"Reference","previous_headings":"","what":"Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 — D24_2014","title":"Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 — D24_2014","text":"five datasets extracted active substance evaluation dossier published EFSA. Kinetic evaluations shown datasets intended illustrate advance kinetic modelling. fact data results shown imply license use context pesticide registrations, use data may constrained data protection regulations.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/D24_2014.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 — D24_2014","text":"","code":"D24_2014"},{"path":"https://pkgdown.jrwb.de/mkin/reference/D24_2014.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 — D24_2014","text":"mkindsg object grouping five datasets","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/D24_2014.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 — D24_2014","text":"Hellenic Ministry Rural Development Agriculture (2014) Final addendum Renewal Assessment Report - public version - 2,4-D Volume 3 Annex B.8 Fate behaviour environment https://open.efsa.europa.eu/study-inventory/EFSA-Q-2013-00811","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/D24_2014.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 — D24_2014","text":"Data first dataset p. 685. Data four datasets used preprocessed versions given kinetics section (p. 761ff.), exception residues smaller 1 DCP soil Site I2, values given p. 694 used. R code used create data object installed package 'dataset_generation' directory. code, page numbers given specific pieces information comments.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/D24_2014.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 — D24_2014","text":"","code":"print(D24_2014) #> <mkindsg> holding 5 mkinds objects #> Title $title: Aerobic soil degradation data on 2,4-D from the EU assessment in 2014 #> Occurrence of observed compounds $observed_n: #> D24 DCP DCA #> 5 4 4 #> Time normalisation factors $f_time_norm: #> [1] 1.6062378 0.7118732 0.7156063 0.7156063 0.8977124 #> Meta information $meta: #> study usda_soil_type study_moisture_ref_type #> Mississippi Cohen 1991 Silt loam <NA> #> Fayette Liu and Adelfinskaya 2011 Silt loam pF1 #> RefSol 03-G Liu and Adelfinskaya 2011 Loam pF1 #> Site E1 Liu and Adelfinskaya 2011 Loam pF1 #> Site I2 Liu and Adelfinskaya 2011 Loamy sand pF1 #> rel_moisture temperature #> Mississippi NA 25 #> Fayette 0.5 20 #> RefSol 03-G 0.5 20 #> Site E1 0.5 20 #> Site I2 0.5 20 # \\dontrun{ print(D24_2014$ds[[1]], data = TRUE) #> <mkinds> with $title: Mississippi #> Observed compounds $observed: D24 #> Sampling times $sampling_times: #> 0, 2, 4, 7, 15, 24, 35, 56, 71, 114, 183, 273, 365 #> With a maximum of 1 replicates #> time D24 #> 1 0 96.8 #> 2 2 81.0 #> 3 4 81.7 #> 4 7 88.2 #> 5 15 66.3 #> 6 24 72.9 #> 7 35 62.6 #> 8 56 54.6 #> 9 71 35.2 #> 10 114 18.0 #> 11 183 11.3 #> 12 273 9.9 #> 13 365 6.3 m_D24 = mkinmod(D24 = mkinsub(\"SFO\", to = \"DCP\"), DCP = mkinsub(\"SFO\", to = \"DCA\"), DCA = mkinsub(\"SFO\")) #> Temporary DLL for differentials generated and loaded print(m_D24) #> <mkinmod> model generated with #> Use of formation fractions $use_of_ff: max #> Specification $spec: #> $D24 #> $type: SFO; $to: DCP; $sink: TRUE #> $DCP #> $type: SFO; $to: DCA; $sink: TRUE #> $DCA #> $type: SFO; $sink: TRUE #> Coefficient matrix $coefmat available #> Compiled model $cf available #> Differential equations: #> d_D24/dt = - k_D24 * D24 #> d_DCP/dt = + f_D24_to_DCP * k_D24 * D24 - k_DCP * DCP #> d_DCA/dt = + f_DCP_to_DCA * k_DCP * DCP - k_DCA * DCA m_D24_2 = mkinmod(D24 = mkinsub(\"DFOP\", to = \"DCP\"), DCP = mkinsub(\"SFO\", to = \"DCA\"), DCA = mkinsub(\"SFO\")) #> Temporary DLL for differentials generated and loaded print(m_D24_2) #> <mkinmod> model generated with #> Use of formation fractions $use_of_ff: max #> Specification $spec: #> $D24 #> $type: DFOP; $to: DCP; $sink: TRUE #> $DCP #> $type: SFO; $to: DCA; $sink: TRUE #> $DCA #> $type: SFO; $sink: TRUE #> Compiled model $cf available #> Differential equations: #> d_D24/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * #> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) #> * D24 #> d_DCP/dt = + f_D24_to_DCP * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * #> exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 #> * time))) * D24 - k_DCP * DCP #> d_DCA/dt = + f_DCP_to_DCA * k_DCP * DCP - k_DCA * DCA # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/DFOP.solution.html","id":null,"dir":"Reference","previous_headings":"","what":"Double First-Order in Parallel kinetics — DFOP.solution","title":"Double First-Order in Parallel kinetics — DFOP.solution","text":"Function describing decline defined starting value using sum two exponential decline functions.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/DFOP.solution.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Double First-Order in Parallel kinetics — DFOP.solution","text":"","code":"DFOP.solution(t, parent_0, k1, k2, g)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/DFOP.solution.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Double First-Order in Parallel kinetics — DFOP.solution","text":"t Time. parent_0 Starting value response variable time zero. k1 First kinetic constant. k2 Second kinetic constant. g Fraction starting value declining according first kinetic constant.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/DFOP.solution.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Double First-Order in Parallel kinetics — DFOP.solution","text":"value response variable time t.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/DFOP.solution.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Double First-Order in Parallel kinetics — DFOP.solution","text":"FOCUS (2006) “Guidance Document Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration” Report FOCUS Work Group Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics FOCUS (2014) “Generic guidance Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration” Report FOCUS Work Group Degradation Kinetics, Version 1.1, 18 December 2014 http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/reference/DFOP.solution.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Double First-Order in Parallel kinetics — DFOP.solution","text":"","code":"plot(function(x) DFOP.solution(x, 100, 5, 0.5, 0.3), 0, 4, ylim = c(0,100))"},{"path":"https://pkgdown.jrwb.de/mkin/reference/Extract.mmkin.html","id":null,"dir":"Reference","previous_headings":"","what":"Subsetting method for mmkin objects — [.mmkin","title":"Subsetting method for mmkin objects — [.mmkin","text":"Subsetting method mmkin objects","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/Extract.mmkin.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subsetting method for mmkin objects — [.mmkin","text":"","code":"# S3 method for mmkin [(x, i, j, ..., drop = FALSE)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/Extract.mmkin.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subsetting method for mmkin objects — [.mmkin","text":"x mmkin object Row index selecting fits specific models j Column index selecting fits specific datasets ... used, satisfy generic method definition drop FALSE, method always returns mmkin object, otherwise either list mkinfit objects single mkinfit object.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/Extract.mmkin.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subsetting method for mmkin objects — [.mmkin","text":"object class mmkin.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/Extract.mmkin.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Subsetting method for mmkin objects — [.mmkin","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/Extract.mmkin.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subsetting method for mmkin objects — [.mmkin","text":"","code":"# Only use one core, to pass R CMD check --as-cran fits <- mmkin(c(\"SFO\", \"FOMC\"), list(B = FOCUS_2006_B, C = FOCUS_2006_C), cores = 1, quiet = TRUE) fits[\"FOMC\", ] #> <mmkin> object #> Status of individual fits: #> #> dataset #> model B C #> FOMC OK OK #> #> OK: No warnings fits[, \"B\"] #> <mmkin> object #> Status of individual fits: #> #> dataset #> model B #> SFO OK #> FOMC OK #> #> OK: No warnings fits[\"SFO\", \"B\"] #> <mmkin> object #> Status of individual fits: #> #> dataset #> model B #> SFO OK #> #> OK: No warnings head( # This extracts an mkinfit object with lots of components fits[[\"FOMC\", \"B\"]] ) #> $par #> parent_0 log_alpha log_beta sigma #> 99.666192 2.549850 5.050587 1.890202 #> #> $objective #> [1] 28.58291 #> #> $convergence #> [1] 0 #> #> $iterations #> [1] 21 #> #> $evaluations #> function gradient #> 25 78 #> #> $message #> [1] \"both X-convergence and relative convergence (5)\" #>"},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_DFOP_ref_A_to_B.html","id":null,"dir":"Reference","previous_headings":"","what":"Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B","title":"Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B","text":"table fitted parameters resulting DT50 DT90 values generated different software packages. Taken directly FOCUS (2006). results fitting data Topfit software removed, initial concentration parent compound fixed value 100 fit.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_DFOP_ref_A_to_B.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B","text":"","code":"FOCUS_2006_DFOP_ref_A_to_B"},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_DFOP_ref_A_to_B.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B","text":"data frame containing following variables. package factor giving name software package M0 fitted initial concentration parent compound f fitted f parameter k1 fitted k1 parameter k2 fitted k2 parameter DT50 resulting half-life parent compound DT90 resulting DT90 parent compound dataset FOCUS dataset used","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_DFOP_ref_A_to_B.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B","text":"FOCUS (2006) “Guidance Document Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration” Report FOCUS Work Group Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_DFOP_ref_A_to_B.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B","text":"","code":"data(FOCUS_2006_DFOP_ref_A_to_B)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_FOMC_ref_A_to_F.html","id":null,"dir":"Reference","previous_headings":"","what":"Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F","title":"Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F","text":"table fitted parameters resulting DT50 DT90 values generated different software packages. Taken directly FOCUS (2006). results fitting data Topfit software removed, initial concentration parent compound fixed value 100 fit.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_FOMC_ref_A_to_F.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F","text":"","code":"FOCUS_2006_FOMC_ref_A_to_F"},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_FOMC_ref_A_to_F.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F","text":"data frame containing following variables. package factor giving name software package M0 fitted initial concentration parent compound alpha fitted alpha parameter beta fitted beta parameter DT50 resulting half-life parent compound DT90 resulting DT90 parent compound dataset FOCUS dataset used","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_FOMC_ref_A_to_F.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F","text":"FOCUS (2006) “Guidance Document Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration” Report FOCUS Work Group Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_FOMC_ref_A_to_F.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F","text":"","code":"data(FOCUS_2006_FOMC_ref_A_to_F)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_HS_ref_A_to_F.html","id":null,"dir":"Reference","previous_headings":"","what":"Results of fitting the HS model to Datasets A to F of FOCUS (2006) — FOCUS_2006_HS_ref_A_to_F","title":"Results of fitting the HS model to Datasets A to F of FOCUS (2006) — FOCUS_2006_HS_ref_A_to_F","text":"table fitted parameters resulting DT50 DT90 values generated different software packages. Taken directly FOCUS (2006). results fitting data Topfit software removed, initial concentration parent compound fixed value 100 fit.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_HS_ref_A_to_F.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Results of fitting the HS model to Datasets A to F of FOCUS (2006) — FOCUS_2006_HS_ref_A_to_F","text":"","code":"FOCUS_2006_HS_ref_A_to_F"},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_HS_ref_A_to_F.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Results of fitting the HS model to Datasets A to F of FOCUS (2006) — FOCUS_2006_HS_ref_A_to_F","text":"data frame containing following variables. package factor giving name software package M0 fitted initial concentration parent compound tb fitted tb parameter k1 fitted k1 parameter k2 fitted k2 parameter DT50 resulting half-life parent compound DT90 resulting DT90 parent compound dataset FOCUS dataset used","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_HS_ref_A_to_F.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Results of fitting the HS model to Datasets A to F of FOCUS (2006) — FOCUS_2006_HS_ref_A_to_F","text":"FOCUS (2006) “Guidance Document Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration” Report FOCUS Work Group Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_HS_ref_A_to_F.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Results of fitting the HS model to Datasets A to F of FOCUS (2006) — FOCUS_2006_HS_ref_A_to_F","text":"","code":"data(FOCUS_2006_HS_ref_A_to_F)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_SFO_ref_A_to_F.html","id":null,"dir":"Reference","previous_headings":"","what":"Results of fitting the SFO model to Datasets A to F of FOCUS (2006) — FOCUS_2006_SFO_ref_A_to_F","title":"Results of fitting the SFO model to Datasets A to F of FOCUS (2006) — FOCUS_2006_SFO_ref_A_to_F","text":"table fitted parameters resulting DT50 DT90 values generated different software packages. Taken directly FOCUS (2006). results fitting data Topfit software removed, initial concentration parent compound fixed value 100 fit.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_SFO_ref_A_to_F.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Results of fitting the SFO model to Datasets A to F of FOCUS (2006) — FOCUS_2006_SFO_ref_A_to_F","text":"","code":"FOCUS_2006_SFO_ref_A_to_F"},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_SFO_ref_A_to_F.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Results of fitting the SFO model to Datasets A to F of FOCUS (2006) — FOCUS_2006_SFO_ref_A_to_F","text":"data frame containing following variables. package factor giving name software package M0 fitted initial concentration parent compound k fitted first-order degradation rate constant DT50 resulting half-life parent compound DT90 resulting DT90 parent compound dataset FOCUS dataset used","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_SFO_ref_A_to_F.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Results of fitting the SFO model to Datasets A to F of FOCUS (2006) — FOCUS_2006_SFO_ref_A_to_F","text":"FOCUS (2006) “Guidance Document Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration” Report FOCUS Work Group Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_SFO_ref_A_to_F.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Results of fitting the SFO model to Datasets A to F of FOCUS (2006) — FOCUS_2006_SFO_ref_A_to_F","text":"","code":"data(FOCUS_2006_SFO_ref_A_to_F)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_datasets.html","id":null,"dir":"Reference","previous_headings":"","what":"Datasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets","title":"Datasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets","text":"Data taken FOCUS (2006), p. 258.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_datasets.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Datasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets","text":"","code":"FOCUS_2006_A FOCUS_2006_B FOCUS_2006_C FOCUS_2006_D FOCUS_2006_E FOCUS_2006_F"},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_datasets.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Datasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets","text":"6 datasets observations following variables. name factor containing name observed variable time numeric vector containing time points value numeric vector containing concentrations percent applied radioactivity","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_datasets.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Datasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets","text":"FOCUS (2006) “Guidance Document Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration” Report FOCUS Work Group Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOCUS_2006_datasets.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Datasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets","text":"","code":"FOCUS_2006_C #> name time value #> 1 parent 0 85.1 #> 2 parent 1 57.9 #> 3 parent 3 29.9 #> 4 parent 7 14.6 #> 5 parent 14 9.7 #> 6 parent 28 6.6 #> 7 parent 63 4.0 #> 8 parent 91 3.9 #> 9 parent 119 0.6"},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOMC.solution.html","id":null,"dir":"Reference","previous_headings":"","what":"First-Order Multi-Compartment kinetics — FOMC.solution","title":"First-Order Multi-Compartment kinetics — FOMC.solution","text":"Function describing exponential decline defined starting value, decreasing rate constant.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOMC.solution.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"First-Order Multi-Compartment kinetics — FOMC.solution","text":"","code":"FOMC.solution(t, parent_0, alpha, beta)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOMC.solution.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"First-Order Multi-Compartment kinetics — FOMC.solution","text":"t Time. parent_0 Starting value response variable time zero. alpha Shape parameter determined coefficient variation rate constant values. beta Location parameter.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOMC.solution.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"First-Order Multi-Compartment kinetics — FOMC.solution","text":"value response variable time t.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOMC.solution.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"First-Order Multi-Compartment kinetics — FOMC.solution","text":"form given differs slightly original reference Gustafson Holden (1990). parameter beta corresponds 1/beta original equation.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOMC.solution.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"First-Order Multi-Compartment kinetics — FOMC.solution","text":"solution FOMC kinetic model reduces SFO.solution large values alpha beta \\(k = \\frac{\\beta}{\\alpha}\\).","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOMC.solution.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"First-Order Multi-Compartment kinetics — FOMC.solution","text":"FOCUS (2006) “Guidance Document Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration” Report FOCUS Work Group Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics FOCUS (2014) “Generic guidance Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration” Report FOCUS Work Group Degradation Kinetics, Version 1.1, 18 December 2014 http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics Gustafson DI Holden LR (1990) Nonlinear pesticide dissipation soil: new model based spatial variability. Environmental Science Technology 24, 1032-1038","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/reference/FOMC.solution.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"First-Order Multi-Compartment kinetics — FOMC.solution","text":"","code":"plot(function(x) FOMC.solution(x, 100, 10, 2), 0, 2, ylim = c(0, 100))"},{"path":"https://pkgdown.jrwb.de/mkin/reference/HS.solution.html","id":null,"dir":"Reference","previous_headings":"","what":"Hockey-Stick kinetics — HS.solution","title":"Hockey-Stick kinetics — HS.solution","text":"Function describing two exponential decline functions break point .","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/HS.solution.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Hockey-Stick kinetics — HS.solution","text":"","code":"HS.solution(t, parent_0, k1, k2, tb)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/HS.solution.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Hockey-Stick kinetics — HS.solution","text":"t Time. parent_0 Starting value response variable time zero. k1 First kinetic constant. k2 Second kinetic constant. tb Break point. time, exponential decline according k1 calculated, time, exponential decline proceeds according k2.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/HS.solution.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Hockey-Stick kinetics — HS.solution","text":"value response variable time t.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/HS.solution.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Hockey-Stick kinetics — HS.solution","text":"FOCUS (2006) “Guidance Document Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration” Report FOCUS Work Group Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics FOCUS (2014) “Generic guidance Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration” Report FOCUS Work Group Degradation Kinetics, Version 1.1, 18 December 2014 http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/reference/HS.solution.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Hockey-Stick kinetics — HS.solution","text":"","code":"plot(function(x) HS.solution(x, 100, 2, 0.3, 0.5), 0, 2, ylim=c(0,100))"},{"path":"https://pkgdown.jrwb.de/mkin/reference/IORE.solution.html","id":null,"dir":"Reference","previous_headings":"","what":"Indeterminate order rate equation kinetics — IORE.solution","title":"Indeterminate order rate equation kinetics — IORE.solution","text":"Function describing exponential decline defined starting value, concentration dependent rate constant.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/IORE.solution.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Indeterminate order rate equation kinetics — IORE.solution","text":"","code":"IORE.solution(t, parent_0, k__iore, N)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/IORE.solution.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Indeterminate order rate equation kinetics — IORE.solution","text":"t Time. parent_0 Starting value response variable time zero. k__iore Rate constant. Note depends concentration units used. N Exponent describing nonlinearity rate equation","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/IORE.solution.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Indeterminate order rate equation kinetics — IORE.solution","text":"value response variable time t.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/IORE.solution.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Indeterminate order rate equation kinetics — IORE.solution","text":"solution IORE kinetic model reduces SFO.solution N = 1. parameters IORE model can transformed equivalent parameters FOMC mode - see NAFTA guidance details.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/IORE.solution.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Indeterminate order rate equation kinetics — IORE.solution","text":"NAFTA Technical Working Group Pesticides (dated) Guidance Evaluating Calculating Degradation Kinetics Environmental Media","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/reference/IORE.solution.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Indeterminate order rate equation kinetics — IORE.solution","text":"","code":"plot(function(x) IORE.solution(x, 100, 0.2, 1.3), 0, 2, ylim = c(0, 100)) # \\dontrun{ fit.fomc <- mkinfit(\"FOMC\", FOCUS_2006_C, quiet = TRUE) fit.iore <- mkinfit(\"IORE\", FOCUS_2006_C, quiet = TRUE) fit.iore.deS <- mkinfit(\"IORE\", FOCUS_2006_C, solution_type = \"deSolve\", quiet = TRUE) #> Error in is.loaded(initfunc, PACKAGE = dllname, type = \"\") : #> invalid 'PACKAGE' argument print(data.frame(fit.fomc$par, fit.iore$par, fit.iore.deS$par, row.names = paste(\"model par\", 1:4))) #> fit.fomc.par fit.iore.par fit.iore.deS.par #> model par 1 85.87489063 85.874890 85.874890 #> model par 2 0.05192238 -4.826631 -4.826631 #> model par 3 0.65096665 1.949403 1.949403 #> model par 4 1.85744396 1.857444 1.857444 print(rbind(fomc = endpoints(fit.fomc)$distimes, iore = endpoints(fit.iore)$distimes, iore.deS = endpoints(fit.iore)$distimes)) #> DT50 DT90 DT50back #> fomc 1.785233 15.1479 4.559973 #> iore 1.785233 15.1479 4.559973 #> iore.deS 1.785233 15.1479 4.559973 # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/NAFTA_SOP_2015.html","id":null,"dir":"Reference","previous_headings":"","what":"Example datasets from the NAFTA SOP published 2015 — NAFTA_SOP_2015","title":"Example datasets from the NAFTA SOP published 2015 — NAFTA_SOP_2015","text":"Data taken US EPA (2015), p. 19 23.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/NAFTA_SOP_2015.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Example datasets from the NAFTA SOP published 2015 — NAFTA_SOP_2015","text":"","code":"NAFTA_SOP_Appendix_B NAFTA_SOP_Appendix_D"},{"path":"https://pkgdown.jrwb.de/mkin/reference/NAFTA_SOP_2015.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Example datasets from the NAFTA SOP published 2015 — NAFTA_SOP_2015","text":"2 datasets observations following variables. name factor containing name observed variable time numeric vector containing time points value numeric vector containing concentrations","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/NAFTA_SOP_2015.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Example datasets from the NAFTA SOP published 2015 — NAFTA_SOP_2015","text":"NAFTA (2011) Guidance evaluating calculating degradation kinetics environmental media. NAFTA Technical Working Group Pesticides https://www.epa.gov/pesticide-science--assessing-pesticide-risks/guidance-evaluating--calculating-degradation accessed 2019-02-22 US EPA (2015) Standard Operating Procedure Using NAFTA Guidance Calculate Representative Half-life Values Characterizing Pesticide Degradation https://www.epa.gov/pesticide-science--assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/NAFTA_SOP_2015.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Example datasets from the NAFTA SOP published 2015 — NAFTA_SOP_2015","text":"","code":"nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D, cores = 1) #> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c #> The representative half-life of the IORE model is longer than the one corresponding #> to the terminal degradation rate found with the DFOP model. #> The representative half-life obtained from the DFOP model may be used print(nafta_evaluation) #> Sums of squares: #> SFO IORE DFOP #> 1378.6832 615.7730 517.8836 #> #> Critical sum of squares for checking the SFO model: #> [1] 717.4598 #> #> Parameters: #> $SFO #> Estimate Pr(>t) Lower Upper #> parent_0 83.7558 1.80e-14 77.18268 90.3288 #> k_parent 0.0017 7.43e-05 0.00112 0.0026 #> sigma 8.7518 1.22e-05 5.64278 11.8608 #> #> $IORE #> Estimate Pr(>t) Lower Upper #> parent_0 9.69e+01 NA 8.88e+01 1.05e+02 #> k__iore_parent 8.40e-14 NA 1.79e-18 3.94e-09 #> N_parent 6.68e+00 NA 4.19e+00 9.17e+00 #> sigma 5.85e+00 NA 3.76e+00 7.94e+00 #> #> $DFOP #> Estimate Pr(>t) Lower Upper #> parent_0 9.76e+01 1.94e-13 9.02e+01 1.05e+02 #> k1 4.24e-02 5.92e-03 2.03e-02 8.88e-02 #> k2 8.24e-04 6.48e-03 3.89e-04 1.75e-03 #> g 2.88e-01 2.47e-05 1.95e-01 4.03e-01 #> sigma 5.36e+00 2.22e-05 3.43e+00 7.30e+00 #> #> #> DTx values: #> DT50 DT90 DT50_rep #> SFO 407 1350 407 #> IORE 541 5190000 1560000 #> DFOP 429 2380 841 #> #> Representative half-life: #> [1] 841.41 plot(nafta_evaluation)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/NAFTA_SOP_Attachment.html","id":null,"dir":"Reference","previous_headings":"","what":"Example datasets from Attachment 1 to the NAFTA SOP published 2015 — NAFTA_SOP_Attachment","title":"Example datasets from Attachment 1 to the NAFTA SOP published 2015 — NAFTA_SOP_Attachment","text":"Data taken Attachment 1 SOP.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/NAFTA_SOP_Attachment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Example datasets from Attachment 1 to the NAFTA SOP published 2015 — NAFTA_SOP_Attachment","text":"","code":"NAFTA_SOP_Attachment"},{"path":"https://pkgdown.jrwb.de/mkin/reference/NAFTA_SOP_Attachment.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Example datasets from Attachment 1 to the NAFTA SOP published 2015 — NAFTA_SOP_Attachment","text":"list (NAFTA_SOP_Attachment) containing 16 datasets suitable evaluation nafta","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/NAFTA_SOP_Attachment.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Example datasets from Attachment 1 to the NAFTA SOP published 2015 — NAFTA_SOP_Attachment","text":"NAFTA (2011) Guidance evaluating calculating degradation kinetics environmental media. NAFTA Technical Working Group Pesticides https://www.epa.gov/pesticide-science--assessing-pesticide-risks/guidance-evaluating--calculating-degradation accessed 2019-02-22 US EPA (2015) Standard Operating Procedure Using NAFTA Guidance Calculate Representative Half-life Values Characterizing Pesticide Degradation https://www.epa.gov/pesticide-science--assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/NAFTA_SOP_Attachment.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Example datasets from Attachment 1 to the NAFTA SOP published 2015 — NAFTA_SOP_Attachment","text":"","code":"nafta_att_p5a <- nafta(NAFTA_SOP_Attachment[[\"p5a\"]], cores = 1) #> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c #> The half-life obtained from the IORE model may be used print(nafta_att_p5a) #> Sums of squares: #> SFO IORE DFOP #> 465.21753 56.27506 32.06401 #> #> Critical sum of squares for checking the SFO model: #> [1] 64.4304 #> #> Parameters: #> $SFO #> Estimate Pr(>t) Lower Upper #> parent_0 95.8401 4.67e-21 92.245 99.4357 #> k_parent 0.0102 3.92e-12 0.009 0.0117 #> sigma 4.8230 3.81e-06 3.214 6.4318 #> #> $IORE #> Estimate Pr(>t) Lower Upper #> parent_0 1.01e+02 NA 9.91e+01 1.02e+02 #> k__iore_parent 1.54e-05 NA 4.08e-06 5.84e-05 #> N_parent 2.57e+00 NA 2.25e+00 2.89e+00 #> sigma 1.68e+00 NA 1.12e+00 2.24e+00 #> #> $DFOP #> Estimate Pr(>t) Lower Upper #> parent_0 9.99e+01 1.41e-26 98.8116 101.0810 #> k1 2.67e-02 5.05e-06 0.0243 0.0295 #> k2 3.41e-12 5.00e-01 0.0000 Inf #> g 6.47e-01 3.67e-06 0.6248 0.6677 #> sigma 1.27e+00 8.91e-06 0.8395 1.6929 #> #> #> DTx values: #> DT50 DT90 DT50_rep #> SFO 67.7 2.25e+02 6.77e+01 #> IORE 58.2 1.07e+03 3.22e+02 #> DFOP 55.5 3.70e+11 2.03e+11 #> #> Representative half-life: #> [1] 321.51 plot(nafta_att_p5a)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/SFO.solution.html","id":null,"dir":"Reference","previous_headings":"","what":"Single First-Order kinetics — SFO.solution","title":"Single First-Order kinetics — SFO.solution","text":"Function describing exponential decline defined starting value.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/SFO.solution.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Single First-Order kinetics — SFO.solution","text":"","code":"SFO.solution(t, parent_0, k)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/SFO.solution.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Single First-Order kinetics — SFO.solution","text":"t Time. parent_0 Starting value response variable time zero. k Kinetic rate constant.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/SFO.solution.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Single First-Order kinetics — SFO.solution","text":"value response variable time t.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/SFO.solution.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Single First-Order kinetics — SFO.solution","text":"FOCUS (2006) “Guidance Document Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration” Report FOCUS Work Group Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics FOCUS (2014) “Generic guidance Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration” Report FOCUS Work Group Degradation Kinetics, Version 1.1, 18 December 2014 http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/reference/SFO.solution.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Single First-Order kinetics — SFO.solution","text":"","code":"plot(function(x) SFO.solution(x, 100, 3), 0, 2)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/SFORB.solution.html","id":null,"dir":"Reference","previous_headings":"","what":"Single First-Order Reversible Binding kinetics — SFORB.solution","title":"Single First-Order Reversible Binding kinetics — SFORB.solution","text":"Function describing solution differential equations describing kinetic model first-order terms two-way transfer free bound fraction, first-order degradation term free fraction. initial condition defined amount free fraction substance bound fraction.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/SFORB.solution.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Single First-Order Reversible Binding kinetics — SFORB.solution","text":"","code":"SFORB.solution(t, parent_0, k_12, k_21, k_1output)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/SFORB.solution.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Single First-Order Reversible Binding kinetics — SFORB.solution","text":"t Time. parent_0 Starting value response variable time zero. k_12 Kinetic constant describing transfer free bound. k_21 Kinetic constant describing transfer bound free. k_1output Kinetic constant describing degradation free fraction.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/SFORB.solution.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Single First-Order Reversible Binding kinetics — SFORB.solution","text":"value response variable, sum free bound fractions time t.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/SFORB.solution.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Single First-Order Reversible Binding kinetics — SFORB.solution","text":"FOCUS (2006) “Guidance Document Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration” Report FOCUS Work Group Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics FOCUS (2014) “Generic guidance Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration” Report FOCUS Work Group Degradation Kinetics, Version 1.1, 18 December 2014 http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/reference/SFORB.solution.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Single First-Order Reversible Binding kinetics — SFORB.solution","text":"","code":"plot(function(x) SFORB.solution(x, 100, 0.5, 2, 3), 0, 2)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/add_err.html","id":null,"dir":"Reference","previous_headings":"","what":"Add normally distributed errors to simulated kinetic degradation data — add_err","title":"Add normally distributed errors to simulated kinetic degradation data — add_err","text":"Normally distributed errors added data predicted specific degradation model using mkinpredict. variance error may depend predicted value specified standard deviation.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/add_err.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add normally distributed errors to simulated kinetic degradation data — add_err","text":"","code":"add_err( prediction, sdfunc, secondary = c(\"M1\", \"M2\"), n = 10, LOD = 0.1, reps = 2, digits = 1, seed = NA )"},{"path":"https://pkgdown.jrwb.de/mkin/reference/add_err.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add normally distributed errors to simulated kinetic degradation data — add_err","text":"prediction prediction kinetic model produced mkinpredict. sdfunc function taking predicted value argument returning standard deviation used generating random error terms value. secondary names state variables initial value zero n number datasets generated. LOD limit detection (LOD). Values LOD adding random error set NA. reps number replicates generated within datasets. digits number digits values rounded. seed seed used generation random numbers. NA, seed set.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/add_err.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add normally distributed errors to simulated kinetic degradation data — add_err","text":"list datasets compatible mmkin, .e. components list datasets compatible mkinfit.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/add_err.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Add normally distributed errors to simulated kinetic degradation data — add_err","text":"Ranke J Lehmann R (2015) t-test t-test, question. XV Symposium Pesticide Chemistry 2-4 September 2015, Piacenza, Italy https://jrwb.de/posters/piacenza_2015.pdf","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/add_err.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Add normally distributed errors to simulated kinetic degradation data — add_err","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/add_err.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add normally distributed errors to simulated kinetic degradation data — add_err","text":"","code":"# The kinetic model m_SFO_SFO <- mkinmod(parent = mkinsub(\"SFO\", \"M1\"), M1 = mkinsub(\"SFO\"), use_of_ff = \"max\") #> Temporary DLL for differentials generated and loaded # Generate a prediction for a specific set of parameters sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) # This is the prediction used for the \"Type 2 datasets\" on the Piacenza poster # from 2015 d_SFO_SFO <- mkinpredict(m_SFO_SFO, c(k_parent = 0.1, f_parent_to_M1 = 0.5, k_M1 = log(2)/1000), c(parent = 100, M1 = 0), sampling_times) # Add an error term with a constant (independent of the value) standard deviation # of 10, and generate three datasets d_SFO_SFO_err <- add_err(d_SFO_SFO, function(x) 10, n = 3, seed = 123456789 ) # Name the datasets for nicer plotting names(d_SFO_SFO_err) <- paste(\"Dataset\", 1:3) # Name the model in the list of models (with only one member in this case) for # nicer plotting later on. Be quiet and use only one core not to offend CRAN # checks # \\dontrun{ f_SFO_SFO <- mmkin(list(\"SFO-SFO\" = m_SFO_SFO), d_SFO_SFO_err, cores = 1, quiet = TRUE) plot(f_SFO_SFO) # We would like to inspect the fit for dataset 3 more closely # Using double brackets makes the returned object an mkinfit object # instead of a list of mkinfit objects, so plot.mkinfit is used plot(f_SFO_SFO[[3]], show_residuals = TRUE) # If we use single brackets, we should give two indices (model and dataset), # and plot.mmkin is used plot(f_SFO_SFO[1, 3]) # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/anova.saem.mmkin.html","id":null,"dir":"Reference","previous_headings":"","what":"Anova method for saem.mmkin objects — anova.saem.mmkin","title":"Anova method for saem.mmkin objects — anova.saem.mmkin","text":"Generate anova object. method calculate BIC saemix package. prominent anova methods, models sorted number parameters, tests (requested) always relative model previous line.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/anova.saem.mmkin.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Anova method for saem.mmkin objects — anova.saem.mmkin","text":"","code":"# S3 method for saem.mmkin anova( object, ..., method = c(\"is\", \"lin\", \"gq\"), test = FALSE, model.names = NULL )"},{"path":"https://pkgdown.jrwb.de/mkin/reference/anova.saem.mmkin.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Anova method for saem.mmkin objects — anova.saem.mmkin","text":"object saem.mmkin object ... objects method Method likelihood calculation: \"\" (importance sampling), \"lin\" (linear approximation), \"gq\" (Gaussian quadrature). Passed saemix::logLik.SaemixObject test likelihood ratio test performed? TRUE, alternative models tested first model. done nested models. model.names Optional character vector model names","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/anova.saem.mmkin.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Anova method for saem.mmkin objects — anova.saem.mmkin","text":"\"anova\" data frame; traditional (S3) result anova()","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/aw.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Akaike weights for model averaging — aw","title":"Calculate Akaike weights for model averaging — aw","text":"Akaike weights calculated based relative expected Kullback-Leibler information specified Burnham Anderson (2004).","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/aw.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Akaike weights for model averaging — aw","text":"","code":"aw(object, ...) # S3 method for mkinfit aw(object, ...) # S3 method for mmkin aw(object, ...) # S3 method for mixed.mmkin aw(object, ...) # S3 method for multistart aw(object, ...)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/aw.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Akaike weights for model averaging — aw","text":"object mmkin column object, containing two mkinfit models fitted data, mkinfit object. latter case, mkinfit objects fitted data specified dots arguments. ... used method mmkin column objects, mkinfit objects method mkinfit objects.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/aw.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate Akaike weights for model averaging — aw","text":"Burnham KP Anderson DR (2004) Multimodel Inference: Understanding AIC BIC Model Selection. Sociological Methods & Research 33(2) 261-304","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/aw.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate Akaike weights for model averaging — aw","text":"","code":"# \\dontrun{ f_sfo <- mkinfit(\"SFO\", FOCUS_2006_D, quiet = TRUE) f_dfop <- mkinfit(\"DFOP\", FOCUS_2006_D, quiet = TRUE) aw_sfo_dfop <- aw(f_sfo, f_dfop) sum(aw_sfo_dfop) #> [1] 1 aw_sfo_dfop # SFO gets more weight as it has less parameters and a similar fit #> [1] 0.5970258 0.4029742 f <- mmkin(c(\"SFO\", \"FOMC\", \"DFOP\"), list(\"FOCUS D\" = FOCUS_2006_D), cores = 1, quiet = TRUE) aw(f) #> [1] 0.4808722 0.1945539 0.3245740 sum(aw(f)) #> [1] 1 aw(f[c(\"SFO\", \"DFOP\")]) #> [1] 0.5970258 0.4029742 # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/confint.mkinfit.html","id":null,"dir":"Reference","previous_headings":"","what":"Confidence intervals for parameters of mkinfit objects — confint.mkinfit","title":"Confidence intervals for parameters of mkinfit objects — confint.mkinfit","text":"default method 'quadratic' based quadratic approximation curvature likelihood function maximum likelihood parameter estimates. alternative method 'profile' based profile likelihood parameter. 'profile' method uses two nested optimisations can take long time, even parallelized specifying 'cores' unixoid platforms. speed method likely improved using method Venzon Moolgavkar (1988).","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/confint.mkinfit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Confidence intervals for parameters of mkinfit objects — confint.mkinfit","text":"","code":"# S3 method for mkinfit confint( object, parm, level = 0.95, alpha = 1 - level, cutoff, method = c(\"quadratic\", \"profile\"), transformed = TRUE, backtransform = TRUE, cores = parallel::detectCores(), rel_tol = 0.01, quiet = FALSE, ... )"},{"path":"https://pkgdown.jrwb.de/mkin/reference/confint.mkinfit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Confidence intervals for parameters of mkinfit objects — confint.mkinfit","text":"object mkinfit object parm vector names parameters given confidence intervals. missing, parameters considered. level confidence level required alpha allowed error probability, overrides 'level' specified. cutoff Possibility specify alternative cutoff difference log-likelihoods confidence boundary. Specifying explicit cutoff value overrides arguments 'level' 'alpha' method 'quadratic' method approximates likelihood function optimised parameters using second term Taylor expansion, using second derivative (hessian) contained object. 'profile' method searches parameter space cutoff confidence intervals means likelihood ratio test. transformed quadratic approximation used, applied likelihood based transformed parameters? backtransform approximate likelihood terms transformed parameters, backtransform parameters confidence intervals? cores number cores used multicore processing. Windows machines, cores > 1 currently supported. rel_tol method 'profile', accuracy lower upper bounds, relative estimate obtained quadratic method? quiet suppress message \"Profiling likelihood\" ... used","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/confint.mkinfit.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Confidence intervals for parameters of mkinfit objects — confint.mkinfit","text":"matrix columns giving lower upper confidence limits parameter.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/confint.mkinfit.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Confidence intervals for parameters of mkinfit objects — confint.mkinfit","text":"Bates DM Watts GW (1988) Nonlinear regression analysis & applications Pawitan Y (2013) likelihood - Statistical modelling inference using likelihood. Clarendon Press, Oxford. Venzon DJ Moolgavkar SH (1988) Method Computing Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, 87–94.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/confint.mkinfit.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Confidence intervals for parameters of mkinfit objects — confint.mkinfit","text":"","code":"f <- mkinfit(\"SFO\", FOCUS_2006_C, quiet = TRUE) confint(f, method = \"quadratic\") #> 2.5% 97.5% #> parent_0 71.8242430 93.1600766 #> k_parent 0.2109541 0.4440528 #> sigma 1.9778868 7.3681380 # \\dontrun{ confint(f, method = \"profile\") #> Profiling the likelihood #> 2.5% 97.5% #> parent_0 73.0641834 92.1392181 #> k_parent 0.2170293 0.4235348 #> sigma 3.1307772 8.0628314 # Set the number of cores for the profiling method for further examples if (identical(Sys.getenv(\"NOT_CRAN\"), \"true\")) { n_cores <- parallel::detectCores() - 1 } else { n_cores <- 1 } if (Sys.getenv(\"TRAVIS\") != \"\") n_cores = 1 if (Sys.info()[\"sysname\"] == \"Windows\") n_cores = 1 SFO_SFO <- mkinmod(parent = mkinsub(\"SFO\", \"m1\"), m1 = mkinsub(\"SFO\"), use_of_ff = \"min\", quiet = TRUE) SFO_SFO.ff <- mkinmod(parent = mkinsub(\"SFO\", \"m1\"), m1 = mkinsub(\"SFO\"), use_of_ff = \"max\", quiet = TRUE) f_d_1 <- mkinfit(SFO_SFO, subset(FOCUS_2006_D, value != 0), quiet = TRUE) system.time(ci_profile <- confint(f_d_1, method = \"profile\", cores = 1, quiet = TRUE)) #> user system elapsed #> 1.203 0.000 1.203 # Using more cores does not save much time here, as parent_0 takes up most of the time # If we additionally exclude parent_0 (the confidence of which is often of # minor interest), we get a nice performance improvement if we use at least 4 cores system.time(ci_profile_no_parent_0 <- confint(f_d_1, method = \"profile\", c(\"k_parent_sink\", \"k_parent_m1\", \"k_m1_sink\", \"sigma\"), cores = n_cores)) #> Profiling the likelihood #> user system elapsed #> 0.438 0.097 0.301 ci_profile #> 2.5% 97.5% #> parent_0 96.456003640 1.027703e+02 #> k_parent_sink 0.040762501 5.549764e-02 #> k_parent_m1 0.046786482 5.500879e-02 #> k_m1_sink 0.003892605 6.702778e-03 #> sigma 2.535612399 3.985263e+00 ci_quadratic_transformed <- confint(f_d_1, method = \"quadratic\") ci_quadratic_transformed #> 2.5% 97.5% #> parent_0 96.403841640 1.027931e+02 #> k_parent_sink 0.041033378 5.596269e-02 #> k_parent_m1 0.046777902 5.511931e-02 #> k_m1_sink 0.004012217 6.897547e-03 #> sigma 2.396089689 3.854918e+00 ci_quadratic_untransformed <- confint(f_d_1, method = \"quadratic\", transformed = FALSE) ci_quadratic_untransformed #> 2.5% 97.5% #> parent_0 96.403841645 102.79312449 #> k_parent_sink 0.040485331 0.05535491 #> k_parent_m1 0.046611582 0.05494364 #> k_m1_sink 0.003835483 0.00668582 #> sigma 2.396089689 3.85491806 # Against the expectation based on Bates and Watts (1988), the confidence # intervals based on the internal parameter transformation are less # congruent with the likelihood based intervals. Note the superiority of the # interval based on the untransformed fit for k_m1_sink rel_diffs_transformed <- abs((ci_quadratic_transformed - ci_profile)/ci_profile) rel_diffs_untransformed <- abs((ci_quadratic_untransformed - ci_profile)/ci_profile) rel_diffs_transformed < rel_diffs_untransformed #> 2.5% 97.5% #> parent_0 FALSE FALSE #> k_parent_sink TRUE FALSE #> k_parent_m1 TRUE FALSE #> k_m1_sink FALSE FALSE #> sigma FALSE FALSE signif(rel_diffs_transformed, 3) #> 2.5% 97.5% #> parent_0 0.000541 0.000222 #> k_parent_sink 0.006650 0.008380 #> k_parent_m1 0.000183 0.002010 #> k_m1_sink 0.030700 0.029100 #> sigma 0.055000 0.032700 signif(rel_diffs_untransformed, 3) #> 2.5% 97.5% #> parent_0 0.000541 0.000222 #> k_parent_sink 0.006800 0.002570 #> k_parent_m1 0.003740 0.001180 #> k_m1_sink 0.014700 0.002530 #> sigma 0.055000 0.032700 # Investigate a case with formation fractions f_d_2 <- mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), quiet = TRUE) ci_profile_ff <- confint(f_d_2, method = \"profile\", cores = n_cores) #> Profiling the likelihood ci_profile_ff #> 2.5% 97.5% #> parent_0 96.456003640 1.027703e+02 #> k_parent 0.090911032 1.071578e-01 #> k_m1 0.003892606 6.702775e-03 #> f_parent_to_m1 0.471328495 5.611550e-01 #> sigma 2.535612399 3.985263e+00 ci_quadratic_transformed_ff <- confint(f_d_2, method = \"quadratic\") ci_quadratic_transformed_ff #> 2.5% 97.5% #> parent_0 96.403833581 102.79311649 #> k_parent 0.090823771 0.10725430 #> k_m1 0.004012219 0.00689755 #> f_parent_to_m1 0.469118824 0.55959615 #> sigma 2.396089689 3.85491806 ci_quadratic_untransformed_ff <- confint(f_d_2, method = \"quadratic\", transformed = FALSE) ci_quadratic_untransformed_ff #> 2.5% 97.5% #> parent_0 96.403833586 1.027931e+02 #> k_parent 0.090491913 1.069035e-01 #> k_m1 0.003835485 6.685823e-03 #> f_parent_to_m1 0.469113477 5.598387e-01 #> sigma 2.396089689 3.854918e+00 rel_diffs_transformed_ff <- abs((ci_quadratic_transformed_ff - ci_profile_ff)/ci_profile_ff) rel_diffs_untransformed_ff <- abs((ci_quadratic_untransformed_ff - ci_profile_ff)/ci_profile_ff) # While the confidence interval for the parent rate constant is closer to # the profile based interval when using the internal parameter # transformation, the interval for the metabolite rate constant is 'better # without internal parameter transformation. rel_diffs_transformed_ff < rel_diffs_untransformed_ff #> 2.5% 97.5% #> parent_0 FALSE FALSE #> k_parent TRUE TRUE #> k_m1 FALSE FALSE #> f_parent_to_m1 TRUE FALSE #> sigma TRUE FALSE rel_diffs_transformed_ff #> 2.5% 97.5% #> parent_0 0.0005408690 0.0002217233 #> k_parent 0.0009598532 0.0009001864 #> k_m1 0.0307283045 0.0290588367 #> f_parent_to_m1 0.0046881768 0.0027780062 #> sigma 0.0550252516 0.0327066836 rel_diffs_untransformed_ff #> 2.5% 97.5% #> parent_0 0.0005408689 0.0002217233 #> k_parent 0.0046102155 0.0023732280 #> k_m1 0.0146740687 0.0025291815 #> f_parent_to_m1 0.0046995210 0.0023457712 #> sigma 0.0550252516 0.0327066836 # The profiling for the following fit does not finish in a reasonable time, # therefore we use the quadratic approximation m_synth_DFOP_par <- mkinmod(parent = mkinsub(\"DFOP\", c(\"M1\", \"M2\")), M1 = mkinsub(\"SFO\"), M2 = mkinsub(\"SFO\"), use_of_ff = \"max\", quiet = TRUE) DFOP_par_c <- synthetic_data_for_UBA_2014[[12]]$data f_tc_2 <- mkinfit(m_synth_DFOP_par, DFOP_par_c, error_model = \"tc\", error_model_algorithm = \"direct\", quiet = TRUE) confint(f_tc_2, method = \"quadratic\") #> 2.5% 97.5% #> parent_0 94.596181875 106.19936592 #> k_M1 0.037605432 0.04490757 #> k_M2 0.008568745 0.01087675 #> f_parent_to_M1 0.021464676 0.62023880 #> f_parent_to_M2 0.015167158 0.37975350 #> k1 0.273897535 0.33388072 #> k2 0.018614555 0.02250379 #> g 0.671943738 0.73583261 #> sigma_low 0.251283679 0.83992102 #> rsd_high 0.040411022 0.07662008 confint(f_tc_2, \"parent_0\", method = \"quadratic\") #> 2.5% 97.5% #> parent_0 94.59618 106.1994 # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/create_deg_func.html","id":null,"dir":"Reference","previous_headings":"","what":"Create degradation functions for known analytical solutions — create_deg_func","title":"Create degradation functions for known analytical solutions — create_deg_func","text":"Create degradation functions known analytical solutions","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/create_deg_func.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create degradation functions for known analytical solutions — create_deg_func","text":"","code":"create_deg_func(spec, use_of_ff = c(\"min\", \"max\"))"},{"path":"https://pkgdown.jrwb.de/mkin/reference/create_deg_func.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create degradation functions for known analytical solutions — create_deg_func","text":"spec List model specifications contained mkinmod objects use_of_ff Minimum maximum use formation fractions","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/create_deg_func.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create degradation functions for known analytical solutions — create_deg_func","text":"Degradation function attached mkinmod objects","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/create_deg_func.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create degradation functions for known analytical solutions — create_deg_func","text":"","code":"SFO_SFO <- mkinmod( parent = mkinsub(\"SFO\", \"m1\"), m1 = mkinsub(\"SFO\")) #> Temporary DLL for differentials generated and loaded FOCUS_D <- subset(FOCUS_2006_D, value != 0) # to avoid warnings fit_1 <- mkinfit(SFO_SFO, FOCUS_D, solution_type = \"analytical\", quiet = TRUE) # \\dontrun{ fit_2 <- mkinfit(SFO_SFO, FOCUS_D, solution_type = \"deSolve\", quiet = TRUE) if (require(rbenchmark)) benchmark( analytical = mkinfit(SFO_SFO, FOCUS_D, solution_type = \"analytical\", quiet = TRUE), deSolve = mkinfit(SFO_SFO, FOCUS_D, solution_type = \"deSolve\", quiet = TRUE), replications = 2) #> Loading required package: rbenchmark #> test replications elapsed relative user.self sys.self user.child #> 1 analytical 2 0.233 1.000 0.232 0.001 0 #> 2 deSolve 2 0.293 1.258 0.293 0.000 0 #> sys.child #> 1 0 #> 2 0 DFOP_SFO <- mkinmod( parent = mkinsub(\"DFOP\", \"m1\"), m1 = mkinsub(\"SFO\")) #> Temporary DLL for differentials generated and loaded benchmark( analytical = mkinfit(DFOP_SFO, FOCUS_D, solution_type = \"analytical\", quiet = TRUE), deSolve = mkinfit(DFOP_SFO, FOCUS_D, solution_type = \"deSolve\", quiet = TRUE), replications = 2) #> test replications elapsed relative user.self sys.self user.child #> 1 analytical 2 0.375 1.000 0.375 0 0 #> 2 deSolve 2 0.508 1.355 0.508 0 0 #> sys.child #> 1 0 #> 2 0 # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/dimethenamid_2018.html","id":null,"dir":"Reference","previous_headings":"","what":"Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018 — dimethenamid_2018","title":"Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018 — dimethenamid_2018","text":"datasets extracted active substance evaluation dossier published EFSA. Kinetic evaluations shown datasets intended illustrate advance kinetic modelling. fact data results shown imply license use context pesticide registrations, use data may constrained data protection regulations.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/dimethenamid_2018.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018 — dimethenamid_2018","text":"","code":"dimethenamid_2018"},{"path":"https://pkgdown.jrwb.de/mkin/reference/dimethenamid_2018.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018 — dimethenamid_2018","text":"mkindsg object grouping seven datasets meta information","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/dimethenamid_2018.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018 — dimethenamid_2018","text":"Rapporteur Member State Germany, Co-Rapporteur Member State Bulgaria (2018) Renewal Assessment Report Dimethenamid-P Volume 3 - B.8 Environmental fate behaviour Rev. 2 - November 2017 https://open.efsa.europa.eu/study-inventory/EFSA-Q-2014-00716","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/dimethenamid_2018.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018 — dimethenamid_2018","text":"R code used create data object installed package 'dataset_generation' directory. code, page numbers given specific pieces information comments.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/dimethenamid_2018.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Aerobic soil degradation data on dimethenamid and dimethenamid-P from the EU assessment in 2018 — dimethenamid_2018","text":"","code":"print(dimethenamid_2018) #> <mkindsg> holding 7 mkinds objects #> Title $title: Aerobic soil degradation data on dimethenamid-P from the EU assessment in 2018 #> Occurrence of observed compounds $observed_n: #> DMTAP M23 M27 M31 DMTA #> 3 7 7 7 4 #> Time normalisation factors $f_time_norm: #> [1] 1.0000000 0.9706477 1.2284784 1.2284784 0.6233856 0.7678922 0.6733938 #> Meta information $meta: #> study usda_soil_type study_moisture_ref_type rel_moisture #> Calke Unsworth 2014 Sandy loam pF2 1.00 #> Borstel Staudenmaier 2009 Sand pF1 0.50 #> Elliot 1 Wendt 1997 Clay loam pF2.5 0.75 #> Elliot 2 Wendt 1997 Clay loam pF2.5 0.75 #> Flaach König 1996 Sandy clay loam pF1 0.40 #> BBA 2.2 König 1995 Loamy sand pF1 0.40 #> BBA 2.3 König 1995 Sandy loam pF1 0.40 #> study_ref_moisture temperature #> Calke NA 20 #> Borstel 23.00 20 #> Elliot 1 33.37 23 #> Elliot 2 33.37 23 #> Flaach NA 20 #> BBA 2.2 NA 20 #> BBA 2.3 NA 20 dmta_ds <- lapply(1:7, function(i) { ds_i <- dimethenamid_2018$ds[[i]]$data ds_i[ds_i$name == \"DMTAP\", \"name\"] <- \"DMTA\" ds_i$time <- ds_i$time * dimethenamid_2018$f_time_norm[i] ds_i }) names(dmta_ds) <- sapply(dimethenamid_2018$ds, function(ds) ds$title) dmta_ds[[\"Elliot\"]] <- rbind(dmta_ds[[\"Elliot 1\"]], dmta_ds[[\"Elliot 2\"]]) dmta_ds[[\"Elliot 1\"]] <- NULL dmta_ds[[\"Elliot 2\"]] <- NULL # \\dontrun{ # We don't use DFOP for the parent compound, as this gives numerical # instabilities in the fits sfo_sfo3p <- mkinmod( DMTA = mkinsub(\"SFO\", c(\"M23\", \"M27\", \"M31\")), M23 = mkinsub(\"SFO\"), M27 = mkinsub(\"SFO\"), M31 = mkinsub(\"SFO\", \"M27\", sink = FALSE), quiet = TRUE ) dmta_sfo_sfo3p_tc <- mmkin(list(\"SFO-SFO3+\" = sfo_sfo3p), dmta_ds, error_model = \"tc\", quiet = TRUE) print(dmta_sfo_sfo3p_tc) #> <mmkin> object #> Status of individual fits: #> #> dataset #> model Calke Borstel Flaach BBA 2.2 BBA 2.3 Elliot #> SFO-SFO3+ OK OK OK OK OK OK #> #> OK: No warnings # The default (test_log_parms = FALSE) gives an undue # influence of ill-defined rate constants that have # extremely small values: plot(mixed(dmta_sfo_sfo3p_tc), test_log_parms = FALSE) # If we disregards ill-defined rate constants, the results # look more plausible, but the truth is likely to be in # between these variants plot(mixed(dmta_sfo_sfo3p_tc), test_log_parms = TRUE) # We can also specify a default value for the failing # log parameters, to mimic FOCUS guidance plot(mixed(dmta_sfo_sfo3p_tc), test_log_parms = TRUE, default_log_parms = log(2)/1000) # As these attempts are not satisfying, we use nonlinear mixed-effects models # f_dmta_nlme_tc <- nlme(dmta_sfo_sfo3p_tc) # nlme reaches maxIter = 50 without convergence f_dmta_saem_tc <- saem(dmta_sfo_sfo3p_tc) # I am commenting out the convergence plot as rendering them # with pkgdown fails (at least without further tweaks to the # graphics device used) #saemix::plot(f_dmta_saem_tc$so, plot.type = \"convergence\") summary(f_dmta_saem_tc) #> saemix version used for fitting: 3.2 #> mkin version used for pre-fitting: 1.2.6 #> R version used for fitting: 4.3.2 #> Date of fit: Thu Nov 16 04:14:53 2023 #> Date of summary: Thu Nov 16 04:14:53 2023 #> #> Equations: #> d_DMTA/dt = - k_DMTA * DMTA #> d_M23/dt = + f_DMTA_to_M23 * k_DMTA * DMTA - k_M23 * M23 #> d_M27/dt = + f_DMTA_to_M27 * k_DMTA * DMTA - k_M27 * M27 + k_M31 * M31 #> d_M31/dt = + f_DMTA_to_M31 * k_DMTA * DMTA - k_M31 * M31 #> #> Data: #> 563 observations of 4 variable(s) grouped in 6 datasets #> #> Model predictions using solution type deSolve #> #> Fitted in 302.335 s #> Using 300, 100 iterations and 9 chains #> #> Variance model: Two-component variance function #> #> Starting values for degradation parameters: #> DMTA_0 log_k_DMTA log_k_M23 log_k_M27 log_k_M31 f_DMTA_ilr_1 #> 95.5662 -2.9048 -3.8130 -4.1600 -4.1486 0.1341 #> f_DMTA_ilr_2 f_DMTA_ilr_3 #> 0.1385 -1.6700 #> #> Fixed degradation parameter values: #> None #> #> Starting values for random effects (square root of initial entries in omega): #> DMTA_0 log_k_DMTA log_k_M23 log_k_M27 log_k_M31 f_DMTA_ilr_1 #> DMTA_0 4.802 0.0000 0.0000 0.000 0.0000 0.0000 #> log_k_DMTA 0.000 0.9834 0.0000 0.000 0.0000 0.0000 #> log_k_M23 0.000 0.0000 0.6983 0.000 0.0000 0.0000 #> log_k_M27 0.000 0.0000 0.0000 1.028 0.0000 0.0000 #> log_k_M31 0.000 0.0000 0.0000 0.000 0.9841 0.0000 #> f_DMTA_ilr_1 0.000 0.0000 0.0000 0.000 0.0000 0.7185 #> f_DMTA_ilr_2 0.000 0.0000 0.0000 0.000 0.0000 0.0000 #> f_DMTA_ilr_3 0.000 0.0000 0.0000 0.000 0.0000 0.0000 #> f_DMTA_ilr_2 f_DMTA_ilr_3 #> DMTA_0 0.0000 0.0000 #> log_k_DMTA 0.0000 0.0000 #> log_k_M23 0.0000 0.0000 #> log_k_M27 0.0000 0.0000 #> log_k_M31 0.0000 0.0000 #> f_DMTA_ilr_1 0.0000 0.0000 #> f_DMTA_ilr_2 0.7378 0.0000 #> f_DMTA_ilr_3 0.0000 0.4451 #> #> Starting values for error model parameters: #> a.1 b.1 #> 1 1 #> #> Results: #> #> Likelihood computed by importance sampling #> AIC BIC logLik #> 2276 2273 -1120 #> #> Optimised parameters: #> est. lower upper #> DMTA_0 88.4862 84.1127 92.8598 #> log_k_DMTA -3.0512 -3.5674 -2.5351 #> log_k_M23 -4.0576 -4.9013 -3.2139 #> log_k_M27 -3.8584 -4.2572 -3.4595 #> log_k_M31 -3.9779 -4.4844 -3.4714 #> f_DMTA_ilr_1 0.1264 -0.2186 0.4714 #> f_DMTA_ilr_2 0.1509 -0.2547 0.5565 #> f_DMTA_ilr_3 -1.3891 -1.6962 -1.0819 #> a.1 0.9196 0.8231 1.0161 #> b.1 0.1377 0.1203 0.1551 #> SD.DMTA_0 3.5956 -0.8154 8.0066 #> SD.log_k_DMTA 0.6437 0.2784 1.0091 #> SD.log_k_M23 0.9929 0.3719 1.6139 #> SD.log_k_M27 0.4530 0.1522 0.7537 #> SD.log_k_M31 0.5773 0.1952 0.9595 #> SD.f_DMTA_ilr_1 0.4063 0.1505 0.6621 #> SD.f_DMTA_ilr_2 0.4800 0.1817 0.7783 #> SD.f_DMTA_ilr_3 0.3582 0.1350 0.5814 #> #> Correlation: #> DMTA_0 l__DMTA lg__M23 lg__M27 lg__M31 f_DMTA__1 f_DMTA__2 #> log_k_DMTA 0.0306 #> log_k_M23 -0.0234 -0.0032 #> log_k_M27 -0.0380 -0.0049 0.0041 #> log_k_M31 -0.0247 -0.0031 0.0022 0.0817 #> f_DMTA_ilr_1 -0.0046 -0.0006 0.0425 -0.0438 0.0319 #> f_DMTA_ilr_2 -0.0008 -0.0002 0.0216 -0.0267 -0.0890 -0.0349 #> f_DMTA_ilr_3 -0.1805 -0.0136 0.0434 0.0791 0.0390 -0.0061 0.0053 #> #> Random effects: #> est. lower upper #> SD.DMTA_0 3.5956 -0.8154 8.0066 #> SD.log_k_DMTA 0.6437 0.2784 1.0091 #> SD.log_k_M23 0.9929 0.3719 1.6139 #> SD.log_k_M27 0.4530 0.1522 0.7537 #> SD.log_k_M31 0.5773 0.1952 0.9595 #> SD.f_DMTA_ilr_1 0.4063 0.1505 0.6621 #> SD.f_DMTA_ilr_2 0.4800 0.1817 0.7783 #> SD.f_DMTA_ilr_3 0.3582 0.1350 0.5814 #> #> Variance model: #> est. lower upper #> a.1 0.9196 0.8231 1.0161 #> b.1 0.1377 0.1203 0.1551 #> #> Backtransformed parameters: #> est. lower upper #> DMTA_0 88.48621 84.112654 92.85977 #> k_DMTA 0.04730 0.028230 0.07926 #> k_M23 0.01729 0.007437 0.04020 #> k_M27 0.02110 0.014162 0.03144 #> k_M31 0.01872 0.011283 0.03107 #> f_DMTA_to_M23 0.14551 NA NA #> f_DMTA_to_M27 0.12169 NA NA #> f_DMTA_to_M31 0.11062 NA NA #> #> Resulting formation fractions: #> ff #> DMTA_M23 0.1455 #> DMTA_M27 0.1217 #> DMTA_M31 0.1106 #> DMTA_sink 0.6222 #> #> Estimated disappearance times: #> DT50 DT90 #> DMTA 14.65 48.68 #> M23 40.09 133.17 #> M27 32.85 109.11 #> M31 37.02 122.97 # As the confidence interval for the random effects of DMTA_0 # includes zero, we could try an alternative model without # such random effects # f_dmta_saem_tc_2 <- saem(dmta_sfo_sfo3p_tc, # covariance.model = diag(c(0, rep(1, 7)))) # saemix::plot(f_dmta_saem_tc_2$so, plot.type = \"convergence\") # This does not perform better judged by AIC and BIC # saemix::compare.saemix(f_dmta_saem_tc$so, f_dmta_saem_tc_2$so) # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/ds_mixed.html","id":null,"dir":"Reference","previous_headings":"","what":"Synthetic data for hierarchical kinetic degradation models — ds_mixed","title":"Synthetic data for hierarchical kinetic degradation models — ds_mixed","text":"R code used create data object installed package 'dataset_generation' directory.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/ds_mixed.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Synthetic data for hierarchical kinetic degradation models — ds_mixed","text":"","code":"# \\dontrun{ sfo_mmkin <- mmkin(\"SFO\", ds_sfo, quiet = TRUE, error_model = \"tc\", cores = 15) sfo_saem <- saem(sfo_mmkin, no_random_effect = \"parent_0\") plot(sfo_saem) # } # This is the code used to generate the datasets cat(readLines(system.file(\"dataset_generation/ds_mixed.R\", package = \"mkin\")), sep = \"\\n\") #> # Synthetic data for hierarchical kinetic models #> # Refactored version of the code previously in tests/testthat/setup_script.R #> # The number of datasets was 3 for FOMC, and 10 for HS in that script, now it #> # is always 15 for consistency #> #> library(mkin) # We use mkinmod and mkinpredict #> sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) #> n <- 15 #> log_sd <- 0.3 #> err_1 = list(const = 1, prop = 0.05) #> tc <- function(value) sigma_twocomp(value, err_1$const, err_1$prop) #> const <- function(value) 2 #> #> set.seed(123456) #> SFO <- mkinmod(parent = mkinsub(\"SFO\")) #> sfo_pop <- list(parent_0 = 100, k_parent = 0.03) #> sfo_parms <- as.matrix(data.frame( #> k_parent = rlnorm(n, log(sfo_pop$k_parent), log_sd))) #> set.seed(123456) #> ds_sfo <- lapply(1:n, function(i) { #> ds_mean <- mkinpredict(SFO, sfo_parms[i, ], #> c(parent = sfo_pop$parent_0), sampling_times) #> add_err(ds_mean, tc, n = 1)[[1]] #> }) #> attr(ds_sfo, \"pop\") <- sfo_pop #> attr(ds_sfo, \"parms\") <- sfo_parms #> #> set.seed(123456) #> FOMC <- mkinmod(parent = mkinsub(\"FOMC\")) #> fomc_pop <- list(parent_0 = 100, alpha = 2, beta = 8) #> fomc_parms <- as.matrix(data.frame( #> alpha = rlnorm(n, log(fomc_pop$alpha), 0.4), #> beta = rlnorm(n, log(fomc_pop$beta), 0.2))) #> set.seed(123456) #> ds_fomc <- lapply(1:n, function(i) { #> ds_mean <- mkinpredict(FOMC, fomc_parms[i, ], #> c(parent = fomc_pop$parent_0), sampling_times) #> add_err(ds_mean, tc, n = 1)[[1]] #> }) #> attr(ds_fomc, \"pop\") <- fomc_pop #> attr(ds_fomc, \"parms\") <- fomc_parms #> #> set.seed(123456) #> DFOP <- mkinmod(parent = mkinsub(\"DFOP\")) #> dfop_pop <- list(parent_0 = 100, k1 = 0.06, k2 = 0.015, g = 0.4) #> dfop_parms <- as.matrix(data.frame( #> k1 = rlnorm(n, log(dfop_pop$k1), log_sd), #> k2 = rlnorm(n, log(dfop_pop$k2), log_sd), #> g = plogis(rnorm(n, qlogis(dfop_pop$g), log_sd)))) #> set.seed(123456) #> ds_dfop <- lapply(1:n, function(i) { #> ds_mean <- mkinpredict(DFOP, dfop_parms[i, ], #> c(parent = dfop_pop$parent_0), sampling_times) #> add_err(ds_mean, tc, n = 1)[[1]] #> }) #> attr(ds_dfop, \"pop\") <- dfop_pop #> attr(ds_dfop, \"parms\") <- dfop_parms #> #> set.seed(123456) #> HS <- mkinmod(parent = mkinsub(\"HS\")) #> hs_pop <- list(parent_0 = 100, k1 = 0.08, k2 = 0.01, tb = 15) #> hs_parms <- as.matrix(data.frame( #> k1 = rlnorm(n, log(hs_pop$k1), log_sd), #> k2 = rlnorm(n, log(hs_pop$k2), log_sd), #> tb = rlnorm(n, log(hs_pop$tb), 0.1))) #> set.seed(123456) #> ds_hs <- lapply(1:n, function(i) { #> ds_mean <- mkinpredict(HS, hs_parms[i, ], #> c(parent = hs_pop$parent_0), sampling_times) #> add_err(ds_mean, const, n = 1)[[1]] #> }) #> attr(ds_hs, \"pop\") <- hs_pop #> attr(ds_hs, \"parms\") <- hs_parms #> #> set.seed(123456) #> DFOP_SFO <- mkinmod( #> parent = mkinsub(\"DFOP\", \"m1\"), #> m1 = mkinsub(\"SFO\"), #> quiet = TRUE) #> dfop_sfo_pop <- list(parent_0 = 100, #> k_m1 = 0.007, f_parent_to_m1 = 0.5, #> k1 = 0.1, k2 = 0.02, g = 0.5) #> dfop_sfo_parms <- as.matrix(data.frame( #> k1 = rlnorm(n, log(dfop_sfo_pop$k1), log_sd), #> k2 = rlnorm(n, log(dfop_sfo_pop$k2), log_sd), #> g = plogis(rnorm(n, qlogis(dfop_sfo_pop$g), log_sd)), #> f_parent_to_m1 = plogis(rnorm(n, #> qlogis(dfop_sfo_pop$f_parent_to_m1), log_sd)), #> k_m1 = rlnorm(n, log(dfop_sfo_pop$k_m1), log_sd))) #> ds_dfop_sfo_mean <- lapply(1:n, #> function(i) { #> mkinpredict(DFOP_SFO, dfop_sfo_parms[i, ], #> c(parent = dfop_sfo_pop$parent_0, m1 = 0), sampling_times) #> } #> ) #> set.seed(123456) #> ds_dfop_sfo <- lapply(ds_dfop_sfo_mean, function(ds) { #> add_err(ds, #> sdfunc = function(value) sqrt(err_1$const^2 + value^2 * err_1$prop^2), #> n = 1, secondary = \"m1\")[[1]] #> }) #> attr(ds_dfop_sfo, \"pop\") <- dfop_sfo_pop #> attr(ds_dfop_sfo, \"parms\") <- dfop_sfo_parms #> #> #save(ds_sfo, ds_fomc, ds_dfop, ds_hs, ds_dfop_sfo, file = \"data/ds_mixed.rda\", version = 2)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/endpoints.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to calculate endpoints for further use from kinetic models fitted\nwith mkinfit — endpoints","title":"Function to calculate endpoints for further use from kinetic models fitted\nwith mkinfit — endpoints","text":"function calculates DT50 DT90 values well formation fractions kinetic models fitted mkinfit. SFORB model specified one parents metabolites, Eigenvalues returned. equivalent rate constants DFOP model, advantage SFORB model can also used metabolites.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/endpoints.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to calculate endpoints for further use from kinetic models fitted\nwith mkinfit — endpoints","text":"","code":"endpoints(fit, covariates = NULL, covariate_quantile = 0.5)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/endpoints.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to calculate endpoints for further use from kinetic models fitted\nwith mkinfit — endpoints","text":"fit object class mkinfit, nlme.mmkin saem.mmkin, another object list components mkinmod containing mkinmod degradation model, two numeric vectors, bparms.optim bparms.fixed, contain parameter values model. covariates Numeric vector covariate values variables covariate models object. given, overrides 'covariate_quantile'. covariate_quantile argument effect fitted object covariate models. , default show endpoints median covariate values (50th percentile).","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/endpoints.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to calculate endpoints for further use from kinetic models fitted\nwith mkinfit — endpoints","text":"list matrix dissipation times named distimes, , applicable, vector formation fractions named ff , SFORB model use, vector eigenvalues SFORB models, equivalent DFOP rate constants","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/endpoints.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Function to calculate endpoints for further use from kinetic models fitted\nwith mkinfit — endpoints","text":"Additional DT50 values calculated FOMC DT90 k1 k2 HS DFOP, well Eigenvalues b1 b2 SFORB models","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/endpoints.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Function to calculate endpoints for further use from kinetic models fitted\nwith mkinfit — endpoints","text":"function used internally summary.mkinfit, summary.nlme.mmkin summary.saem.mmkin.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/endpoints.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Function to calculate endpoints for further use from kinetic models fitted\nwith mkinfit — endpoints","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/endpoints.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Function to calculate endpoints for further use from kinetic models fitted\nwith mkinfit — endpoints","text":"","code":"fit <- mkinfit(\"FOMC\", FOCUS_2006_C, quiet = TRUE) endpoints(fit) #> $distimes #> DT50 DT90 DT50back #> parent 1.785233 15.1479 4.559973 #> # \\dontrun{ fit_2 <- mkinfit(\"DFOP\", FOCUS_2006_C, quiet = TRUE) endpoints(fit_2) #> $distimes #> DT50 DT90 DT50back DT50_k1 DT50_k2 #> parent 1.886925 21.25106 6.397207 1.508293 38.83438 #> fit_3 <- mkinfit(\"SFORB\", FOCUS_2006_C, quiet = TRUE) endpoints(fit_3) #> $ff #> parent_free #> 1 #> #> $SFORB #> parent_b1 parent_b2 parent_g #> 0.4595574 0.0178488 0.8539454 #> #> $distimes #> DT50 DT90 DT50back DT50_parent_b1 DT50_parent_b2 #> parent 1.886925 21.25106 6.397208 1.508293 38.83438 #> # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/experimental_data_for_UBA.html","id":null,"dir":"Reference","previous_headings":"","what":"Experimental datasets used for development and testing of error models — experimental_data_for_UBA_2019","title":"Experimental datasets used for development and testing of error models — experimental_data_for_UBA_2019","text":"12 datasets extracted active substance evaluation dossiers published EFSA. Kinetic evaluations shown datasets intended illustrate advance error model specifications. fact data results shown imply license use context pesticide registrations, use data may constrained data protection regulations. Preprocessing data performed based recommendations FOCUS kinetics workgroup (FOCUS, 2014) described . Datasets 1 2 Renewal Assessment Report (RAR) imazamox (France, 2015, p. 15). setting values reported zero, LOQ 0.1 assumed. Metabolite residues reported day zero added parent compound residues. Datasets 3 4 Renewal Assessment Report (RAR) isofetamid (Belgium, 2014, p. 8) show data two different radiolabels. dataset 4, value given metabolite day zero sampling replicate B added parent compound, following respective FOCUS recommendation. Dataset 5 Renewal Assessment Report (RAR) ethofumesate (Austria, 2015, p. 16). Datasets 6 10 Renewal Assessment Report (RAR) glyphosate (Germany, 2013, pages 8, 28, 50, 51). initial sampling, residues given metabolite added parent value, following recommendation FOCUS kinetics workgroup. Dataset 11 Renewal Assessment Report (RAR) 2,4-D (Hellas, 2013, p. 644). Values reported zero set NA, exception day three sampling metabolite A2, set one half LOD reported 1% AR. Dataset 12 Renewal Assessment Report (RAR) thifensulfuron-methyl (United Kingdom, 2014, p. 81).","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/experimental_data_for_UBA.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Experimental datasets used for development and testing of error models — experimental_data_for_UBA_2019","text":"","code":"experimental_data_for_UBA_2019"},{"path":"https://pkgdown.jrwb.de/mkin/reference/experimental_data_for_UBA.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Experimental datasets used for development and testing of error models — experimental_data_for_UBA_2019","text":"list containing twelve datasets R6 class defined mkinds, containing, among others, following components title name dataset, e.g. Soil 1 data data frame data form expected mkinfit","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/experimental_data_for_UBA.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Experimental datasets used for development and testing of error models — experimental_data_for_UBA_2019","text":"Austria (2015). Ethofumesate Renewal Assessment Report Volume 3 Annex B.8 () Belgium (2014). Isofetamid (IKF-5411) Draft Assessment Report Volume 3 Annex B.8 () France (2015). Imazamox Draft Renewal Assessment Report Volume 3 Annex B.8 () FOCUS (2014) “Generic guidance Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration” Report FOCUS Work Group Degradation Kinetics, Version 1.1, 18 December 2014 http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics Germany (2013). Renewal Assessment Report Glyphosate Volume 3 Annex B.8: Environmental Fate Behaviour Hellas (2013). Renewal Assessment Report 2,4-D Volume 3 Annex B.8: Fate behaviour environment Ranke (2019) Documentation results obtained error model expertise written German Umweltbundesamt. United Kingdom (2014). Thifensulfuron-methyl - Annex B.8 (Volume 3) Report Proposed Decision United Kingdom made European Commission Regulation (EC) . 1141/2010 renewal active substance","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/experimental_data_for_UBA.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Experimental datasets used for development and testing of error models — experimental_data_for_UBA_2019","text":"","code":"# \\dontrun{ # Model definitions sfo_sfo <- mkinmod( parent = mkinsub(\"SFO\", to = \"A1\"), A1 = mkinsub(\"SFO\"), use_of_ff = \"max\" ) #> Temporary DLL for differentials generated and loaded dfop_sfo <- mkinmod( parent = mkinsub(\"DFOP\", to = \"A1\"), A1 = mkinsub(\"SFO\"), use_of_ff = \"max\" ) #> Temporary DLL for differentials generated and loaded sfo_sfo_sfo <- mkinmod( parent = mkinsub(\"SFO\", to = \"A1\"), A1 = mkinsub(\"SFO\", to = \"A2\"), A2 = mkinsub(\"SFO\"), use_of_ff = \"max\" ) #> Temporary DLL for differentials generated and loaded dfop_sfo_sfo <- mkinmod( parent = mkinsub(\"DFOP\", to = \"A1\"), A1 = mkinsub(\"SFO\", to = \"A2\"), A2 = mkinsub(\"SFO\"), use_of_ff = \"max\" ) #> Temporary DLL for differentials generated and loaded d_1_2 <- lapply(experimental_data_for_UBA_2019[1:2], function(x) x$data) names(d_1_2) <- paste(\"Soil\", 1:2) f_1_2_tc <- mmkin(list(\"DFOP-SFO-SFO\" = dfop_sfo_sfo), d_1_2, error_model = \"tc\") plot(f_1_2_tc, resplot = \"errmod\") # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/f_time_norm_focus.html","id":null,"dir":"Reference","previous_headings":"","what":"Normalisation factors for aerobic soil degradation according to FOCUS guidance — f_time_norm_focus","title":"Normalisation factors for aerobic soil degradation according to FOCUS guidance — f_time_norm_focus","text":"Time step normalisation factors aerobic soil degradation described Appendix 8 FOCUS kinetics guidance (FOCUS 2014, p. 369).","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/f_time_norm_focus.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Normalisation factors for aerobic soil degradation according to FOCUS guidance — f_time_norm_focus","text":"","code":"f_time_norm_focus(object, ...) # S3 method for numeric f_time_norm_focus( object, moisture = NA, field_moisture = NA, temperature = object, Q10 = 2.58, walker = 0.7, f_na = NA, ... ) # S3 method for mkindsg f_time_norm_focus( object, study_moisture_ref_source = c(\"auto\", \"meta\", \"focus\"), Q10 = 2.58, walker = 0.7, f_na = NA, ... )"},{"path":"https://pkgdown.jrwb.de/mkin/reference/f_time_norm_focus.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Normalisation factors for aerobic soil degradation according to FOCUS guidance — f_time_norm_focus","text":"object object containing information used calculations ... Currently used moisture Numeric vector moisture contents \\% w/w field_moisture Numeric vector moisture contents field capacity (pF2) \\% w/w temperature Numeric vector temperatures °C Q10 Q10 value used temperature normalisation walker Walker exponent used moisture normalisation f_na factor use NA values. set NA, factors complete cases returned. study_moisture_ref_source Source reference value used calculate study moisture. 'auto', preference given reference moisture given meta information, otherwise focus soil moisture soil class used","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/f_time_norm_focus.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Normalisation factors for aerobic soil degradation according to FOCUS guidance — f_time_norm_focus","text":"FOCUS (2006) “Guidance Document Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration” Report FOCUS Work Group Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics FOCUS (2014) “Generic guidance Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration” Report FOCUS Work Group Degradation Kinetics, Version 1.1, 18 December 2014 http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/reference/f_time_norm_focus.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Normalisation factors for aerobic soil degradation according to FOCUS guidance — f_time_norm_focus","text":"","code":"f_time_norm_focus(25, 20, 25) # 1.37, compare FOCUS 2014 p. 184 #> [1] 1.373956 D24_2014$meta #> study usda_soil_type study_moisture_ref_type #> Mississippi Cohen 1991 Silt loam <NA> #> Fayette Liu and Adelfinskaya 2011 Silt loam pF1 #> RefSol 03-G Liu and Adelfinskaya 2011 Loam pF1 #> Site E1 Liu and Adelfinskaya 2011 Loam pF1 #> Site I2 Liu and Adelfinskaya 2011 Loamy sand pF1 #> rel_moisture temperature #> Mississippi NA 25 #> Fayette 0.5 20 #> RefSol 03-G 0.5 20 #> Site E1 0.5 20 #> Site I2 0.5 20 # No moisture normalisation in the first dataset, so we use f_na = 1 to get # temperature only normalisation as in the EU evaluation f_time_norm_focus(D24_2014, study_moisture_ref_source = \"focus\", f_na = 1) #> $f_time_norm was (re)set to normalised values"},{"path":"https://pkgdown.jrwb.de/mkin/reference/focus_soil_moisture.html","id":null,"dir":"Reference","previous_headings":"","what":"FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar — focus_soil_moisture","title":"FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar — focus_soil_moisture","text":"value transcribed p. 36. table assumes field capacity corresponds pF2, MWHC pF 1 1/3 bar pF 2.5.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/focus_soil_moisture.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar — focus_soil_moisture","text":"","code":"focus_soil_moisture"},{"path":"https://pkgdown.jrwb.de/mkin/reference/focus_soil_moisture.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar — focus_soil_moisture","text":"matrix upper case USDA soil classes row names, water tension ('pF1', 'pF2', 'pF 2.5') column names","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/focus_soil_moisture.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar — focus_soil_moisture","text":"Anonymous (2014) Generic Guidance Tier 1 FOCUS Ground Water Assessment Version 2.2, May 2014 https://esdac.jrc.ec.europa.eu/projects/ground-water","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/focus_soil_moisture.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"FOCUS default values for soil moisture contents at field capacity, MWHC and 1/3 bar — focus_soil_moisture","text":"","code":"focus_soil_moisture #> pF1 pF2 pF2.5 #> Sand 24 12 7 #> Loamy sand 24 14 9 #> Sandy loam 27 19 15 #> Sandy clay loam 28 22 18 #> Clay loam 32 28 25 #> Loam 31 25 21 #> Silt loam 32 26 21 #> Silty clay loam 34 30 27 #> Silt 31 27 21 #> Sandy clay 41 35 31 #> Silty clay 44 40 36 #> Clay 53 48 43"},{"path":"https://pkgdown.jrwb.de/mkin/reference/get_deg_func.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve a degradation function from the mmkin namespace — get_deg_func","title":"Retrieve a degradation function from the mmkin namespace — get_deg_func","text":"Retrieve degradation function mmkin namespace","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/get_deg_func.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve a degradation function from the mmkin namespace — get_deg_func","text":"","code":"get_deg_func()"},{"path":"https://pkgdown.jrwb.de/mkin/reference/get_deg_func.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve a degradation function from the mmkin namespace — get_deg_func","text":"function likely previously assigned within nlme.mmkin","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/hierarchical_kinetics.html","id":null,"dir":"Reference","previous_headings":"","what":"Hierarchical kinetics template — hierarchical_kinetics","title":"Hierarchical kinetics template — hierarchical_kinetics","text":"R markdown format setting hierarchical kinetics based template provided mkin package. format based rmarkdown::pdf_document. Chunk options adapted. Echoing R code code chunks caching turned per default. character prepending output code chunks set empty string, code tidying , figure alignment defaults centering, positioning figures set \"H\", means figures move around document, stay user includes .","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/hierarchical_kinetics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Hierarchical kinetics template — hierarchical_kinetics","text":"","code":"hierarchical_kinetics(..., keep_tex = FALSE)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/hierarchical_kinetics.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Hierarchical kinetics template — hierarchical_kinetics","text":"... Arguments rmarkdown::pdf_document keep_tex Keep intermediate tex file used conversion PDF","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/hierarchical_kinetics.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Hierarchical kinetics template — hierarchical_kinetics","text":"R Markdown output format pass render","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/hierarchical_kinetics.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Hierarchical kinetics template — hierarchical_kinetics","text":"latter feature (positioning figures \"H\") depends LaTeX package 'float'. addition, LaTeX package 'listing' used template showing model fit summaries Appendix. means LaTeX packages 'float' 'listing' need installed TeX distribution used. Windows, easiest way achieve (TeX distribution present ) install 'tinytex' R package, run 'tinytex::install_tinytex()' get basic tiny Tex distribution, run 'tinytex::tlmgr_install(c(\"float\", \"listing\"))'.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/hierarchical_kinetics.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Hierarchical kinetics template — hierarchical_kinetics","text":"","code":"# \\dontrun{ library(rmarkdown) # The following is now commented out after the relase of v1.2.3 for the generation # of online docs, as the command creates a directory and opens an editor #draft(\"example_analysis.rmd\", template = \"hierarchical_kinetics\", package = \"mkin\") # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/illparms.html","id":null,"dir":"Reference","previous_headings":"","what":"Method to get the names of ill-defined parameters — illparms","title":"Method to get the names of ill-defined parameters — illparms","text":"method generalised nonlinear regression fits obtained mkinfit mmkin checks degradation parameters pass Wald test (degradation kinetics often simply called t-test) significant difference zero. test, parameterisation without parameter transformations used.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/illparms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Method to get the names of ill-defined parameters — illparms","text":"","code":"illparms(object, ...) # S3 method for mkinfit illparms(object, conf.level = 0.95, ...) # S3 method for illparms.mkinfit print(x, ...) # S3 method for mmkin illparms(object, conf.level = 0.95, ...) # S3 method for illparms.mmkin print(x, ...) # S3 method for saem.mmkin illparms( object, conf.level = 0.95, random = TRUE, errmod = TRUE, slopes = TRUE, ... ) # S3 method for illparms.saem.mmkin print(x, ...) # S3 method for mhmkin illparms(object, conf.level = 0.95, random = TRUE, errmod = TRUE, ...) # S3 method for illparms.mhmkin print(x, ...)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/illparms.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Method to get the names of ill-defined parameters — illparms","text":"object object investigate ... potential future extensions conf.level confidence level checking p values x object printed random hierarchical fits, random effects tested? errmod hierarchical fits, error model parameters tested? slopes hierarchical saem fits using saemix backend, slope parameters covariate model(starting 'beta_') tested?","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/illparms.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Method to get the names of ill-defined parameters — illparms","text":"mkinfit saem objects, character vector parameter names. mmkin mhmkin objects, matrix like object class 'illparms.mmkin' 'illparms.mhmkin'.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/illparms.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Method to get the names of ill-defined parameters — illparms","text":"method hierarchical model fits, also known nonlinear mixed-effects model fits obtained saem mhmkin checks confidence intervals random effects expressed standard deviations include zero, confidence intervals error model parameters include zero.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/illparms.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Method to get the names of ill-defined parameters — illparms","text":"return objects printing methods. single fits, printing output anything case ill-defined parameters found.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/illparms.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Method to get the names of ill-defined parameters — illparms","text":"","code":"fit <- mkinfit(\"FOMC\", FOCUS_2006_A, quiet = TRUE) #> Warning: Optimisation did not converge: #> false convergence (8) illparms(fit) #> [1] \"parent_0\" \"alpha\" \"beta\" \"sigma\" # \\dontrun{ fits <- mmkin( c(\"SFO\", \"FOMC\"), list(\"FOCUS A\" = FOCUS_2006_A, \"FOCUS C\" = FOCUS_2006_C), quiet = TRUE) illparms(fits) #> dataset #> model FOCUS A FOCUS C #> SFO #> FOMC parent_0, alpha, beta, sigma # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/ilr.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to perform isometric log-ratio transformation — ilr","title":"Function to perform isometric log-ratio transformation — ilr","text":"implementation special case class isometric log-ratio transformations.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/ilr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to perform isometric log-ratio transformation — ilr","text":"","code":"ilr(x) invilr(x)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/ilr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to perform isometric log-ratio transformation — ilr","text":"x numeric vector. Naturally, forward transformation sensible vectors elements greater zero.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/ilr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to perform isometric log-ratio transformation — ilr","text":"result forward backward transformation. returned components always sum 1 case inverse log-ratio transformation.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/ilr.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Function to perform isometric log-ratio transformation — ilr","text":"Peter Filzmoser, Karel Hron (2008) Outlier Detection Compositional Data Using Robust Methods. Math Geosci 40 233-248","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/reference/ilr.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Function to perform isometric log-ratio transformation — ilr","text":"René Lehmann Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/ilr.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Function to perform isometric log-ratio transformation — ilr","text":"","code":"# Order matters ilr(c(0.1, 1, 10)) #> [1] -1.628174 -2.820079 ilr(c(10, 1, 0.1)) #> [1] 1.628174 2.820079 # Equal entries give ilr transformations with zeros as elements ilr(c(3, 3, 3)) #> [1] 0 0 # Almost equal entries give small numbers ilr(c(0.3, 0.4, 0.3)) #> [1] -0.2034219 0.1174457 # Only the ratio between the numbers counts, not their sum invilr(ilr(c(0.7, 0.29, 0.01))) #> [1] 0.70 0.29 0.01 invilr(ilr(2.1 * c(0.7, 0.29, 0.01))) #> [1] 0.70 0.29 0.01 # Inverse transformation of larger numbers gives unequal elements invilr(-10) #> [1] 7.213536e-07 9.999993e-01 invilr(c(-10, 0)) #> [1] 7.207415e-07 9.991507e-01 8.486044e-04 # The sum of the elements of the inverse ilr is 1 sum(invilr(c(-10, 0))) #> [1] 1 # This is why we do not need all elements of the inverse transformation to go back: a <- c(0.1, 0.3, 0.5) b <- invilr(a) length(b) # Four elements #> [1] 4 ilr(c(b[1:3], 1 - sum(b[1:3]))) # Gives c(0.1, 0.3, 0.5) #> [1] 0.1 0.3 0.5"},{"path":"https://pkgdown.jrwb.de/mkin/reference/intervals.saem.mmkin.html","id":null,"dir":"Reference","previous_headings":"","what":"Confidence intervals for parameters in saem.mmkin objects — intervals.saem.mmkin","title":"Confidence intervals for parameters in saem.mmkin objects — intervals.saem.mmkin","text":"Confidence intervals parameters saem.mmkin objects","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/intervals.saem.mmkin.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Confidence intervals for parameters in saem.mmkin objects — intervals.saem.mmkin","text":"","code":"# S3 method for saem.mmkin intervals(object, level = 0.95, backtransform = TRUE, ...)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/intervals.saem.mmkin.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Confidence intervals for parameters in saem.mmkin objects — intervals.saem.mmkin","text":"object fitted saem.mmkin object level confidence level. Must default 0.95 available saemix object backtransform case model fitted mkin transformations, backtransform parameters one one correlation transformed backtransformed parameters exists? ... compatibility generic method","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/intervals.saem.mmkin.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Confidence intervals for parameters in saem.mmkin objects — intervals.saem.mmkin","text":"object 'intervals.saem.mmkin' 'intervals.lme' class attribute","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/llhist.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the distribution of log likelihoods from multistart objects — llhist","title":"Plot the distribution of log likelihoods from multistart objects — llhist","text":"Produces histogram log-likelihoods. addition, likelihood original fit shown red vertical line.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/llhist.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the distribution of log likelihoods from multistart objects — llhist","text":"","code":"llhist(object, breaks = \"Sturges\", lpos = \"topleft\", main = \"\", ...)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/llhist.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the distribution of log likelihoods from multistart objects — llhist","text":"object multistart object breaks Passed hist lpos Positioning legend. main Title plot ... Passed hist","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/reference/loftest.html","id":null,"dir":"Reference","previous_headings":"","what":"Lack-of-fit test for models fitted to data with replicates — loftest","title":"Lack-of-fit test for models fitted to data with replicates — loftest","text":"generic function method currently defined mkinfit objects. fits anova model data contained object compares likelihoods using likelihood ratio test lrtest.default lmtest package.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/loftest.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Lack-of-fit test for models fitted to data with replicates — loftest","text":"","code":"loftest(object, ...) # S3 method for mkinfit loftest(object, ...)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/loftest.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Lack-of-fit test for models fitted to data with replicates — loftest","text":"object model object defined loftest method ... used","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/loftest.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Lack-of-fit test for models fitted to data with replicates — loftest","text":"anova model interpreted simplest form mkinfit model, assuming constant variance means, enforcing structure means, one model parameter every mean replicate samples.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/reference/loftest.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Lack-of-fit test for models fitted to data with replicates — loftest","text":"","code":"# \\dontrun{ test_data <- subset(synthetic_data_for_UBA_2014[[12]]$data, name == \"parent\") sfo_fit <- mkinfit(\"SFO\", test_data, quiet = TRUE) plot_res(sfo_fit) # We see a clear pattern in the residuals loftest(sfo_fit) # We have a clear lack of fit #> Likelihood ratio test #> #> Model 1: ANOVA with error model const #> Model 2: SFO with error model const #> #Df LogLik Df Chisq Pr(>Chisq) #> 1 10 -40.710 #> 2 3 -63.954 -7 46.487 7.027e-08 *** #> --- #> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 # # We try a different model (the one that was used to generate the data) dfop_fit <- mkinfit(\"DFOP\", test_data, quiet = TRUE) plot_res(dfop_fit) # We don't see systematic deviations, but heteroscedastic residuals # therefore we should consider adapting the error model, although we have loftest(dfop_fit) # no lack of fit #> Likelihood ratio test #> #> Model 1: ANOVA with error model const #> Model 2: DFOP with error model const #> #Df LogLik Df Chisq Pr(>Chisq) #> 1 10 -40.710 #> 2 5 -42.453 -5 3.485 0.6257 # # This is the anova model used internally for the comparison test_data_anova <- test_data test_data_anova$time <- as.factor(test_data_anova$time) anova_fit <- lm(value ~ time, data = test_data_anova) summary(anova_fit) #> #> Call: #> lm(formula = value ~ time, data = test_data_anova) #> #> Residuals: #> Min 1Q Median 3Q Max #> -6.1000 -0.5625 0.0000 0.5625 6.1000 #> #> Coefficients: #> Estimate Std. Error t value Pr(>|t|) #> (Intercept) 103.150 2.323 44.409 7.44e-12 *** #> time1 -19.950 3.285 -6.073 0.000185 *** #> time3 -50.800 3.285 -15.465 8.65e-08 *** #> time7 -68.500 3.285 -20.854 6.28e-09 *** #> time14 -79.750 3.285 -24.278 1.63e-09 *** #> time28 -86.000 3.285 -26.181 8.35e-10 *** #> time60 -94.900 3.285 -28.891 3.48e-10 *** #> time90 -98.500 3.285 -29.986 2.49e-10 *** #> time120 -100.450 3.285 -30.580 2.09e-10 *** #> --- #> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 #> #> Residual standard error: 3.285 on 9 degrees of freedom #> Multiple R-squared: 0.9953,\tAdjusted R-squared: 0.9912 #> F-statistic: 240.5 on 8 and 9 DF, p-value: 1.417e-09 #> logLik(anova_fit) # We get the same likelihood and degrees of freedom #> 'log Lik.' -40.71015 (df=10) # test_data_2 <- synthetic_data_for_UBA_2014[[12]]$data m_synth_SFO_lin <- mkinmod(parent = list(type = \"SFO\", to = \"M1\"), M1 = list(type = \"SFO\", to = \"M2\"), M2 = list(type = \"SFO\"), use_of_ff = \"max\") #> Temporary DLL for differentials generated and loaded sfo_lin_fit <- mkinfit(m_synth_SFO_lin, test_data_2, quiet = TRUE) plot_res(sfo_lin_fit) # not a good model, we try parallel formation loftest(sfo_lin_fit) #> Likelihood ratio test #> #> Model 1: ANOVA with error model const #> Model 2: m_synth_SFO_lin with error model const and fixed parameter(s) M1_0, M2_0 #> #Df LogLik Df Chisq Pr(>Chisq) #> 1 28 -93.606 #> 2 7 -171.927 -21 156.64 < 2.2e-16 *** #> --- #> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 # m_synth_SFO_par <- mkinmod(parent = list(type = \"SFO\", to = c(\"M1\", \"M2\")), M1 = list(type = \"SFO\"), M2 = list(type = \"SFO\"), use_of_ff = \"max\") #> Temporary DLL for differentials generated and loaded sfo_par_fit <- mkinfit(m_synth_SFO_par, test_data_2, quiet = TRUE) plot_res(sfo_par_fit) # much better for metabolites loftest(sfo_par_fit) #> Likelihood ratio test #> #> Model 1: ANOVA with error model const #> Model 2: m_synth_SFO_par with error model const and fixed parameter(s) M1_0, M2_0 #> #Df LogLik Df Chisq Pr(>Chisq) #> 1 28 -93.606 #> 2 7 -156.331 -21 125.45 < 2.2e-16 *** #> --- #> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 # m_synth_DFOP_par <- mkinmod(parent = list(type = \"DFOP\", to = c(\"M1\", \"M2\")), M1 = list(type = \"SFO\"), M2 = list(type = \"SFO\"), use_of_ff = \"max\") #> Temporary DLL for differentials generated and loaded dfop_par_fit <- mkinfit(m_synth_DFOP_par, test_data_2, quiet = TRUE) plot_res(dfop_par_fit) # No visual lack of fit loftest(dfop_par_fit) # no lack of fit found by the test #> Likelihood ratio test #> #> Model 1: ANOVA with error model const #> Model 2: m_synth_DFOP_par with error model const and fixed parameter(s) M1_0, M2_0 #> #Df LogLik Df Chisq Pr(>Chisq) #> 1 28 -93.606 #> 2 9 -102.763 -19 18.313 0.5016 # # The anova model used for comparison in the case of transformation products test_data_anova_2 <- dfop_par_fit$data test_data_anova_2$variable <- as.factor(test_data_anova_2$variable) test_data_anova_2$time <- as.factor(test_data_anova_2$time) anova_fit_2 <- lm(observed ~ time:variable - 1, data = test_data_anova_2) summary(anova_fit_2) #> #> Call: #> lm(formula = observed ~ time:variable - 1, data = test_data_anova_2) #> #> Residuals: #> Min 1Q Median 3Q Max #> -6.1000 -0.5875 0.0000 0.5875 6.1000 #> #> Coefficients: (2 not defined because of singularities) #> Estimate Std. Error t value Pr(>|t|) #> time0:variableparent 103.150 1.573 65.562 < 2e-16 *** #> time1:variableparent 83.200 1.573 52.882 < 2e-16 *** #> time3:variableparent 52.350 1.573 33.274 < 2e-16 *** #> time7:variableparent 34.650 1.573 22.024 < 2e-16 *** #> time14:variableparent 23.400 1.573 14.873 6.35e-14 *** #> time28:variableparent 17.150 1.573 10.901 5.47e-11 *** #> time60:variableparent 8.250 1.573 5.244 1.99e-05 *** #> time90:variableparent 4.650 1.573 2.956 0.006717 ** #> time120:variableparent 2.700 1.573 1.716 0.098507 . #> time0:variableM1 NA NA NA NA #> time1:variableM1 11.850 1.573 7.532 6.93e-08 *** #> time3:variableM1 22.700 1.573 14.428 1.26e-13 *** #> time7:variableM1 33.050 1.573 21.007 < 2e-16 *** #> time14:variableM1 31.250 1.573 19.863 < 2e-16 *** #> time28:variableM1 18.900 1.573 12.013 7.02e-12 *** #> time60:variableM1 7.550 1.573 4.799 6.28e-05 *** #> time90:variableM1 3.850 1.573 2.447 0.021772 * #> time120:variableM1 2.050 1.573 1.303 0.204454 #> time0:variableM2 NA NA NA NA #> time1:variableM2 6.700 1.573 4.259 0.000254 *** #> time3:variableM2 16.750 1.573 10.646 8.93e-11 *** #> time7:variableM2 25.800 1.573 16.399 6.89e-15 *** #> time14:variableM2 28.600 1.573 18.178 6.35e-16 *** #> time28:variableM2 25.400 1.573 16.144 9.85e-15 *** #> time60:variableM2 21.600 1.573 13.729 3.81e-13 *** #> time90:variableM2 17.800 1.573 11.314 2.51e-11 *** #> time120:variableM2 14.100 1.573 8.962 2.79e-09 *** #> --- #> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 #> #> Residual standard error: 2.225 on 25 degrees of freedom #> Multiple R-squared: 0.9979,\tAdjusted R-squared: 0.9957 #> F-statistic: 469.2 on 25 and 25 DF, p-value: < 2.2e-16 #> # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/logLik.mkinfit.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculated the log-likelihood of a fitted mkinfit object — logLik.mkinfit","title":"Calculated the log-likelihood of a fitted mkinfit object — logLik.mkinfit","text":"function returns product likelihood densities observed value, calculated part fitting procedure using dnorm, .e. assuming normal distribution, means predicted degradation model, standard deviations predicted error model.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/logLik.mkinfit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculated the log-likelihood of a fitted mkinfit object — logLik.mkinfit","text":"","code":"# S3 method for mkinfit logLik(object, ...)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/logLik.mkinfit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculated the log-likelihood of a fitted mkinfit object — logLik.mkinfit","text":"object object class mkinfit. ... compatibility generic method","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/logLik.mkinfit.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculated the log-likelihood of a fitted mkinfit object — logLik.mkinfit","text":"object class logLik number estimated parameters (degradation model parameters plus variance model parameters) attribute.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/logLik.mkinfit.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculated the log-likelihood of a fitted mkinfit object — logLik.mkinfit","text":"total number estimated parameters returned value likelihood calculated sum fitted degradation model parameters fitted error model parameters.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/reference/logLik.mkinfit.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculated the log-likelihood of a fitted mkinfit object — logLik.mkinfit","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/logLik.mkinfit.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculated the log-likelihood of a fitted mkinfit object — logLik.mkinfit","text":"","code":"# \\dontrun{ sfo_sfo <- mkinmod( parent = mkinsub(\"SFO\", to = \"m1\"), m1 = mkinsub(\"SFO\") ) #> Temporary DLL for differentials generated and loaded d_t <- subset(FOCUS_2006_D, value != 0) f_nw <- mkinfit(sfo_sfo, d_t, quiet = TRUE) # no weighting (weights are unity) f_obs <- update(f_nw, error_model = \"obs\") f_tc <- update(f_nw, error_model = \"tc\") AIC(f_nw, f_obs, f_tc) #> df AIC #> f_nw 5 204.4486 #> f_obs 6 205.8727 #> f_tc 6 141.9656 # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/logLik.saem.mmkin.html","id":null,"dir":"Reference","previous_headings":"","what":"logLik method for saem.mmkin objects — logLik.saem.mmkin","title":"logLik method for saem.mmkin objects — logLik.saem.mmkin","text":"logLik method saem.mmkin objects","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/logLik.saem.mmkin.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"logLik method for saem.mmkin objects — logLik.saem.mmkin","text":"","code":"# S3 method for saem.mmkin logLik(object, ..., method = c(\"is\", \"lin\", \"gq\"))"},{"path":"https://pkgdown.jrwb.de/mkin/reference/logLik.saem.mmkin.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"logLik method for saem.mmkin objects — logLik.saem.mmkin","text":"object fitted saem.mmkin object ... Passed saemix::logLik.SaemixObject method Passed saemix::logLik.SaemixObject","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/logistic.solution.html","id":null,"dir":"Reference","previous_headings":"","what":"Logistic kinetics — logistic.solution","title":"Logistic kinetics — logistic.solution","text":"Function describing exponential decline defined starting value, increasing rate constant, supposedly caused microbial growth","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/logistic.solution.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Logistic kinetics — logistic.solution","text":"","code":"logistic.solution(t, parent_0, kmax, k0, r)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/logistic.solution.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Logistic kinetics — logistic.solution","text":"t Time. parent_0 Starting value response variable time zero. kmax Maximum rate constant. k0 Minimum rate constant effective time zero. r Growth rate increase rate constant.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/logistic.solution.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Logistic kinetics — logistic.solution","text":"value response variable time t.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/logistic.solution.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Logistic kinetics — logistic.solution","text":"solution logistic model reduces SFO.solution k0 equal kmax.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/logistic.solution.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Logistic kinetics — logistic.solution","text":"FOCUS (2006) “Guidance Document Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration” Report FOCUS Work Group Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics FOCUS (2014) “Generic guidance Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration” Report FOCUS Work Group Degradation Kinetics, Version 1.1, 18 December 2014 http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/reference/logistic.solution.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Logistic kinetics — logistic.solution","text":"","code":"# Reproduce the plot on page 57 of FOCUS (2014) plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.2), from = 0, to = 100, ylim = c(0, 100), xlab = \"Time\", ylab = \"Residue\") plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.4), from = 0, to = 100, add = TRUE, lty = 2, col = 2) plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.8), from = 0, to = 100, add = TRUE, lty = 3, col = 3) plot(function(x) logistic.solution(x, 100, 0.08, 0.001, 0.2), from = 0, to = 100, add = TRUE, lty = 4, col = 4) plot(function(x) logistic.solution(x, 100, 0.08, 0.08, 0.2), from = 0, to = 100, add = TRUE, lty = 5, col = 5) legend(\"topright\", inset = 0.05, legend = paste0(\"k0 = \", c(0.0001, 0.0001, 0.0001, 0.001, 0.08), \", r = \", c(0.2, 0.4, 0.8, 0.2, 0.2)), lty = 1:5, col = 1:5) # Fit with synthetic data logistic <- mkinmod(parent = mkinsub(\"logistic\")) sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) parms_logistic <- c(kmax = 0.08, k0 = 0.0001, r = 0.2) d_logistic <- mkinpredict(logistic, parms_logistic, c(parent = 100), sampling_times) d_2_1 <- add_err(d_logistic, sdfunc = function(x) sigma_twocomp(x, 0.5, 0.07), n = 1, reps = 2, digits = 5, LOD = 0.1, seed = 123456)[[1]] m <- mkinfit(\"logistic\", d_2_1, quiet = TRUE) plot_sep(m) summary(m)$bpar #> Estimate se_notrans t value Pr(>t) Lower #> parent_0 1.057896e+02 1.9023449604 55.610120 3.768360e-16 1.016451e+02 #> kmax 6.398190e-02 0.0143201030 4.467978 3.841828e-04 3.929235e-02 #> k0 1.612775e-04 0.0005866813 0.274898 3.940351e-01 5.846688e-08 #> r 2.263946e-01 0.1718110664 1.317695 1.061043e-01 4.335843e-02 #> sigma 5.332935e+00 0.9145907310 5.830952 4.036926e-05 3.340213e+00 #> Upper #> parent_0 109.9341588 #> kmax 0.1041853 #> k0 0.4448749 #> r 1.1821120 #> sigma 7.3256566 endpoints(m)$distimes #> DT50 DT90 DT50_k0 DT50_kmax #> parent 36.86533 62.41511 4297.853 10.83349"},{"path":"https://pkgdown.jrwb.de/mkin/reference/lrtest.mkinfit.html","id":null,"dir":"Reference","previous_headings":"","what":"Likelihood ratio test for mkinfit models — lrtest.mkinfit","title":"Likelihood ratio test for mkinfit models — lrtest.mkinfit","text":"Compare two mkinfit models based likelihood. two fitted mkinfit objects given arguments, checked fitted data. responsibility user make sure models nested, .e. one less degrees freedom can expressed fixing parameters .","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/lrtest.mkinfit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Likelihood ratio test for mkinfit models — lrtest.mkinfit","text":"","code":"# S3 method for mkinfit lrtest(object, object_2 = NULL, ...) # S3 method for mmkin lrtest(object, ...)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/lrtest.mkinfit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Likelihood ratio test for mkinfit models — lrtest.mkinfit","text":"object mkinfit object, mmkin column object containing two fits data. object_2 Optionally, another mkinfit object fitted data. ... Argument mkinfit, passed update.mkinfit creating alternative fitted object.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/lrtest.mkinfit.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Likelihood ratio test for mkinfit models — lrtest.mkinfit","text":"Alternatively, argument mkinfit can given passed update.mkinfit obtain alternative model. comparison made lrtest.default method lmtest package. model higher number fitted parameters (alternative hypothesis) listed first, model lower number fitted parameters (null hypothesis).","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/lrtest.mkinfit.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Likelihood ratio test for mkinfit models — lrtest.mkinfit","text":"","code":"# \\dontrun{ test_data <- subset(synthetic_data_for_UBA_2014[[12]]$data, name == \"parent\") sfo_fit <- mkinfit(\"SFO\", test_data, quiet = TRUE) dfop_fit <- mkinfit(\"DFOP\", test_data, quiet = TRUE) lrtest(dfop_fit, sfo_fit) #> Likelihood ratio test #> #> Model 1: DFOP with error model const #> Model 2: SFO with error model const #> #Df LogLik Df Chisq Pr(>Chisq) #> 1 5 -42.453 #> 2 3 -63.954 -2 43.002 4.594e-10 *** #> --- #> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 lrtest(sfo_fit, dfop_fit) #> Likelihood ratio test #> #> Model 1: DFOP with error model const #> Model 2: SFO with error model const #> #Df LogLik Df Chisq Pr(>Chisq) #> 1 5 -42.453 #> 2 3 -63.954 -2 43.002 4.594e-10 *** #> --- #> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 # The following two examples are commented out as they fail during # generation of the static help pages by pkgdown #lrtest(dfop_fit, error_model = \"tc\") #lrtest(dfop_fit, fixed_parms = c(k2 = 0)) # However, this equivalent syntax also works for static help pages lrtest(dfop_fit, update(dfop_fit, error_model = \"tc\")) #> Likelihood ratio test #> #> Model 1: DFOP with error model tc #> Model 2: DFOP with error model const #> #Df LogLik Df Chisq Pr(>Chisq) #> 1 6 -34.587 #> 2 5 -42.453 -1 15.731 7.302e-05 *** #> --- #> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 lrtest(dfop_fit, update(dfop_fit, fixed_parms = c(k2 = 0))) #> Likelihood ratio test #> #> Model 1: DFOP with error model const #> Model 2: DFOP with error model const and fixed parameter(s) k2 #> #Df LogLik Df Chisq Pr(>Chisq) #> 1 5 -42.453 #> 2 4 -57.340 -1 29.776 4.851e-08 *** #> --- #> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/max_twa_parent.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to calculate maximum time weighted average concentrations from\nkinetic models fitted with mkinfit — max_twa_parent","title":"Function to calculate maximum time weighted average concentrations from\nkinetic models fitted with mkinfit — max_twa_parent","text":"function calculates maximum moving window time weighted average concentrations (TWAs) kinetic models fitted mkinfit. Currently, calculations parent implemented SFO, FOMC, DFOP HS models, using analytical formulas given PEC soil section FOCUS guidance.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/max_twa_parent.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to calculate maximum time weighted average concentrations from\nkinetic models fitted with mkinfit — max_twa_parent","text":"","code":"max_twa_parent(fit, windows) max_twa_sfo(M0 = 1, k, t) max_twa_fomc(M0 = 1, alpha, beta, t) max_twa_dfop(M0 = 1, k1, k2, g, t) max_twa_hs(M0 = 1, k1, k2, tb, t)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/max_twa_parent.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to calculate maximum time weighted average concentrations from\nkinetic models fitted with mkinfit — max_twa_parent","text":"fit object class mkinfit. windows width time windows TWAs calculated. M0 initial concentration maximum time weighted average decline curve calculated. default use value 1, means relative maximum time weighted average factor (f_twa) calculated. k rate constant case SFO kinetics. t width time window. alpha Parameter FOMC model. beta Parameter FOMC model. k1 first rate constant DFOP HS kinetics. k2 second rate constant DFOP HS kinetics. g Parameter DFOP model. tb Parameter HS model.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/max_twa_parent.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to calculate maximum time weighted average concentrations from\nkinetic models fitted with mkinfit — max_twa_parent","text":"max_twa_parent, numeric vector, named using windows argument. functions, numeric vector length one (also known 'number').","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/max_twa_parent.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Function to calculate maximum time weighted average concentrations from\nkinetic models fitted with mkinfit — max_twa_parent","text":"FOCUS (2006) “Guidance Document Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration” Report FOCUS Work Group Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/max_twa_parent.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Function to calculate maximum time weighted average concentrations from\nkinetic models fitted with mkinfit — max_twa_parent","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/max_twa_parent.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Function to calculate maximum time weighted average concentrations from\nkinetic models fitted with mkinfit — max_twa_parent","text":"","code":"fit <- mkinfit(\"FOMC\", FOCUS_2006_C, quiet = TRUE) max_twa_parent(fit, c(7, 21)) #> 7 21 #> 34.71343 18.22124"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mccall81_245T.html","id":null,"dir":"Reference","previous_headings":"","what":"Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T","title":"Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T","text":"Time course 2,4,5-trichlorophenoxyacetic acid, corresponding 2,4,5-trichlorophenol 2,4,5-trichloroanisole recovered diethylether extracts.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mccall81_245T.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T","text":"","code":"mccall81_245T"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mccall81_245T.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T","text":"dataframe containing following variables. name name compound observed. Note T245 used acronym 2,4,5-T. T245 legitimate object name R, necessary specifying models using mkinmod. time numeric vector containing sampling times days treatment value numeric vector containing concentrations percent applied radioactivity soil factor containing name soil","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mccall81_245T.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T","text":"McCall P, Vrona SA, Kelley SS (1981) Fate uniformly carbon-14 ring labelled 2,4,5-Trichlorophenoxyacetic acid 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107 doi:10.1021/jf00103a026","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mccall81_245T.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T","text":"","code":"SFO_SFO_SFO <- mkinmod(T245 = list(type = \"SFO\", to = \"phenol\"), phenol = list(type = \"SFO\", to = \"anisole\"), anisole = list(type = \"SFO\")) #> Temporary DLL for differentials generated and loaded # \\dontrun{ fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == \"Commerce\"), quiet = TRUE) #> Warning: Observations with value of zero were removed from the data summary(fit.1)$bpar #> Estimate se_notrans t value Pr(>t) #> T245_0 1.038550e+02 2.1847074943 47.537272 4.472189e-18 #> k_T245 4.337042e-02 0.0018983965 22.845818 2.276911e-13 #> k_phenol 4.050581e-01 0.2986993738 1.356073 9.756990e-02 #> k_anisole 6.678742e-03 0.0008021439 8.326114 2.623177e-07 #> f_T245_to_phenol 6.227599e-01 0.3985340721 1.562626 6.949414e-02 #> f_phenol_to_anisole 1.000000e+00 0.6718440131 1.488441 7.867790e-02 #> sigma 2.514628e+00 0.4907558973 5.123989 6.233159e-05 #> Lower Upper #> T245_0 99.246061490 1.084640e+02 #> k_T245 0.039631621 4.746194e-02 #> k_phenol 0.218013879 7.525762e-01 #> k_anisole 0.005370739 8.305299e-03 #> f_T245_to_phenol 0.547559080 6.924813e-01 #> f_phenol_to_anisole 0.000000000 1.000000e+00 #> sigma 1.706607296 3.322649e+00 endpoints(fit.1) #> $ff #> T245_phenol T245_sink phenol_anisole phenol_sink #> 6.227599e-01 3.772401e-01 1.000000e+00 3.072478e-10 #> #> $distimes #> DT50 DT90 #> T245 15.982025 53.09114 #> phenol 1.711229 5.68458 #> anisole 103.784093 344.76329 #> # formation fraction from phenol to anisol is practically 1. As we cannot # fix formation fractions when using the ilr transformation, we can turn of # the sink in the model generation SFO_SFO_SFO_2 <- mkinmod(T245 = list(type = \"SFO\", to = \"phenol\"), phenol = list(type = \"SFO\", to = \"anisole\", sink = FALSE), anisole = list(type = \"SFO\")) #> Temporary DLL for differentials generated and loaded fit.2 <- mkinfit(SFO_SFO_SFO_2, subset(mccall81_245T, soil == \"Commerce\"), quiet = TRUE) #> Warning: Observations with value of zero were removed from the data summary(fit.2)$bpar #> Estimate se_notrans t value Pr(>t) Lower #> T245_0 1.038550e+02 2.1623653059 48.028439 4.993108e-19 99.271020328 #> k_T245 4.337042e-02 0.0018343666 23.643268 3.573556e-14 0.039650976 #> k_phenol 4.050582e-01 0.1177237651 3.440752 1.679255e-03 0.218746589 #> k_anisole 6.678742e-03 0.0006829745 9.778903 1.872894e-08 0.005377083 #> f_T245_to_phenol 6.227599e-01 0.0342197873 18.198824 2.039411e-12 0.547975634 #> sigma 2.514628e+00 0.3790944250 6.633250 2.875782e-06 1.710983655 #> Upper #> T245_0 108.43904079 #> k_T245 0.04743877 #> k_phenol 0.75005593 #> k_anisole 0.00829550 #> f_T245_to_phenol 0.69212307 #> sigma 3.31827222 endpoints(fit.1) #> $ff #> T245_phenol T245_sink phenol_anisole phenol_sink #> 6.227599e-01 3.772401e-01 1.000000e+00 3.072478e-10 #> #> $distimes #> DT50 DT90 #> T245 15.982025 53.09114 #> phenol 1.711229 5.68458 #> anisole 103.784093 344.76329 #> plot_sep(fit.2) # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mean_degparms.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate mean degradation parameters for an mmkin row object — mean_degparms","title":"Calculate mean degradation parameters for an mmkin row object — mean_degparms","text":"Calculate mean degradation parameters mmkin row object","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mean_degparms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate mean degradation parameters for an mmkin row object — mean_degparms","text":"","code":"mean_degparms( object, random = FALSE, test_log_parms = FALSE, conf.level = 0.6, default_log_parms = NA )"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mean_degparms.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate mean degradation parameters for an mmkin row object — mean_degparms","text":"object mmkin row object containing several fits model different datasets random list fixed random effects returned? test_log_parms TRUE, log parameters considered mean calculations untransformed counterparts (likely rate constants) pass t-test significant difference zero. conf.level Possibility adjust required confidence level parameter tested requested 'test_log_parms'. default_log_parms set numeric value, used default value tested log parameters failed t-test.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mean_degparms.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate mean degradation parameters for an mmkin row object — mean_degparms","text":"random FALSE (default), named vector containing mean values fitted degradation model parameters. random TRUE, list fixed random effects, format required start argument nlme case single grouping variable ds.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mhmkin.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit nonlinear mixed-effects models built from one or more kinetic\ndegradation models and one or more error models — mhmkin","title":"Fit nonlinear mixed-effects models built from one or more kinetic\ndegradation models and one or more error models — mhmkin","text":"name methods expresses (multiple) hierarchichal (also known multilevel) multicompartment kinetic models fitted. kinetic models nonlinear, can use various nonlinear mixed-effects model fitting functions.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mhmkin.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit nonlinear mixed-effects models built from one or more kinetic\ndegradation models and one or more error models — mhmkin","text":"","code":"mhmkin(objects, ...) # S3 method for mmkin mhmkin(objects, ...) # S3 method for list mhmkin( objects, backend = \"saemix\", algorithm = \"saem\", no_random_effect = NULL, ..., cores = if (Sys.info()[\"sysname\"] == \"Windows\") 1 else parallel::detectCores(), cluster = NULL ) # S3 method for mhmkin [(x, i, j, ..., drop = FALSE) # S3 method for mhmkin print(x, ...)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mhmkin.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit nonlinear mixed-effects models built from one or more kinetic\ndegradation models and one or more error models — mhmkin","text":"objects list mmkin objects containing fits degradation models data, using different error models. Alternatively, single mmkin object containing fits several degradation models data ... arguments passed nonlinear mixed-effects model fitting function. backend backend used fitting. Currently, saemix supported algorithm algorithm used fitting (currently used) no_random_effect Default NULL passed saem. character vector supplied, passed calls saem, exclude random effects matching parameters. Alternatively, list character vectors object class illparms.mhmkin can specified. dimensions return object current call , .e. number rows must match number degradation models mmkin object(s), number columns must match number error models used mmkin object(s). cores number cores used multicore processing. used cluster argument NULL. Windows machines, cores > 1 supported, need use cluster argument use multiple logical processors. Per default, cores detected parallel::detectCores() used, except Windows default 1. cluster cluster returned makeCluster used parallel execution. x mhmkin object. Row index selecting fits specific models j Column index selecting fits specific datasets drop FALSE, method always returns mhmkin object, otherwise either list fit objects single fit object.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mhmkin.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fit nonlinear mixed-effects models built from one or more kinetic\ndegradation models and one or more error models — mhmkin","text":"two-dimensional array fit objects /try-errors can indexed using degradation model names first index (row index) error model names second index (column index), class attribute 'mhmkin'. object inheriting mhmkin.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/reference/mhmkin.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fit nonlinear mixed-effects models built from one or more kinetic\ndegradation models and one or more error models — mhmkin","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mhmkin.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fit nonlinear mixed-effects models built from one or more kinetic\ndegradation models and one or more error models — mhmkin","text":"","code":"# \\dontrun{ # We start with separate evaluations of all the first six datasets with two # degradation models and two error models f_sep_const <- mmkin(c(\"SFO\", \"FOMC\"), ds_fomc[1:6], cores = 2, quiet = TRUE) f_sep_tc <- update(f_sep_const, error_model = \"tc\") # The mhmkin function sets up hierarchical degradation models aka # nonlinear mixed-effects models for all four combinations, specifying # uncorrelated random effects for all degradation parameters f_saem_1 <- mhmkin(list(f_sep_const, f_sep_tc), cores = 2) status(f_saem_1) #> error #> degradation const tc #> SFO OK OK #> FOMC OK OK #> #> OK: Fit terminated successfully # The 'illparms' function shows that in all hierarchical fits, at least # one random effect is ill-defined (the confidence interval for the # random effect expressed as standard deviation includes zero) illparms(f_saem_1) #> error #> degradation const tc #> SFO sd(parent_0) sd(parent_0) #> FOMC sd(log_beta) sd(parent_0), sd(log_beta) # Therefore we repeat the fits, excluding the ill-defined random effects f_saem_2 <- update(f_saem_1, no_random_effect = illparms(f_saem_1)) status(f_saem_2) #> error #> degradation const tc #> SFO OK OK #> FOMC OK OK #> #> OK: Fit terminated successfully illparms(f_saem_2) #> error #> degradation const tc #> SFO #> FOMC # Model comparisons show that FOMC with two-component error is preferable, # and confirms our reduction of the default parameter model anova(f_saem_1) #> Data: 95 observations of 1 variable(s) grouped in 6 datasets #> #> npar AIC BIC Lik #> SFO const 5 574.40 573.35 -282.20 #> SFO tc 6 543.72 542.47 -265.86 #> FOMC const 7 489.67 488.22 -237.84 #> FOMC tc 8 406.11 404.44 -195.05 anova(f_saem_2) #> Data: 95 observations of 1 variable(s) grouped in 6 datasets #> #> npar AIC BIC Lik #> SFO const 4 572.22 571.39 -282.11 #> SFO tc 5 541.63 540.59 -265.81 #> FOMC const 6 487.38 486.13 -237.69 #> FOMC tc 6 402.12 400.88 -195.06 # The convergence plot for the selected model looks fine saemix::plot(f_saem_2[[\"FOMC\", \"tc\"]]$so, plot.type = \"convergence\") # The plot of predictions versus data shows that we have a pretty data-rich # situation with homogeneous distribution of residuals, because we used the # same degradation model, error model and parameter distribution model that # was used in the data generation. plot(f_saem_2[[\"FOMC\", \"tc\"]]) # We can specify the same parameter model reductions manually no_ranef <- list(\"parent_0\", \"log_beta\", \"parent_0\", c(\"parent_0\", \"log_beta\")) dim(no_ranef) <- c(2, 2) f_saem_2m <- update(f_saem_1, no_random_effect = no_ranef) anova(f_saem_2m) #> Data: 95 observations of 1 variable(s) grouped in 6 datasets #> #> npar AIC BIC Lik #> SFO const 4 572.22 571.39 -282.11 #> SFO tc 5 541.63 540.59 -265.81 #> FOMC const 6 487.38 486.13 -237.69 #> FOMC tc 6 402.12 400.88 -195.06 # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mixed.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a mixed effects model from an mmkin row object — mixed","title":"Create a mixed effects model from an mmkin row object — mixed","text":"Create mixed effects model mmkin row object","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mixed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a mixed effects model from an mmkin row object — mixed","text":"","code":"mixed(object, ...) # S3 method for mmkin mixed(object, method = c(\"none\"), ...) # S3 method for mixed.mmkin print(x, digits = max(3, getOption(\"digits\") - 3), ...)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mixed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a mixed effects model from an mmkin row object — mixed","text":"object mmkin row object ... Currently used method method used x mixed.mmkin object print digits Number digits use printing.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mixed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a mixed effects model from an mmkin row object — mixed","text":"object class 'mixed.mmkin' observed data single dataframe convenient plotting","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mixed.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a mixed effects model from an mmkin row object — mixed","text":"","code":"sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) n_biphasic <- 8 err_1 = list(const = 1, prop = 0.07) DFOP_SFO <- mkinmod( parent = mkinsub(\"DFOP\", \"m1\"), m1 = mkinsub(\"SFO\"), quiet = TRUE) set.seed(123456) log_sd <- 0.3 syn_biphasic_parms <- as.matrix(data.frame( k1 = rlnorm(n_biphasic, log(0.05), log_sd), k2 = rlnorm(n_biphasic, log(0.01), log_sd), g = plogis(rnorm(n_biphasic, 0, log_sd)), f_parent_to_m1 = plogis(rnorm(n_biphasic, 0, log_sd)), k_m1 = rlnorm(n_biphasic, log(0.002), log_sd))) ds_biphasic_mean <- lapply(1:n_biphasic, function(i) { mkinpredict(DFOP_SFO, syn_biphasic_parms[i, ], c(parent = 100, m1 = 0), sampling_times) } ) set.seed(123456L) ds_biphasic <- lapply(ds_biphasic_mean, function(ds) { add_err(ds, sdfunc = function(value) sqrt(err_1$const^2 + value^2 * err_1$prop^2), n = 1, secondary = \"m1\")[[1]] }) # \\dontrun{ f_mmkin <- mmkin(list(\"DFOP-SFO\" = DFOP_SFO), ds_biphasic, error_model = \"tc\", quiet = TRUE) f_mixed <- mixed(f_mmkin) print(f_mixed) #> Kinetic model fitted by nonlinear regression to each dataset #> Structural model: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * #> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) #> * parent #> d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) #> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * #> exp(-k2 * time))) * parent - k_m1 * m1 #> #> Data: #> 271 observations of 2 variable(s) grouped in 8 datasets #> #> <mmkin> object #> Status of individual fits: #> #> dataset #> model 1 2 3 4 5 6 7 8 #> DFOP-SFO OK OK OK OK OK C OK OK #> #> C: Optimisation did not converge: #> iteration limit reached without convergence (10) #> OK: No warnings #> #> Mean fitted parameters: #> parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 #> 100.605312 -8.758664 -0.001917 -3.350887 -3.990017 #> g_qlogis #> -0.091167 plot(f_mixed) # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkin_long_to_wide.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a dataframe from long to wide format — mkin_long_to_wide","title":"Convert a dataframe from long to wide format — mkin_long_to_wide","text":"function takes dataframe long form, .e. row observed value, converts dataframe one independent variable several dependent variables columns.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkin_long_to_wide.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a dataframe from long to wide format — mkin_long_to_wide","text":"","code":"mkin_long_to_wide(long_data, time = \"time\", outtime = \"time\")"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkin_long_to_wide.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a dataframe from long to wide format — mkin_long_to_wide","text":"long_data dataframe must contain one variable called \"time\" time values specified time argument, one column called \"name\" grouping observed values, finally one column observed values called \"value\". time name time variable long input data. outtime name time variable wide output data.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkin_long_to_wide.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a dataframe from long to wide format — mkin_long_to_wide","text":"Dataframe wide format.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkin_long_to_wide.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Convert a dataframe from long to wide format — mkin_long_to_wide","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkin_long_to_wide.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert a dataframe from long to wide format — mkin_long_to_wide","text":"","code":"mkin_long_to_wide(FOCUS_2006_D) #> time parent m1 #> 1 0 99.46 0.00 #> 2 0 102.04 0.00 #> 3 1 93.50 4.84 #> 4 1 92.50 5.64 #> 5 3 63.23 12.91 #> 6 3 68.99 12.96 #> 7 7 52.32 22.97 #> 8 7 55.13 24.47 #> 9 14 27.27 41.69 #> 10 14 26.64 33.21 #> 11 21 11.50 44.37 #> 12 21 11.64 46.44 #> 13 35 2.85 41.22 #> 14 35 2.91 37.95 #> 15 50 0.69 41.19 #> 16 50 0.63 40.01 #> 17 75 0.05 40.09 #> 18 75 0.06 33.85 #> 19 100 NA 31.04 #> 20 100 NA 33.13 #> 21 120 NA 25.15 #> 22 120 NA 33.31"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkin_wide_to_long.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a dataframe with observations over time into long format — mkin_wide_to_long","title":"Convert a dataframe with observations over time into long format — mkin_wide_to_long","text":"function simply takes dataframe one independent variable several dependent variable converts long form required mkinfit.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkin_wide_to_long.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a dataframe with observations over time into long format — mkin_wide_to_long","text":"","code":"mkin_wide_to_long(wide_data, time = \"t\")"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkin_wide_to_long.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a dataframe with observations over time into long format — mkin_wide_to_long","text":"wide_data dataframe must contain one variable time values specified time argument usually one column observed values. time name time variable.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkin_wide_to_long.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a dataframe with observations over time into long format — mkin_wide_to_long","text":"Dataframe long format needed mkinfit.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkin_wide_to_long.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Convert a dataframe with observations over time into long format — mkin_wide_to_long","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkin_wide_to_long.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert a dataframe with observations over time into long format — mkin_wide_to_long","text":"","code":"wide <- data.frame(t = c(1,2,3), x = c(1,4,7), y = c(3,4,5)) mkin_wide_to_long(wide) #> name time value #> 1 x 1 1 #> 2 x 2 4 #> 3 x 3 7 #> 4 y 1 3 #> 5 y 2 4 #> 6 y 3 5"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinds.html","id":null,"dir":"Reference","previous_headings":"","what":"A dataset class for mkin — mkinds","title":"A dataset class for mkin — mkinds","text":"moment dataset class hardly used mkin. example, mkinfit take mkinds datasets argument, works dataframes contained data field mkinds objects. datasets provided package come mkinds objects nevertheless.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinds.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A dataset class for mkin — mkinds","text":"","code":"# S3 method for mkinds print(x, data = FALSE, ...)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinds.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A dataset class for mkin — mkinds","text":"x mkinds object. data data printed? ... used.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinds.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"A dataset class for mkin — mkinds","text":"title full title dataset sampling_times sampling times time_unit time unit observed Names observed variables unit unit observations replicates maximum number replicates per sampling time data data frame least columns name, time value order compatible mkinfit","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinds.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"A dataset class for mkin — mkinds","text":"mkinds$new() mkinds$clone()","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinds.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"A dataset class for mkin — mkinds","text":"Create new mkinds object","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinds.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A dataset class for mkin — mkinds","text":"","code":"mkinds$new(title = \"\", data, time_unit = NA, unit = NA)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinds.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"A dataset class for mkin — mkinds","text":"title dataset title data data time_unit time unit unit unit observations","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinds.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"A dataset class for mkin — mkinds","text":"objects class cloneable method.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinds.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"A dataset class for mkin — mkinds","text":"","code":"mkinds$clone(deep = FALSE)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinds.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"A dataset class for mkin — mkinds","text":"deep Whether make deep clone.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinds.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"A dataset class for mkin — mkinds","text":"","code":"mds <- mkinds$new(\"FOCUS A\", FOCUS_2006_A) print(mds) #> <mkinds> with $title: FOCUS A #> Observed compounds $observed: parent #> Sampling times $sampling_times: #> 0, 3, 7, 14, 30, 62, 90, 118 #> With a maximum of 1 replicates"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkindsg.html","id":null,"dir":"Reference","previous_headings":"","what":"A class for dataset groups for mkin — mkindsg","title":"A class for dataset groups for mkin — mkindsg","text":"container working datasets share least one compound, combined evaluations desirable. Time normalisation factors initialised value 1 dataset data supplied.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkindsg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A class for dataset groups for mkin — mkindsg","text":"","code":"# S3 method for mkindsg print(x, data = FALSE, verbose = data, ...)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkindsg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"A class for dataset groups for mkin — mkindsg","text":"x mkindsg object. data mkinds objects printed data? verbose mkinds objects printed? ... used.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkindsg.html","id":"public-fields","dir":"Reference","previous_headings":"","what":"Public fields","title":"A class for dataset groups for mkin — mkindsg","text":"title title dataset group ds list mkinds objects observed_n Occurrence counts compounds datasets f_time_norm Time normalisation factors meta data frame row dataset, containing additional information form categorical data (factors) numerical data (e.g. temperature, moisture, covariates like soil pH).","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkindsg.html","id":"public-methods","dir":"Reference","previous_headings":"","what":"Public methods","title":"A class for dataset groups for mkin — mkindsg","text":"mkindsg$new() mkindsg$clone()","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkindsg.html","id":"method-new-","dir":"Reference","previous_headings":"","what":"Method new()","title":"A class for dataset groups for mkin — mkindsg","text":"Create new mkindsg object","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkindsg.html","id":"usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A class for dataset groups for mkin — mkindsg","text":"","code":"mkindsg$new(title = \"\", ds, f_time_norm = rep(1, length(ds)), meta)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkindsg.html","id":"arguments-1","dir":"Reference","previous_headings":"","what":"Arguments","title":"A class for dataset groups for mkin — mkindsg","text":"title title ds list mkinds objects f_time_norm Time normalisation factors meta meta data","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkindsg.html","id":"method-clone-","dir":"Reference","previous_headings":"","what":"Method clone()","title":"A class for dataset groups for mkin — mkindsg","text":"objects class cloneable method.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkindsg.html","id":"usage-1","dir":"Reference","previous_headings":"","what":"Usage","title":"A class for dataset groups for mkin — mkindsg","text":"","code":"mkindsg$clone(deep = FALSE)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkindsg.html","id":"arguments-2","dir":"Reference","previous_headings":"","what":"Arguments","title":"A class for dataset groups for mkin — mkindsg","text":"deep Whether make deep clone.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkindsg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"A class for dataset groups for mkin — mkindsg","text":"","code":"mdsg <- mkindsg$new(\"Experimental X\", experimental_data_for_UBA_2019[6:10]) print(mdsg) #> <mkindsg> holding 5 mkinds objects #> Title $title: Experimental X #> Occurrence of observed compounds $observed_n: #> parent A1 #> 5 5 print(mdsg, verbose = TRUE) #> <mkindsg> holding 5 mkinds objects #> Title $title: Experimental X #> Occurrence of observed compounds $observed_n: #> parent A1 #> 5 5 #> #> Datasets $ds: #> <mkinds> with $title: Soil 6 #> Observed compounds $observed: parent, A1 #> Sampling times $sampling_times: #> 0, 3, 6, 10, 20, 34, 55, 90, 112, 132 #> With a maximum of 2 replicates #> Time unit: days #> Observation unit: \\%AR #> #> <mkinds> with $title: Soil 7 #> Observed compounds $observed: parent, A1 #> Sampling times $sampling_times: #> 0, 3, 7, 14, 30, 60, 90, 120, 180 #> With a maximum of 2 replicates #> Time unit: days #> Observation unit: \\%AR #> #> <mkinds> with $title: Soil 8 #> Observed compounds $observed: parent, A1 #> Sampling times $sampling_times: #> 0, 1, 3, 8, 14, 27, 48, 70 #> With a maximum of 2 replicates #> Time unit: days #> Observation unit: \\%AR #> #> <mkinds> with $title: Soil 9 #> Observed compounds $observed: parent, A1 #> Sampling times $sampling_times: #> 0, 1, 3, 8, 14, 27, 48, 70, 91, 120 #> With a maximum of 2 replicates #> Time unit: days #> Observation unit: \\%AR #> #> <mkinds> with $title: Soil 10 #> Observed compounds $observed: parent, A1 #> Sampling times $sampling_times: #> 0, 8, 14, 21, 41, 63, 91, 120 #> With a maximum of 2 replicates #> Time unit: days #> Observation unit: \\%AR print(mdsg, verbose = TRUE, data = TRUE) #> <mkindsg> holding 5 mkinds objects #> Title $title: Experimental X #> Occurrence of observed compounds $observed_n: #> parent A1 #> 5 5 #> #> Datasets $ds: #> <mkinds> with $title: Soil 6 #> Observed compounds $observed: parent, A1 #> Sampling times $sampling_times: #> 0, 3, 6, 10, 20, 34, 55, 90, 112, 132 #> With a maximum of 2 replicates #> Time unit: days #> Observation unit: \\%AR #> time parent A1 #> 1 0 97.2 NA #> 2 0 96.4 NA #> 3 3 71.1 4.3 #> 4 3 69.2 4.6 #> 5 6 58.1 7.0 #> 6 6 56.6 7.2 #> 7 10 44.4 8.2 #> 8 10 43.4 8.0 #> 9 20 33.3 11.0 #> 10 20 29.2 13.7 #> 11 34 17.6 11.5 #> 12 34 18.0 12.7 #> 13 55 10.5 14.9 #> 14 55 9.3 14.5 #> 15 90 4.5 12.1 #> 16 90 4.7 12.3 #> 17 112 3.0 9.9 #> 18 112 3.4 10.2 #> 19 132 2.3 8.8 #> 20 132 2.7 7.8 #> #> <mkinds> with $title: Soil 7 #> Observed compounds $observed: parent, A1 #> Sampling times $sampling_times: #> 0, 3, 7, 14, 30, 60, 90, 120, 180 #> With a maximum of 2 replicates #> Time unit: days #> Observation unit: \\%AR #> time parent A1 #> 1 0 93.6 NA #> 2 0 92.3 NA #> 3 3 87.0 3.9 #> 4 3 82.2 3.1 #> 5 7 74.0 6.9 #> 6 7 73.9 6.6 #> 7 14 64.2 10.4 #> 8 14 69.5 8.3 #> 9 30 54.0 14.4 #> 10 30 54.6 13.7 #> 11 60 41.1 22.1 #> 12 60 38.4 22.3 #> 13 90 32.5 27.5 #> 14 90 35.5 25.4 #> 15 120 28.1 28.0 #> 16 120 29.0 26.6 #> 17 180 26.5 25.8 #> 18 180 27.6 25.3 #> #> <mkinds> with $title: Soil 8 #> Observed compounds $observed: parent, A1 #> Sampling times $sampling_times: #> 0, 1, 3, 8, 14, 27, 48, 70 #> With a maximum of 2 replicates #> Time unit: days #> Observation unit: \\%AR #> time parent A1 #> 1 0 91.9 NA #> 2 0 90.8 NA #> 3 1 64.9 9.6 #> 4 1 66.2 7.7 #> 5 3 43.5 15.0 #> 6 3 44.1 15.1 #> 7 8 18.3 21.2 #> 8 8 18.1 21.1 #> 9 14 10.2 19.7 #> 10 14 10.8 18.9 #> 11 27 4.9 17.5 #> 12 27 3.3 15.9 #> 13 48 1.6 9.5 #> 14 48 1.5 9.8 #> 15 70 1.1 6.2 #> 16 70 0.9 6.1 #> #> <mkinds> with $title: Soil 9 #> Observed compounds $observed: parent, A1 #> Sampling times $sampling_times: #> 0, 1, 3, 8, 14, 27, 48, 70, 91, 120 #> With a maximum of 2 replicates #> Time unit: days #> Observation unit: \\%AR #> time parent A1 #> 1 0 99.8 NA #> 2 0 98.3 NA #> 3 1 77.1 4.2 #> 4 1 77.2 3.9 #> 5 3 59.0 7.4 #> 6 3 58.1 7.9 #> 7 8 27.4 14.5 #> 8 8 29.2 13.7 #> 9 14 19.1 14.2 #> 10 14 29.6 12.2 #> 11 27 10.1 13.7 #> 12 27 18.2 13.2 #> 13 48 4.5 13.6 #> 14 48 9.1 15.4 #> 15 70 2.3 10.4 #> 16 70 2.9 11.6 #> 17 91 2.0 10.0 #> 18 91 1.8 9.5 #> 19 120 2.0 9.1 #> 20 120 2.2 9.0 #> #> <mkinds> with $title: Soil 10 #> Observed compounds $observed: parent, A1 #> Sampling times $sampling_times: #> 0, 8, 14, 21, 41, 63, 91, 120 #> With a maximum of 2 replicates #> Time unit: days #> Observation unit: \\%AR #> time parent A1 #> 1 0 96.1 NA #> 2 0 94.3 NA #> 3 8 73.9 3.3 #> 4 8 73.9 3.4 #> 5 14 69.4 3.9 #> 6 14 73.1 2.9 #> 7 21 65.6 6.4 #> 8 21 65.3 7.2 #> 9 41 55.9 9.1 #> 10 41 54.4 8.5 #> 11 63 47.0 11.7 #> 12 63 49.3 12.0 #> 13 91 44.7 13.3 #> 14 91 46.7 13.2 #> 15 120 42.1 14.3 #> 16 120 41.3 12.1"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinerrmin.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate the minimum error to assume in order to pass the variance test — mkinerrmin","title":"Calculate the minimum error to assume in order to pass the variance test — mkinerrmin","text":"function finds smallest relative error still resulting passing chi-squared test defined FOCUS kinetics report 2006.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinerrmin.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate the minimum error to assume in order to pass the variance test — mkinerrmin","text":"","code":"mkinerrmin(fit, alpha = 0.05)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinerrmin.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate the minimum error to assume in order to pass the variance test — mkinerrmin","text":"fit object class mkinfit. alpha confidence level chosen chi-squared test.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinerrmin.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate the minimum error to assume in order to pass the variance test — mkinerrmin","text":"dataframe following components: err.min relative error, expressed fraction. n.optim number optimised parameters attributed data series. df number remaining degrees freedom chi2 error level calculations. Note mean values used chi2 statistic therefore every time point observed values series counts one time. dataframe one row total dataset one row observed state variable model.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinerrmin.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate the minimum error to assume in order to pass the variance test — mkinerrmin","text":"function used internally summary.mkinfit.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinerrmin.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Calculate the minimum error to assume in order to pass the variance test — mkinerrmin","text":"FOCUS (2006) “Guidance Document Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration” Report FOCUS Work Group Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinerrmin.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate the minimum error to assume in order to pass the variance test — mkinerrmin","text":"","code":"SFO_SFO = mkinmod(parent = mkinsub(\"SFO\", to = \"m1\"), m1 = mkinsub(\"SFO\"), use_of_ff = \"max\") #> Temporary DLL for differentials generated and loaded fit_FOCUS_D = mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE) #> Warning: Observations with value of zero were removed from the data round(mkinerrmin(fit_FOCUS_D), 4) #> err.min n.optim df #> All data 0.0640 4 15 #> parent 0.0646 2 7 #> m1 0.0469 2 8 # \\dontrun{ fit_FOCUS_E = mkinfit(SFO_SFO, FOCUS_2006_E, quiet = TRUE) round(mkinerrmin(fit_FOCUS_E), 4) #> err.min n.optim df #> All data 0.1544 4 13 #> parent 0.1659 2 7 #> m1 0.1095 2 6 # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinerrplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to plot squared residuals and the error model for an mkin object — mkinerrplot","title":"Function to plot squared residuals and the error model for an mkin object — mkinerrplot","text":"function plots squared residuals specified subset observed variables mkinfit object. addition, one dashed line(s) show fitted error model. combined plot fitted model error model plot can obtained plot.mkinfit using argument show_errplot = TRUE.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinerrplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to plot squared residuals and the error model for an mkin object — mkinerrplot","text":"","code":"mkinerrplot( object, obs_vars = names(object$mkinmod$map), xlim = c(0, 1.1 * max(object$data$predicted)), xlab = \"Predicted\", ylab = \"Squared residual\", maxy = \"auto\", legend = TRUE, lpos = \"topright\", col_obs = \"auto\", pch_obs = \"auto\", frame = TRUE, ... )"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinerrplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to plot squared residuals and the error model for an mkin object — mkinerrplot","text":"object fit represented mkinfit object. obs_vars character vector names observed variables residuals plotted. Defaults observed variables model xlim plot range x direction. xlab Label x axis. ylab Label y axis. maxy Maximum value residuals. used scaling y axis defaults \"auto\". legend legend plotted? lpos legend placed? Default \"topright\". passed legend. col_obs Colors observed variables. pch_obs Symbols used observed variables. frame frame drawn around plots? ... arguments passed plot.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinerrplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to plot squared residuals and the error model for an mkin object — mkinerrplot","text":"Nothing returned function, called side effect, namely produce plot.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinerrplot.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Function to plot squared residuals and the error model for an mkin object — mkinerrplot","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinerrplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Function to plot squared residuals and the error model for an mkin object — mkinerrplot","text":"","code":"# \\dontrun{ model <- mkinmod(parent = mkinsub(\"SFO\", \"m1\"), m1 = mkinsub(\"SFO\")) #> Temporary DLL for differentials generated and loaded fit <- mkinfit(model, FOCUS_2006_D, error_model = \"tc\", quiet = TRUE) #> Warning: Observations with value of zero were removed from the data mkinerrplot(fit) # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinfit.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit a kinetic model to data with one or more state variables — mkinfit","title":"Fit a kinetic model to data with one or more state variables — mkinfit","text":"function maximises likelihood observed data using Port algorithm stats::nlminb(), specified initial fixed parameters starting values. step optimisation, kinetic model solved using function mkinpredict(), except analytical solution implemented, case model solved using degradation function mkinmod object. parameters selected error model fitted simultaneously degradation model parameters, arguments likelihood function.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinfit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit a kinetic model to data with one or more state variables — mkinfit","text":"","code":"mkinfit( mkinmod, observed, parms.ini = \"auto\", state.ini = \"auto\", err.ini = \"auto\", fixed_parms = NULL, fixed_initials = names(mkinmod$diffs)[-1], from_max_mean = FALSE, solution_type = c(\"auto\", \"analytical\", \"eigen\", \"deSolve\"), method.ode = \"lsoda\", use_compiled = \"auto\", control = list(eval.max = 300, iter.max = 200), transform_rates = TRUE, transform_fractions = TRUE, quiet = FALSE, atol = 1e-08, rtol = 1e-10, error_model = c(\"const\", \"obs\", \"tc\"), error_model_algorithm = c(\"auto\", \"d_3\", \"direct\", \"twostep\", \"threestep\", \"fourstep\", \"IRLS\", \"OLS\"), reweight.tol = 1e-08, reweight.max.iter = 10, trace_parms = FALSE, test_residuals = FALSE, ... )"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinfit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit a kinetic model to data with one or more state variables — mkinfit","text":"mkinmod list class mkinmod, containing kinetic model fitted data, one shorthand names (\"SFO\", \"FOMC\", \"DFOP\", \"HS\", \"SFORB\", \"IORE\"). shorthand name given, parent degradation model generated variable highest value observed. observed dataframe observed data. first column called \"name\" must contain name observed variable data point. second column must contain times observation, named \"time\". third column must named \"value\" contain observed values. Zero values \"value\" column removed, warning, order avoid problems fitting two-component error model. expected problem, general, values zero observed degradation data, lower limit detection. parms.ini named vector initial values parameters, including parameters optimised potentially also fixed parameters indicated fixed_parms. set \"auto\", initial values rate constants set default values. Using parameter names model gives error. possible specify subset parameters model needs. can use parameter lists \"bparms.ode\" previously fitted model, contains differential equation parameters model. works nicely models nested. example given . state.ini named vector initial values state variables model. case observed variables represented one model variable, names differ names observed variables (see map component mkinmod). default set initial value first model variable mean time zero values variable maximum observed value, others 0. variable time zero observations, initial value set 100. err.ini named vector initial values error model parameters optimised. set \"auto\", initial values set default values. Otherwise, inital values error model parameters must given. fixed_parms names parameters optimised rather kept values specified parms.ini. Alternatively, named numeric vector parameters fixed, regardless values parms.ini. fixed_initials names model variables initial state time 0 excluded optimisation. Defaults state variables except first one. from_max_mean set TRUE, model one observed variable, data time maximum observed value (averaging sampling time) discarded, time subtracted remaining time values, time maximum observed mean value new time zero. solution_type set \"eigen\", solution system differential equations based spectral decomposition coefficient matrix cases possible. set \"deSolve\", numerical ode solver package deSolve used. set \"analytical\", analytical solution model used. implemented relatively simple degradation models. default \"auto\", uses \"analytical\" possible, otherwise \"deSolve\" compiler present, \"eigen\" compiler present model can expressed using eigenvalues eigenvectors. method.ode solution method passed via mkinpredict() deSolve::ode() case solution type \"deSolve\". default \"lsoda\" performant, sometimes fails converge. use_compiled set FALSE, compiled version mkinmod model used calls mkinpredict() even compiled version present. control list control arguments passed stats::nlminb(). transform_rates Boolean specifying kinetic rate constants transformed model specification used fitting better compliance assumption normal distribution estimator. TRUE, also alpha beta parameters FOMC model log-transformed, well k1 k2 rate constants DFOP HS models break point tb HS model. FALSE, zero used lower bound rates optimisation. transform_fractions Boolean specifying formation fractions transformed model specification used fitting better compliance assumption normal distribution estimator. default (TRUE) transformations. TRUE, g parameter DFOP model also transformed. Transformations described transform_odeparms. quiet Suppress printing current value negative log-likelihood improvement? atol Absolute error tolerance, passed deSolve::ode(). Default 1e-8, lower default deSolve::lsoda() function used per default. rtol Absolute error tolerance, passed deSolve::ode(). Default 1e-10, much lower deSolve::lsoda(). error_model error model \"const\", constant standard deviation assumed. error model \"obs\", observed variable assumed variance. error model \"tc\" (two-component error model), two component error model similar one described Rocke Lorenzato (1995) used setting likelihood function. Note model deviates model Rocke Lorenzato, model implies errors follow lognormal distribution large values, normal distribution assumed method. error_model_algorithm \"auto\", selected algorithm depends error model. error model \"const\", unweighted nonlinear least squares fitting (\"OLS\") selected. error model \"obs\", \"tc\", \"d_3\" algorithm selected. algorithm \"d_3\" directly minimize negative log-likelihood independently also use three step algorithm described . fit higher likelihood returned. algorithm \"direct\" directly minimize negative log-likelihood. algorithm \"twostep\" minimize negative log-likelihood initial unweighted least squares optimisation step. algorithm \"threestep\" starts unweighted least squares, optimizes error model using degradation model parameters found, minimizes negative log-likelihood free degradation error model parameters. algorithm \"fourstep\" starts unweighted least squares, optimizes error model using degradation model parameters found, optimizes degradation model fixed error model parameters, finally minimizes negative log-likelihood free degradation error model parameters. algorithm \"IRLS\" (Iteratively Reweighted Least Squares) starts unweighted least squares, iterates optimization error model parameters subsequent optimization degradation model using error model parameters, error model parameters converge. reweight.tol Tolerance convergence criterion calculated error model parameters IRLS fits. reweight.max.iter Maximum number iterations IRLS fits. trace_parms trace parameter values listed? test_residuals residuals tested normal distribution? ... arguments passed deSolve::ode().","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinfit.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fit a kinetic model to data with one or more state variables — mkinfit","text":"list \"mkinfit\" class attribute.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinfit.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fit a kinetic model to data with one or more state variables — mkinfit","text":"Per default, parameters kinetic models internally transformed order better satisfy assumption normal distribution estimators.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinfit.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Fit a kinetic model to data with one or more state variables — mkinfit","text":"using \"IORE\" submodel metabolites, fitting \"transform_rates = TRUE\" (default) often leads failures numerical ODE solver. situation may help switch internal rate transformation.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinfit.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Fit a kinetic model to data with one or more state variables — mkinfit","text":"Rocke DM Lorenzato S (1995) two-component model measurement error analytical chemistry. Technometrics 37(2), 176-184. Ranke J Meinecke S (2019) Error Models Kinetic Evaluation Chemical Degradation Data. Environments 6(12) 124 doi:10.3390/environments6120124 .","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinfit.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fit a kinetic model to data with one or more state variables — mkinfit","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinfit.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fit a kinetic model to data with one or more state variables — mkinfit","text":"","code":"# Use shorthand notation for parent only degradation fit <- mkinfit(\"FOMC\", FOCUS_2006_C, quiet = TRUE) summary(fit) #> mkin version used for fitting: 1.2.6 #> R version used for fitting: 4.3.2 #> Date of fit: Thu Nov 16 04:15:31 2023 #> Date of summary: Thu Nov 16 04:15:31 2023 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> #> Fitted using 222 model solutions performed in 0.014 s #> #> Error model: Constant variance #> #> Error model algorithm: OLS #> #> Starting values for parameters to be optimised: #> value type #> parent_0 85.1 state #> alpha 1.0 deparm #> beta 10.0 deparm #> #> Starting values for the transformed parameters actually optimised: #> value lower upper #> parent_0 85.100000 -Inf Inf #> log_alpha 0.000000 -Inf Inf #> log_beta 2.302585 -Inf Inf #> #> Fixed parameter values: #> None #> #> Results: #> #> AIC BIC logLik #> 44.68652 45.47542 -18.34326 #> #> Optimised, transformed parameters with symmetric confidence intervals: #> Estimate Std. Error Lower Upper #> parent_0 85.87000 1.8070 81.23000 90.5200 #> log_alpha 0.05192 0.1353 -0.29580 0.3996 #> log_beta 0.65100 0.2287 0.06315 1.2390 #> sigma 1.85700 0.4378 0.73200 2.9830 #> #> Parameter correlation: #> parent_0 log_alpha log_beta sigma #> parent_0 1.000e+00 -1.565e-01 -3.142e-01 4.681e-08 #> log_alpha -1.565e-01 1.000e+00 9.564e-01 1.013e-07 #> log_beta -3.142e-01 9.564e-01 1.000e+00 8.637e-08 #> sigma 4.681e-08 1.013e-07 8.637e-08 1.000e+00 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. #> t-test (unrealistically) based on the assumption of normal distribution #> for estimators of untransformed parameters. #> Estimate t value Pr(>t) Lower Upper #> parent_0 85.870 47.530 3.893e-08 81.2300 90.520 #> alpha 1.053 7.393 3.562e-04 0.7439 1.491 #> beta 1.917 4.373 3.601e-03 1.0650 3.451 #> sigma 1.857 4.243 4.074e-03 0.7320 2.983 #> #> FOCUS Chi2 error levels in percent: #> err.min n.optim df #> All data 6.657 3 6 #> parent 6.657 3 6 #> #> Estimated disappearance times: #> DT50 DT90 DT50back #> parent 1.785 15.15 4.56 #> #> Data: #> time variable observed predicted residual #> 0 parent 85.1 85.875 -0.7749 #> 1 parent 57.9 55.191 2.7091 #> 3 parent 29.9 31.845 -1.9452 #> 7 parent 14.6 17.012 -2.4124 #> 14 parent 9.7 9.241 0.4590 #> 28 parent 6.6 4.754 1.8460 #> 63 parent 4.0 2.102 1.8977 #> 91 parent 3.9 1.441 2.4590 #> 119 parent 0.6 1.092 -0.4919 # One parent compound, one metabolite, both single first order. # We remove zero values from FOCUS dataset D in order to avoid warnings FOCUS_D <- subset(FOCUS_2006_D, value != 0) # Use mkinsub for convenience in model formulation. Pathway to sink included per default. SFO_SFO <- mkinmod( parent = mkinsub(\"SFO\", \"m1\"), m1 = mkinsub(\"SFO\")) #> Temporary DLL for differentials generated and loaded # Fit the model quietly to the FOCUS example dataset D using defaults fit <- mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE) plot_sep(fit) # As lower parent values appear to have lower variance, we try an alternative error model fit.tc <- mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE, error_model = \"tc\") # This avoids the warning, and the likelihood ratio test confirms it is preferable lrtest(fit.tc, fit) #> Likelihood ratio test #> #> Model 1: SFO_SFO with error model tc and fixed parameter(s) m1_0 #> Model 2: SFO_SFO with error model const and fixed parameter(s) m1_0 #> #Df LogLik Df Chisq Pr(>Chisq) #> 1 6 -64.983 #> 2 5 -97.224 -1 64.483 9.737e-16 *** #> --- #> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 # We can also allow for different variances of parent and metabolite as error model fit.obs <- mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE, error_model = \"obs\") # The two-component error model has significantly higher likelihood lrtest(fit.obs, fit.tc) #> Likelihood ratio test #> #> Model 1: SFO_SFO with error model tc and fixed parameter(s) m1_0 #> Model 2: SFO_SFO with error model obs and fixed parameter(s) m1_0 #> #Df LogLik Df Chisq Pr(>Chisq) #> 1 6 -64.983 #> 2 6 -96.936 0 63.907 < 2.2e-16 *** #> --- #> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 parms(fit.tc) #> parent_0 k_parent k_m1 f_parent_to_m1 sigma_low #> 1.007343e+02 1.005562e-01 5.166712e-03 5.083933e-01 3.049883e-03 #> rsd_high #> 7.928118e-02 endpoints(fit.tc) #> $ff #> parent_m1 parent_sink #> 0.5083933 0.4916067 #> #> $distimes #> DT50 DT90 #> parent 6.89313 22.89848 #> m1 134.15634 445.65771 #> # We can show a quick (only one replication) benchmark for this case, as we # have several alternative solution methods for the model. We skip # uncompiled deSolve, as it is so slow. More benchmarks are found in the # benchmark vignette # \\dontrun{ if(require(rbenchmark)) { benchmark(replications = 1, order = \"relative\", columns = c(\"test\", \"relative\", \"elapsed\"), deSolve_compiled = mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE, error_model = \"tc\", solution_type = \"deSolve\", use_compiled = TRUE), eigen = mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE, error_model = \"tc\", solution_type = \"eigen\"), analytical = mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE, error_model = \"tc\", solution_type = \"analytical\")) } #> test relative elapsed #> 3 analytical 1.000 0.223 #> 2 eigen 1.973 0.440 #> 1 deSolve_compiled 2.072 0.462 # } # Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO # \\dontrun{ FOMC_SFO <- mkinmod( parent = mkinsub(\"FOMC\", \"m1\"), m1 = mkinsub(\"SFO\")) #> Temporary DLL for differentials generated and loaded fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_D, quiet = TRUE) # Again, we get a warning and try a more sophisticated error model fit.FOMC_SFO.tc <- mkinfit(FOMC_SFO, FOCUS_D, quiet = TRUE, error_model = \"tc\") # This model has a higher likelihood, but not significantly so lrtest(fit.tc, fit.FOMC_SFO.tc) #> Likelihood ratio test #> #> Model 1: FOMC_SFO with error model tc and fixed parameter(s) m1_0 #> Model 2: SFO_SFO with error model tc and fixed parameter(s) m1_0 #> #Df LogLik Df Chisq Pr(>Chisq) #> 1 7 -64.829 #> 2 6 -64.983 -1 0.3075 0.5792 # Also, the missing standard error for log_beta and the t-tests for alpha # and beta indicate overparameterisation summary(fit.FOMC_SFO.tc, data = FALSE) #> Warning: NaNs produced #> Warning: NaNs produced #> Warning: diag(.) had 0 or NA entries; non-finite result is doubtful #> mkin version used for fitting: 1.2.6 #> R version used for fitting: 4.3.2 #> Date of fit: Thu Nov 16 04:15:35 2023 #> Date of summary: Thu Nov 16 04:15:35 2023 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> d_m1/dt = + f_parent_to_m1 * (alpha/beta) * 1/((time/beta) + 1) * #> parent - k_m1 * m1 #> #> Model predictions using solution type deSolve #> #> Fitted using 4062 model solutions performed in 0.768 s #> #> Error model: Two-component variance function #> #> Error model algorithm: d_3 #> Direct fitting and three-step fitting yield approximately the same likelihood #> #> Starting values for parameters to be optimised: #> value type #> parent_0 100.75 state #> alpha 1.00 deparm #> beta 10.00 deparm #> k_m1 0.10 deparm #> f_parent_to_m1 0.50 deparm #> sigma_low 0.10 error #> rsd_high 0.10 error #> #> Starting values for the transformed parameters actually optimised: #> value lower upper #> parent_0 100.750000 -Inf Inf #> log_k_m1 -2.302585 -Inf Inf #> f_parent_qlogis 0.000000 -Inf Inf #> log_alpha 0.000000 -Inf Inf #> log_beta 2.302585 -Inf Inf #> sigma_low 0.100000 0 Inf #> rsd_high 0.100000 0 Inf #> #> Fixed parameter values: #> value type #> m1_0 0 state #> #> Results: #> #> AIC BIC logLik #> 143.658 155.1211 -64.82902 #> #> Optimised, transformed parameters with symmetric confidence intervals: #> Estimate Std. Error Lower Upper #> parent_0 101.600000 2.6400000 96.240000 107.000000 #> log_k_m1 -5.284000 0.0929100 -5.474000 -5.095000 #> f_parent_qlogis 0.001426 0.0766900 -0.155000 0.157800 #> log_alpha 5.522000 0.0077320 5.506000 5.538000 #> log_beta 7.806000 NaN NaN NaN #> sigma_low 0.002488 0.0002431 0.001992 0.002984 #> rsd_high 0.079210 0.0093280 0.060180 0.098230 #> #> Parameter correlation: #> parent_0 log_k_m1 f_parent_qlogis log_alpha log_beta #> parent_0 1.000000 -0.095161 -0.76675 0.70542 NaN #> log_k_m1 -0.095161 1.000000 0.51429 -0.14382 NaN #> f_parent_qlogis -0.766750 0.514286 1.00000 -0.61393 NaN #> log_alpha 0.705417 -0.143821 -0.61393 1.00000 NaN #> log_beta NaN NaN NaN NaN 1 #> sigma_low 0.016086 0.001583 0.01547 5.87036 NaN #> rsd_high 0.006618 -0.011695 -0.05356 0.04848 NaN #> sigma_low rsd_high #> parent_0 0.016086 0.006618 #> log_k_m1 0.001583 -0.011695 #> f_parent_qlogis 0.015466 -0.053560 #> log_alpha 5.870361 0.048483 #> log_beta NaN NaN #> sigma_low 1.000000 -0.652545 #> rsd_high -0.652545 1.000000 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. #> t-test (unrealistically) based on the assumption of normal distribution #> for estimators of untransformed parameters. #> Estimate t value Pr(>t) Lower Upper #> parent_0 1.016e+02 32.7800 6.310e-26 9.624e+01 1.070e+02 #> k_m1 5.072e-03 10.1200 1.216e-11 4.196e-03 6.130e-03 #> f_parent_to_m1 5.004e-01 20.8300 4.316e-20 4.613e-01 5.394e-01 #> alpha 2.502e+02 0.5624 2.889e-01 2.463e+02 2.542e+02 #> beta 2.455e+03 0.5549 2.915e-01 NA NA #> sigma_low 2.488e-03 0.4843 3.158e-01 1.992e-03 2.984e-03 #> rsd_high 7.921e-02 8.4300 8.001e-10 6.018e-02 9.823e-02 #> #> FOCUS Chi2 error levels in percent: #> err.min n.optim df #> All data 6.781 5 14 #> parent 7.141 3 6 #> m1 4.640 2 8 #> #> Resulting formation fractions: #> ff #> parent_m1 0.5004 #> parent_sink 0.4996 #> #> Estimated disappearance times: #> DT50 DT90 DT50back #> parent 6.812 22.7 6.834 #> m1 136.661 454.0 NA # We can easily use starting parameters from the parent only fit (only for illustration) fit.FOMC = mkinfit(\"FOMC\", FOCUS_2006_D, quiet = TRUE, error_model = \"tc\") fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_D, quiet = TRUE, parms.ini = fit.FOMC$bparms.ode, error_model = \"tc\") # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinmod.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to set up a kinetic model with one or more state variables — mkinmod","title":"Function to set up a kinetic model with one or more state variables — mkinmod","text":"function usually called using call mkinsub() observed variable, specifying corresponding submodel well outgoing pathways (see examples). Print mkinmod objects way user finds way get components.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinmod.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to set up a kinetic model with one or more state variables — mkinmod","text":"","code":"mkinmod( ..., use_of_ff = \"max\", name = NULL, speclist = NULL, quiet = FALSE, verbose = FALSE, dll_dir = NULL, unload = FALSE, overwrite = FALSE ) # S3 method for mkinmod print(x, ...) mkinsub(submodel, to = NULL, sink = TRUE, full_name = NA)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinmod.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to set up a kinetic model with one or more state variables — mkinmod","text":"... observed variable, list obtained mkinsub() specified argument (see examples). Currently, single first order kinetics \"SFO\", indeterminate order rate equation kinetics \"IORE\", single first order reversible binding \"SFORB\" implemented variables, \"FOMC\", \"DFOP\", \"HS\" \"logistic\" can additionally chosen first variable assumed source compartment. Additionally, mkinsub() argument , specifying names variables transfer assumed model. argument use_of_ff set \"min\" model compartment \"SFO\" \"SFORB\", additional mkinsub() argument can sink = FALSE, effectively fixing flux sink zero. print.mkinmod, argument currently used. use_of_ff Specification use formation fractions model equations , applicable, coefficient matrix. \"max\", formation fractions always used (default). \"min\", minimum use formation fractions made, .e. first-order pathway metabolite rate constant. name name model. valid R object name. speclist specification observed variables submodel types pathways can given single list using argument. Default NULL. quiet messages suppressed? verbose TRUE, passed inline::cfunction() applicable give detailed information C function built. dll_dir Directory DLL object, generated internally inline::cfunction(), saved. DLL stored permanent location use future sessions, 'dll_dir' 'name' specified. helpful fit objects cached e.g. knitr, cache remains functional across sessions DLL stored user defined location. unload DLL target location 'dll_dir' already loaded, unloaded first? overwrite file exists target DLL location 'dll_dir', overwritten? x mkinmod object. submodel Character vector length one specify submodel type. See mkinmod list allowed submodel names. Vector names state variable transformation shall included model. sink pathway sink included model addition pathways state variables? full_name optional name used e.g. plotting fits performed model. can use non-ASCII characters , R code portable, .e. may produce unintended plot results operating systems system configurations.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinmod.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to set up a kinetic model with one or more state variables — mkinmod","text":"list class mkinmod use mkinfit(), containing, among others, diffs vector string representations differential equations, one modelling variable. map list containing named character vectors observed variable, specifying modelling variables represented. use_of_ff content use_of_ff passed list component. deg_func generated, function containing solution degradation model. coefmat coefficient matrix, system differential equations can represented one. cf generated, compiled function calculating derivatives returned cfunction. list use mkinmod.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinmod.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Function to set up a kinetic model with one or more state variables — mkinmod","text":"definition model types parameters, equations given FOCUS NAFTA guidance documents used. kinetic models one observed variable, symbolic solution system differential equations included resulting mkinmod object cases, speeding solution. C compiler found pkgbuild::has_compiler() one observed variable specification, C code generated evaluating differential equations, compiled using inline::cfunction() added resulting mkinmod object.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinmod.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Function to set up a kinetic model with one or more state variables — mkinmod","text":"IORE submodel well tested metabolites. using model metabolites, may want read note help page mkinfit.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinmod.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Function to set up a kinetic model with one or more state variables — mkinmod","text":"FOCUS (2006) “Guidance Document Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration” Report FOCUS Work Group Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics NAFTA Technical Working Group Pesticides (dated) Guidance Evaluating Calculating Degradation Kinetics Environmental Media","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinmod.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Function to set up a kinetic model with one or more state variables — mkinmod","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinmod.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Function to set up a kinetic model with one or more state variables — mkinmod","text":"","code":"# Specify the SFO model (this is not needed any more, as we can now mkinfit(\"SFO\", ...) SFO <- mkinmod(parent = mkinsub(\"SFO\")) # One parent compound, one metabolite, both single first order SFO_SFO <- mkinmod( parent = mkinsub(\"SFO\", \"m1\"), m1 = mkinsub(\"SFO\")) #> Temporary DLL for differentials generated and loaded print(SFO_SFO) #> <mkinmod> model generated with #> Use of formation fractions $use_of_ff: max #> Specification $spec: #> $parent #> $type: SFO; $to: m1; $sink: TRUE #> $m1 #> $type: SFO; $sink: TRUE #> Coefficient matrix $coefmat available #> Compiled model $cf available #> Differential equations: #> d_parent/dt = - k_parent * parent #> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1 # \\dontrun{ fit_sfo_sfo <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, solution_type = \"deSolve\") #> Warning: Observations with value of zero were removed from the data # Now supplying compound names used for plotting, and write to user defined location # We need to choose a path outside the session tempdir because this gets removed DLL_dir <- \"~/.local/share/mkin\" if (!dir.exists(DLL_dir)) dir.create(DLL_dir) SFO_SFO.2 <- mkinmod( parent = mkinsub(\"SFO\", \"m1\", full_name = \"Test compound\"), m1 = mkinsub(\"SFO\", full_name = \"Metabolite M1\"), name = \"SFO_SFO\", dll_dir = DLL_dir, unload = TRUE, overwrite = TRUE) #> Temporary DLL for differentials generated and loaded #> Copied DLL from /tmp/Rtmpjn19MY/filee5f2f55ca8372.so to /home/jranke/.local/share/mkin/SFO_SFO.so # Now we can save the model and restore it in a new session saveRDS(SFO_SFO.2, file = \"~/SFO_SFO.rds\") # Terminate the R session here if you would like to check, and then do library(mkin) SFO_SFO.3 <- readRDS(\"~/SFO_SFO.rds\") fit_sfo_sfo <- mkinfit(SFO_SFO.3, FOCUS_2006_D, quiet = TRUE, solution_type = \"deSolve\") #> Warning: Observations with value of zero were removed from the data # Show details of creating the C function SFO_SFO <- mkinmod( parent = mkinsub(\"SFO\", \"m1\"), m1 = mkinsub(\"SFO\"), verbose = TRUE) #> Program source: #> 1: #include <R.h> #> 2: #> 3: #> 4: static double parms [3]; #> 5: #define k_parent parms[0] #> 6: #define f_parent_to_m1 parms[1] #> 7: #define k_m1 parms[2] #> 8: #> 9: void initpar(void (* odeparms)(int *, double *)) { #> 10: int N = 3; #> 11: odeparms(&N, parms); #> 12: } #> 13: #> 14: #> 15: void diffs ( int * n, double * t, double * y, double * f, double * rpar, int * ipar ) { #> 16: #> 17: f[0] = - k_parent * y[0]; #> 18: f[1] = + f_parent_to_m1 * k_parent * y[0] - k_m1 * y[1]; #> 19: } #> Temporary DLL for differentials generated and loaded # The symbolic solution which is available in this case is not # made for human reading but for speed of computation SFO_SFO$deg_func #> function (observed, odeini, odeparms) #> { #> predicted <- numeric(0) #> with(as.list(odeparms), { #> t <- observed[observed$name == \"parent\", \"time\"] #> predicted <<- c(predicted, SFO.solution(t, odeini[\"parent\"], #> k_parent)) #> t <- observed[observed$name == \"m1\", \"time\"] #> predicted <<- c(predicted, (((k_m1 - k_parent) * odeini[\"m1\"] - #> f_parent_to_m1 * k_parent * odeini[\"parent\"]) * exp(-k_m1 * #> t) + f_parent_to_m1 * k_parent * odeini[\"parent\"] * #> exp(-k_parent * t))/(k_m1 - k_parent)) #> }) #> return(predicted) #> } #> <environment: 0x555555f44b28> # If we have several parallel metabolites # (compare tests/testthat/test_synthetic_data_for_UBA_2014.R) m_synth_DFOP_par <- mkinmod( parent = mkinsub(\"DFOP\", c(\"M1\", \"M2\")), M1 = mkinsub(\"SFO\"), M2 = mkinsub(\"SFO\"), quiet = TRUE) fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, synthetic_data_for_UBA_2014[[12]]$data, quiet = TRUE) # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinparplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to plot the confidence intervals obtained using mkinfit — mkinparplot","title":"Function to plot the confidence intervals obtained using mkinfit — mkinparplot","text":"function plots confidence intervals parameters fitted using mkinfit.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinparplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to plot the confidence intervals obtained using mkinfit — mkinparplot","text":"","code":"mkinparplot(object)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinparplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to plot the confidence intervals obtained using mkinfit — mkinparplot","text":"object fit represented mkinfit object.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinparplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to plot the confidence intervals obtained using mkinfit — mkinparplot","text":"Nothing returned function, called side effect, namely produce plot.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinparplot.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Function to plot the confidence intervals obtained using mkinfit — mkinparplot","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinparplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Function to plot the confidence intervals obtained using mkinfit — mkinparplot","text":"","code":"# \\dontrun{ model <- mkinmod( T245 = mkinsub(\"SFO\", to = c(\"phenol\"), sink = FALSE), phenol = mkinsub(\"SFO\", to = c(\"anisole\")), anisole = mkinsub(\"SFO\"), use_of_ff = \"max\") #> Temporary DLL for differentials generated and loaded fit <- mkinfit(model, subset(mccall81_245T, soil == \"Commerce\"), quiet = TRUE) #> Warning: Observations with value of zero were removed from the data mkinparplot(fit) # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the observed data and the fitted model of an mkinfit object — mkinplot","title":"Plot the observed data and the fitted model of an mkinfit object — mkinplot","text":"Deprecated function. now calls plot method plot.mkinfit.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the observed data and the fitted model of an mkinfit object — mkinplot","text":"","code":"mkinplot(fit, ...)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the observed data and the fitted model of an mkinfit object — mkinplot","text":"fit object class mkinfit. ... arguments passed plot.mkinfit.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot the observed data and the fitted model of an mkinfit object — mkinplot","text":"function called side effect.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinplot.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plot the observed data and the fitted model of an mkinfit object — mkinplot","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinpredict.html","id":null,"dir":"Reference","previous_headings":"","what":"Produce predictions from a kinetic model using specific parameters — mkinpredict","title":"Produce predictions from a kinetic model using specific parameters — mkinpredict","text":"function produces time series observed variables kinetic model specified mkinmod, using specific set kinetic parameters initial values state variables.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinpredict.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Produce predictions from a kinetic model using specific parameters — mkinpredict","text":"","code":"mkinpredict(x, odeparms, odeini, outtimes, ...) # S3 method for mkinmod mkinpredict( x, odeparms = c(k_parent_sink = 0.1), odeini = c(parent = 100), outtimes = seq(0, 120, by = 0.1), solution_type = \"deSolve\", use_compiled = \"auto\", use_symbols = FALSE, method.ode = \"lsoda\", atol = 1e-08, rtol = 1e-10, maxsteps = 20000L, map_output = TRUE, na_stop = TRUE, ... ) # S3 method for mkinfit mkinpredict( x, odeparms = x$bparms.ode, odeini = x$bparms.state, outtimes = seq(0, 120, by = 0.1), solution_type = \"deSolve\", use_compiled = \"auto\", method.ode = \"lsoda\", atol = 1e-08, rtol = 1e-10, map_output = TRUE, ... )"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinpredict.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Produce predictions from a kinetic model using specific parameters — mkinpredict","text":"x kinetic model produced mkinmod, kinetic fit fitted mkinfit. latter case, fitted parameters used prediction. odeparms numeric vector specifying parameters used kinetic model, generally defined set ordinary differential equations. odeini numeric vector containing initial values state variables model. Note state variables can differ observed variables, example case SFORB model. outtimes numeric vector specifying time points model predictions generated. ... arguments passed ode solver case solver used. solution_type method used producing predictions. generally \"analytical\" one observed variable, usually \"deSolve\" case several observed variables. third possibility \"eigen\" fast comparison uncompiled ODE models, applicable models, e.g. using FOMC parent compound. use_compiled set FALSE, compiled version mkinmod model used, even present. use_symbols set TRUE (default), symbol info present mkinmod object used available accessing compiled code method.ode solution method passed via mkinpredict ode] case solution type \"deSolve\" using compiled code. using compiled code, lsoda supported. atol Absolute error tolerance, passed ode solver. rtol Absolute error tolerance, passed ode solver. maxsteps Maximum number steps, passed ode solver. map_output Boolean specify output list values observed variables (default) state variables (set FALSE). Setting FALSE effect analytical solutions, always return mapped output. na_stop error ode returns NaN values","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinpredict.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Produce predictions from a kinetic model using specific parameters — mkinpredict","text":"matrix numeric solution wide format","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinpredict.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Produce predictions from a kinetic model using specific parameters — mkinpredict","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinpredict.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Produce predictions from a kinetic model using specific parameters — mkinpredict","text":"","code":"SFO <- mkinmod(degradinol = mkinsub(\"SFO\")) # Compare solution types mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20, solution_type = \"analytical\") #> time degradinol #> 0 0 100.0000000 #> 1 1 74.0818221 #> 2 2 54.8811636 #> 3 3 40.6569660 #> 4 4 30.1194212 #> 5 5 22.3130160 #> 6 6 16.5298888 #> 7 7 12.2456428 #> 8 8 9.0717953 #> 9 9 6.7205513 #> 10 10 4.9787068 #> 11 11 3.6883167 #> 12 12 2.7323722 #> 13 13 2.0241911 #> 14 14 1.4995577 #> 15 15 1.1108997 #> 16 16 0.8229747 #> 17 17 0.6096747 #> 18 18 0.4516581 #> 19 19 0.3345965 #> 20 20 0.2478752 mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20, solution_type = \"deSolve\") #> time degradinol #> 0 0 100.0000000 #> 1 1 74.0818221 #> 2 2 54.8811636 #> 3 3 40.6569660 #> 4 4 30.1194212 #> 5 5 22.3130160 #> 6 6 16.5298888 #> 7 7 12.2456428 #> 8 8 9.0717953 #> 9 9 6.7205513 #> 10 10 4.9787068 #> 11 11 3.6883167 #> 12 12 2.7323722 #> 13 13 2.0241911 #> 14 14 1.4995577 #> 15 15 1.1108996 #> 16 16 0.8229747 #> 17 17 0.6096747 #> 18 18 0.4516581 #> 19 19 0.3345965 #> 20 20 0.2478752 mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20, solution_type = \"deSolve\", use_compiled = FALSE) #> time degradinol #> 0 0 100.0000000 #> 1 1 74.0818221 #> 2 2 54.8811636 #> 3 3 40.6569660 #> 4 4 30.1194212 #> 5 5 22.3130160 #> 6 6 16.5298888 #> 7 7 12.2456428 #> 8 8 9.0717953 #> 9 9 6.7205513 #> 10 10 4.9787068 #> 11 11 3.6883167 #> 12 12 2.7323722 #> 13 13 2.0241911 #> 14 14 1.4995577 #> 15 15 1.1108996 #> 16 16 0.8229747 #> 17 17 0.6096747 #> 18 18 0.4516581 #> 19 19 0.3345965 #> 20 20 0.2478752 mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20, solution_type = \"eigen\") #> time degradinol #> 0 0 100.0000000 #> 1 1 74.0818221 #> 2 2 54.8811636 #> 3 3 40.6569660 #> 4 4 30.1194212 #> 5 5 22.3130160 #> 6 6 16.5298888 #> 7 7 12.2456428 #> 8 8 9.0717953 #> 9 9 6.7205513 #> 10 10 4.9787068 #> 11 11 3.6883167 #> 12 12 2.7323722 #> 13 13 2.0241911 #> 14 14 1.4995577 #> 15 15 1.1108997 #> 16 16 0.8229747 #> 17 17 0.6096747 #> 18 18 0.4516581 #> 19 19 0.3345965 #> 20 20 0.2478752 # Compare integration methods to analytical solution mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20, solution_type = \"analytical\")[21,] #> time degradinol #> 20.0000000 0.2478752 mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20, method = \"lsoda\", use_compiled = FALSE)[21,] #> time degradinol #> 20.0000000 0.2478752 mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20, method = \"ode45\", use_compiled = FALSE)[21,] #> time degradinol #> 20.0000000 0.2478752 mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20, method = \"rk4\", use_compiled = FALSE)[21,] #> time degradinol #> 20.0000000 0.2480043 # rk4 is not as precise here # The number of output times used to make a lot of difference until the # default for atol was adjusted mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), seq(0, 20, by = 0.1))[201,] #> time degradinol #> 20.0000000 0.2478752 mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), seq(0, 20, by = 0.01))[2001,] #> time degradinol #> 20.0000000 0.2478752 # Comparison of the performance of solution types SFO_SFO = mkinmod(parent = list(type = \"SFO\", to = \"m1\"), m1 = list(type = \"SFO\"), use_of_ff = \"max\") #> Temporary DLL for differentials generated and loaded if(require(rbenchmark)) { benchmark(replications = 10, order = \"relative\", columns = c(\"test\", \"relative\", \"elapsed\"), eigen = mkinpredict(SFO_SFO, c(k_parent = 0.15, f_parent_to_m1 = 0.5, k_m1 = 0.01), c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = \"eigen\")[201,], deSolve_compiled = mkinpredict(SFO_SFO, c(k_parent = 0.15, f_parent_to_m1 = 0.5, k_m1 = 0.01), c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = \"deSolve\")[201,], deSolve = mkinpredict(SFO_SFO, c(k_parent = 0.15, f_parent_to_m1 = 0.5, k_m1 = 0.01), c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = \"deSolve\", use_compiled = FALSE)[201,], analytical = mkinpredict(SFO_SFO, c(k_parent = 0.15, f_parent_to_m1 = 0.5, k_m1 = 0.01), c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = \"analytical\", use_compiled = FALSE)[201,]) } #> test relative elapsed #> 4 analytical 1 0.001 #> 2 deSolve_compiled 2 0.002 #> 1 eigen 8 0.008 #> 3 deSolve 64 0.064 # \\dontrun{ # Predict from a fitted model f <- mkinfit(SFO_SFO, FOCUS_2006_C, quiet = TRUE) f <- mkinfit(SFO_SFO, FOCUS_2006_C, quiet = TRUE, solution_type = \"deSolve\") head(mkinpredict(f)) #> Error in !is.null(x$symbols) & use_symbols: operations are possible only for numeric, logical or complex types # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinresplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Function to plot residuals stored in an mkin object — mkinresplot","title":"Function to plot residuals stored in an mkin object — mkinresplot","text":"function plots residuals specified subset observed variables mkinfit object. combined plot fitted model residuals can obtained using plot.mkinfit using argument show_residuals = TRUE.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinresplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function to plot residuals stored in an mkin object — mkinresplot","text":"","code":"mkinresplot( object, obs_vars = names(object$mkinmod$map), xlim = c(0, 1.1 * max(object$data$time)), standardized = FALSE, xlab = \"Time\", ylab = ifelse(standardized, \"Standardized residual\", \"Residual\"), maxabs = \"auto\", legend = TRUE, lpos = \"topright\", col_obs = \"auto\", pch_obs = \"auto\", frame = TRUE, ... )"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinresplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function to plot residuals stored in an mkin object — mkinresplot","text":"object fit represented mkinfit object. obs_vars character vector names observed variables residuals plotted. Defaults observed variables model xlim plot range x direction. standardized residuals standardized dividing standard deviation given error model fit? xlab Label x axis. ylab Label y axis. maxabs Maximum absolute value residuals. used scaling y axis defaults \"auto\". legend legend plotted? lpos legend placed? Default \"topright\". passed legend. col_obs Colors observed variables. pch_obs Symbols used observed variables. frame frame drawn around plots? ... arguments passed plot.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinresplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function to plot residuals stored in an mkin object — mkinresplot","text":"Nothing returned function, called side effect, namely produce plot.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinresplot.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Function to plot residuals stored in an mkin object — mkinresplot","text":"Johannes Ranke Katrin Lindenberger","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mkinresplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Function to plot residuals stored in an mkin object — mkinresplot","text":"","code":"model <- mkinmod(parent = mkinsub(\"SFO\", \"m1\"), m1 = mkinsub(\"SFO\")) #> Temporary DLL for differentials generated and loaded fit <- mkinfit(model, FOCUS_2006_D, quiet = TRUE) #> Warning: Observations with value of zero were removed from the data mkinresplot(fit, \"m1\")"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mmkin.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit one or more kinetic models with one or more state variables to one or\nmore datasets — mmkin","title":"Fit one or more kinetic models with one or more state variables to one or\nmore datasets — mmkin","text":"function calls mkinfit combinations models datasets specified first two arguments.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mmkin.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit one or more kinetic models with one or more state variables to one or\nmore datasets — mmkin","text":"","code":"mmkin( models = c(\"SFO\", \"FOMC\", \"DFOP\"), datasets, cores = if (Sys.info()[\"sysname\"] == \"Windows\") 1 else parallel::detectCores(), cluster = NULL, ... ) # S3 method for mmkin print(x, ...)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/mmkin.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit one or more kinetic models with one or more state variables to one or\nmore datasets — mmkin","text":"models Either character vector shorthand names like c(\"SFO\", \"FOMC\", \"DFOP\", \"HS\", \"SFORB\"), optionally named list mkinmod objects. datasets optionally named list datasets suitable observed data mkinfit. cores number cores used multicore processing. used cluster argument NULL. Windows machines, cores > 1 supported, need use cluster argument use multiple logical processors. Per default, cores detected parallel::detectCores() used, except Windows default 1. cluster cluster returned makeCluster used parallel execution. ... used. x mmkin object.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mmkin.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fit one or more kinetic models with one or more state variables to one or\nmore datasets — mmkin","text":"two-dimensional array mkinfit objects /try-errors can indexed using model names first index (row index) dataset names second index (column index).","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/reference/mmkin.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Fit one or more kinetic models with one or more state variables to one or\nmore datasets — mmkin","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/mmkin.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fit one or more kinetic models with one or more state variables to one or\nmore datasets — mmkin","text":"","code":"# \\dontrun{ m_synth_SFO_lin <- mkinmod(parent = mkinsub(\"SFO\", \"M1\"), M1 = mkinsub(\"SFO\", \"M2\"), M2 = mkinsub(\"SFO\"), use_of_ff = \"max\") #> Temporary DLL for differentials generated and loaded m_synth_FOMC_lin <- mkinmod(parent = mkinsub(\"FOMC\", \"M1\"), M1 = mkinsub(\"SFO\", \"M2\"), M2 = mkinsub(\"SFO\"), use_of_ff = \"max\") #> Temporary DLL for differentials generated and loaded models <- list(SFO_lin = m_synth_SFO_lin, FOMC_lin = m_synth_FOMC_lin) datasets <- lapply(synthetic_data_for_UBA_2014[1:3], function(x) x$data) names(datasets) <- paste(\"Dataset\", 1:3) time_default <- system.time(fits.0 <- mmkin(models, datasets, quiet = TRUE)) time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE)) time_default #> user system elapsed #> 1.653 0.553 0.654 time_1 #> user system elapsed #> 2.013 0.008 2.021 endpoints(fits.0[[\"SFO_lin\", 2]]) #> $ff #> parent_M1 parent_sink M1_M2 M1_sink #> 0.7340481 0.2659519 0.7505690 0.2494310 #> #> $distimes #> DT50 DT90 #> parent 0.8777689 2.915885 #> M1 2.3257403 7.725942 #> M2 33.7201060 112.015767 #> # plot.mkinfit handles rows or columns of mmkin result objects plot(fits.0[1, ]) plot(fits.0[1, ], obs_var = c(\"M1\", \"M2\")) plot(fits.0[, 1]) # Use double brackets to extract a single mkinfit object, which will be plotted # by plot.mkinfit and can be plotted using plot_sep plot(fits.0[[1, 1]], sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE) plot_sep(fits.0[[1, 1]]) # Plotting with mmkin (single brackets, extracting an mmkin object) does not # allow to plot the observed variables separately plot(fits.0[1, 1]) # On Windows, we can use multiple cores by making a cluster first cl <- parallel::makePSOCKcluster(12) f <- mmkin(c(\"SFO\", \"FOMC\", \"DFOP\"), list(A = FOCUS_2006_A, B = FOCUS_2006_B, C = FOCUS_2006_C, D = FOCUS_2006_D), cluster = cl, quiet = TRUE) print(f) #> <mmkin> object #> Status of individual fits: #> #> dataset #> model A B C D #> SFO OK OK OK OK #> FOMC C OK OK OK #> DFOP OK OK OK OK #> #> C: Optimisation did not converge: #> false convergence (8) #> OK: No warnings # We get false convergence for the FOMC fit to FOCUS_2006_A because this # dataset is really SFO, and the FOMC fit is overparameterised parallel::stopCluster(cl) # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/multistart.html","id":null,"dir":"Reference","previous_headings":"","what":"Perform a hierarchical model fit with multiple starting values — multistart","title":"Perform a hierarchical model fit with multiple starting values — multistart","text":"purpose method check certain algorithm fitting nonlinear hierarchical models (also known nonlinear mixed-effects models) reliably yield results sufficiently similar , started certain range reasonable starting parameters. inspired article practical identifiabiliy frame nonlinear mixed-effects models Duchesne et al (2021).","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/multistart.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Perform a hierarchical model fit with multiple starting values — multistart","text":"","code":"multistart( object, n = 50, cores = if (Sys.info()[\"sysname\"] == \"Windows\") 1 else parallel::detectCores(), cluster = NULL, ... ) # S3 method for saem.mmkin multistart(object, n = 50, cores = 1, cluster = NULL, ...) # S3 method for multistart print(x, ...) best(object, ...) # S3 method for default best(object, ...) which.best(object, ...) # S3 method for default which.best(object, ...)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/multistart.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Perform a hierarchical model fit with multiple starting values — multistart","text":"object fit object work n many different combinations starting parameters used? cores many fits run parallel (posix platforms)? cluster cluster returned parallel::makeCluster used parallel execution. ... Passed update function. x multistart object print","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/multistart.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Perform a hierarchical model fit with multiple starting values — multistart","text":"list saem.mmkin objects, class attributes 'multistart.saem.mmkin' 'multistart'. object highest likelihood index object highest likelihood","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/multistart.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Perform a hierarchical model fit with multiple starting values — multistart","text":"Duchesne R, Guillemin , Gandrillon O, Crauste F. Practical identifiability frame nonlinear mixed effects models: example vitro erythropoiesis. BMC Bioinformatics. 2021 Oct 4;22(1):478. doi: 10.1186/s12859-021-04373-4.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/reference/multistart.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Perform a hierarchical model fit with multiple starting values — multistart","text":"","code":"# \\dontrun{ library(mkin) dmta_ds <- lapply(1:7, function(i) { ds_i <- dimethenamid_2018$ds[[i]]$data ds_i[ds_i$name == \"DMTAP\", \"name\"] <- \"DMTA\" ds_i$time <- ds_i$time * dimethenamid_2018$f_time_norm[i] ds_i }) names(dmta_ds) <- sapply(dimethenamid_2018$ds, function(ds) ds$title) dmta_ds[[\"Elliot\"]] <- rbind(dmta_ds[[\"Elliot 1\"]], dmta_ds[[\"Elliot 2\"]]) dmta_ds[[\"Elliot 1\"]] <- dmta_ds[[\"Elliot 2\"]] <- NULL f_mmkin <- mmkin(\"DFOP\", dmta_ds, error_model = \"tc\", cores = 7, quiet = TRUE) f_saem_full <- saem(f_mmkin) f_saem_full_multi <- multistart(f_saem_full, n = 16, cores = 16) parplot(f_saem_full_multi, lpos = \"topleft\") illparms(f_saem_full) #> [1] \"sd(log_k2)\" f_saem_reduced <- update(f_saem_full, no_random_effect = \"log_k2\") illparms(f_saem_reduced) # On Windows, we need to create a PSOCK cluster first and refer to it # in the call to multistart() library(parallel) cl <- makePSOCKcluster(12) f_saem_reduced_multi <- multistart(f_saem_reduced, n = 16, cluster = cl) parplot(f_saem_reduced_multi, lpos = \"topright\", ylim = c(0.5, 2)) stopCluster(cl) # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/nafta.html","id":null,"dir":"Reference","previous_headings":"","what":"Evaluate parent kinetics using the NAFTA guidance — nafta","title":"Evaluate parent kinetics using the NAFTA guidance — nafta","text":"function fits SFO, IORE DFOP models using mmkin returns object class nafta methods printing plotting. Print nafta objects. results three models printed order increasing model complexity, .e. SFO, IORE, finally DFOP.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/nafta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Evaluate parent kinetics using the NAFTA guidance — nafta","text":"","code":"nafta(ds, title = NA, quiet = FALSE, ...) # S3 method for nafta print(x, quiet = TRUE, digits = 3, ...)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/nafta.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Evaluate parent kinetics using the NAFTA guidance — nafta","text":"NAFTA (2011) Guidance evaluating calculating degradation kinetics environmental media. NAFTA Technical Working Group Pesticides https://www.epa.gov/pesticide-science--assessing-pesticide-risks/guidance-evaluating--calculating-degradation accessed 2019-02-22 US EPA (2015) Standard Operating Procedure Using NAFTA Guidance Calculate Representative Half-life Values Characterizing Pesticide Degradation https://www.epa.gov/pesticide-science--assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/nafta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Evaluate parent kinetics using the NAFTA guidance — nafta","text":"ds dataframe must contain one variable called \"time\" time values specified time argument, one column called \"name\" grouping observed values, finally one column observed values called \"value\". title Optional title dataset quiet evaluation text shown? ... arguments passed mmkin (printing method). x nafta object. digits Number digits used printing parameters dissipation times.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/nafta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Evaluate parent kinetics using the NAFTA guidance — nafta","text":"list class nafta. list element named \"mmkin\" mmkin object containing fits three models. list element named \"title\" contains title dataset used. list element \"data\" contains dataset used fits.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/nafta.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Evaluate parent kinetics using the NAFTA guidance — nafta","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/nafta.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Evaluate parent kinetics using the NAFTA guidance — nafta","text":"","code":"nafta_evaluation <- nafta(NAFTA_SOP_Appendix_D, cores = 1) #> The SFO model is rejected as S_SFO is equal or higher than the critical value S_c #> The representative half-life of the IORE model is longer than the one corresponding #> to the terminal degradation rate found with the DFOP model. #> The representative half-life obtained from the DFOP model may be used print(nafta_evaluation) #> Sums of squares: #> SFO IORE DFOP #> 1378.6832 615.7730 517.8836 #> #> Critical sum of squares for checking the SFO model: #> [1] 717.4598 #> #> Parameters: #> $SFO #> Estimate Pr(>t) Lower Upper #> parent_0 83.7558 1.80e-14 77.18268 90.3288 #> k_parent 0.0017 7.43e-05 0.00112 0.0026 #> sigma 8.7518 1.22e-05 5.64278 11.8608 #> #> $IORE #> Estimate Pr(>t) Lower Upper #> parent_0 9.69e+01 NA 8.88e+01 1.05e+02 #> k__iore_parent 8.40e-14 NA 1.79e-18 3.94e-09 #> N_parent 6.68e+00 NA 4.19e+00 9.17e+00 #> sigma 5.85e+00 NA 3.76e+00 7.94e+00 #> #> $DFOP #> Estimate Pr(>t) Lower Upper #> parent_0 9.76e+01 1.94e-13 9.02e+01 1.05e+02 #> k1 4.24e-02 5.92e-03 2.03e-02 8.88e-02 #> k2 8.24e-04 6.48e-03 3.89e-04 1.75e-03 #> g 2.88e-01 2.47e-05 1.95e-01 4.03e-01 #> sigma 5.36e+00 2.22e-05 3.43e+00 7.30e+00 #> #> #> DTx values: #> DT50 DT90 DT50_rep #> SFO 407 1350 407 #> IORE 541 5190000 1560000 #> DFOP 429 2380 841 #> #> Representative half-life: #> [1] 841.41 plot(nafta_evaluation)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/nlme.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper functions to create nlme models from mmkin row objects — nlme_function","title":"Helper functions to create nlme models from mmkin row objects — nlme_function","text":"functions facilitate setting nonlinear mixed effects model mmkin row object. mmkin row object essentially list mkinfit objects obtained fitting model list datasets. used internally nlme.mmkin() method.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/nlme.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper functions to create nlme models from mmkin row objects — nlme_function","text":"","code":"nlme_function(object) nlme_data(object)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/nlme.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper functions to create nlme models from mmkin row objects — nlme_function","text":"object mmkin row object containing several fits model different datasets","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/nlme.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper functions to create nlme models from mmkin row objects — nlme_function","text":"function can used nlme groupedData object","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/reference/nlme.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper functions to create nlme models from mmkin row objects — nlme_function","text":"","code":"sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) m_SFO <- mkinmod(parent = mkinsub(\"SFO\")) d_SFO_1 <- mkinpredict(m_SFO, c(k_parent = 0.1), c(parent = 98), sampling_times) d_SFO_1_long <- mkin_wide_to_long(d_SFO_1, time = \"time\") d_SFO_2 <- mkinpredict(m_SFO, c(k_parent = 0.05), c(parent = 102), sampling_times) d_SFO_2_long <- mkin_wide_to_long(d_SFO_2, time = \"time\") d_SFO_3 <- mkinpredict(m_SFO, c(k_parent = 0.02), c(parent = 103), sampling_times) d_SFO_3_long <- mkin_wide_to_long(d_SFO_3, time = \"time\") d1 <- add_err(d_SFO_1, function(value) 3, n = 1) d2 <- add_err(d_SFO_2, function(value) 2, n = 1) d3 <- add_err(d_SFO_3, function(value) 4, n = 1) ds <- c(d1 = d1, d2 = d2, d3 = d3) f <- mmkin(\"SFO\", ds, cores = 1, quiet = TRUE) mean_dp <- mean_degparms(f) grouped_data <- nlme_data(f) nlme_f <- nlme_function(f) # These assignments are necessary for these objects to be # visible to nlme and augPred when evaluation is done by # pkgdown to generate the html docs. assign(\"nlme_f\", nlme_f, globalenv()) assign(\"grouped_data\", grouped_data, globalenv()) library(nlme) m_nlme <- nlme(value ~ nlme_f(name, time, parent_0, log_k_parent_sink), data = grouped_data, fixed = parent_0 + log_k_parent_sink ~ 1, random = pdDiag(parent_0 + log_k_parent_sink ~ 1), start = mean_dp) summary(m_nlme) #> Nonlinear mixed-effects model fit by maximum likelihood #> Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink) #> Data: grouped_data #> AIC BIC logLik #> 266.6428 275.8935 -128.3214 #> #> Random effects: #> Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1) #> Level: ds #> Structure: Diagonal #> parent_0 log_k_parent_sink Residual #> StdDev: 0.0003775775 0.7058039 3.065183 #> #> Fixed effects: parent_0 + log_k_parent_sink ~ 1 #> Value Std.Error DF t-value p-value #> parent_0 101.18323 0.7900461 43 128.07257 0 #> log_k_parent_sink -3.08708 0.4171755 43 -7.39995 0 #> Correlation: #> prnt_0 #> log_k_parent_sink 0.031 #> #> Standardized Within-Group Residuals: #> Min Q1 Med Q3 Max #> -2.38427070 -0.52059848 0.03593021 0.39987268 2.73188969 #> #> Number of Observations: 47 #> Number of Groups: 3 plot(augPred(m_nlme, level = 0:1), layout = c(3, 1)) # augPred does not work on fits with more than one state # variable # # The procedure is greatly simplified by the nlme.mmkin function f_nlme <- nlme(f) plot(f_nlme)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/nlme.mmkin.html","id":null,"dir":"Reference","previous_headings":"","what":"Create an nlme model for an mmkin row object — nlme.mmkin","title":"Create an nlme model for an mmkin row object — nlme.mmkin","text":"functions sets nonlinear mixed effects model mmkin row object. mmkin row object essentially list mkinfit objects obtained fitting model list datasets.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/nlme.mmkin.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create an nlme model for an mmkin row object — nlme.mmkin","text":"","code":"# S3 method for mmkin nlme( model, data = \"auto\", fixed = lapply(as.list(names(mean_degparms(model))), function(el) eval(parse(text = paste(el, 1, sep = \"~\")))), random = pdDiag(fixed), groups, start = mean_degparms(model, random = TRUE, test_log_parms = TRUE), correlation = NULL, weights = NULL, subset, method = c(\"ML\", \"REML\"), na.action = na.fail, naPattern, control = list(), verbose = FALSE ) # S3 method for nlme.mmkin print(x, digits = max(3, getOption(\"digits\") - 3), ...) # S3 method for nlme.mmkin update(object, ...)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/nlme.mmkin.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create an nlme model for an mmkin row object — nlme.mmkin","text":"model mmkin row object. data Ignored, data taken mmkin model fixed Ignored, degradation parameters fitted mmkin model used fixed parameters random specified, correlations random effects set optimised degradation model parameters. achieved using nlme::pdDiag method. groups See documentation nlme start specified, mean values fitted degradation parameters taken mmkin object used correlation See documentation nlme weights passed nlme subset passed nlme method passed nlme na.action passed nlme naPattern passed nlme control passed nlme verbose passed nlme x nlme.mmkin object print digits Number digits use printing ... Update specifications passed update.nlme object nlme.mmkin object update","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/nlme.mmkin.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create an nlme model for an mmkin row object — nlme.mmkin","text":"Upon success, fitted 'nlme.mmkin' object, nlme object additional elements. also inherits 'mixed.mmkin'.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/nlme.mmkin.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create an nlme model for an mmkin row object — nlme.mmkin","text":"Note convergence nlme algorithms depends quality data. degradation kinetics, often datasets (e.g. data soils) complicated degradation models, may make impossible obtain convergence nlme.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/nlme.mmkin.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Create an nlme model for an mmkin row object — nlme.mmkin","text":"object inherits nlme::nlme, wealth methods automatically work 'nlme.mmkin' objects, nlme::intervals(), nlme::anova.lme() nlme::coef.lme().","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/reference/nlme.mmkin.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create an nlme model for an mmkin row object — nlme.mmkin","text":"","code":"ds <- lapply(experimental_data_for_UBA_2019[6:10], function(x) subset(x$data[c(\"name\", \"time\", \"value\")], name == \"parent\")) # \\dontrun{ f <- mmkin(c(\"SFO\", \"DFOP\"), ds, quiet = TRUE, cores = 1) library(nlme) f_nlme_sfo <- nlme(f[\"SFO\", ]) f_nlme_dfop <- nlme(f[\"DFOP\", ]) anova(f_nlme_sfo, f_nlme_dfop) #> Model df AIC BIC logLik Test L.Ratio p-value #> f_nlme_sfo 1 5 625.0539 637.5529 -307.5269 #> f_nlme_dfop 2 9 495.1270 517.6253 -238.5635 1 vs 2 137.9269 <.0001 print(f_nlme_dfop) #> Kinetic nonlinear mixed-effects model fit by maximum likelihood #> #> Structural model: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * #> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) #> * parent #> #> Data: #> 90 observations of 1 variable(s) grouped in 5 datasets #> #> Log-likelihood: -238.6 #> #> Fixed effects: #> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) #> parent_0 log_k1 log_k2 g_qlogis #> 94.1702 -1.8002 -4.1474 0.0324 #> #> Random effects: #> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) #> Level: ds #> Structure: Diagonal #> parent_0 log_k1 log_k2 g_qlogis Residual #> StdDev: 2.488 0.8447 1.33 0.4652 2.321 #> plot(f_nlme_dfop) endpoints(f_nlme_dfop) #> $distimes #> DT50 DT90 DT50back DT50_k1 DT50_k2 #> parent 10.79857 100.7937 30.34192 4.193937 43.85442 #> ds_2 <- lapply(experimental_data_for_UBA_2019[6:10], function(x) x$data[c(\"name\", \"time\", \"value\")]) m_sfo_sfo <- mkinmod(parent = mkinsub(\"SFO\", \"A1\"), A1 = mkinsub(\"SFO\"), use_of_ff = \"min\", quiet = TRUE) m_sfo_sfo_ff <- mkinmod(parent = mkinsub(\"SFO\", \"A1\"), A1 = mkinsub(\"SFO\"), use_of_ff = \"max\", quiet = TRUE) m_dfop_sfo <- mkinmod(parent = mkinsub(\"DFOP\", \"A1\"), A1 = mkinsub(\"SFO\"), quiet = TRUE) f_2 <- mmkin(list(\"SFO-SFO\" = m_sfo_sfo, \"SFO-SFO-ff\" = m_sfo_sfo_ff, \"DFOP-SFO\" = m_dfop_sfo), ds_2, quiet = TRUE) f_nlme_sfo_sfo <- nlme(f_2[\"SFO-SFO\", ]) plot(f_nlme_sfo_sfo) # With formation fractions this does not coverge with defaults # f_nlme_sfo_sfo_ff <- nlme(f_2[\"SFO-SFO-ff\", ]) #plot(f_nlme_sfo_sfo_ff) # For the following, we need to increase pnlsMaxIter and the tolerance # to get convergence f_nlme_dfop_sfo <- nlme(f_2[\"DFOP-SFO\", ], control = list(pnlsMaxIter = 120, tolerance = 5e-4)) plot(f_nlme_dfop_sfo) anova(f_nlme_dfop_sfo, f_nlme_sfo_sfo) #> Model df AIC BIC logLik Test L.Ratio p-value #> f_nlme_dfop_sfo 1 13 843.8547 884.620 -408.9273 #> f_nlme_sfo_sfo 2 9 1085.1821 1113.404 -533.5910 1 vs 2 249.3274 <.0001 endpoints(f_nlme_sfo_sfo) #> $ff #> parent_sink parent_A1 A1_sink #> 0.5912432 0.4087568 1.0000000 #> #> $distimes #> DT50 DT90 #> parent 19.13518 63.5657 #> A1 66.02155 219.3189 #> endpoints(f_nlme_dfop_sfo) #> $ff #> parent_A1 parent_sink #> 0.2768574 0.7231426 #> #> $distimes #> DT50 DT90 DT50back DT50_k1 DT50_k2 #> parent 11.07091 104.6320 31.49737 4.462383 46.20825 #> A1 162.30550 539.1672 NA NA NA #> if (length(findFunction(\"varConstProp\")) > 0) { # tc error model for nlme available # Attempts to fit metabolite kinetics with the tc error model are possible, # but need tweeking of control values and sometimes do not converge f_tc <- mmkin(c(\"SFO\", \"DFOP\"), ds, quiet = TRUE, error_model = \"tc\") f_nlme_sfo_tc <- nlme(f_tc[\"SFO\", ]) f_nlme_dfop_tc <- nlme(f_tc[\"DFOP\", ]) AIC(f_nlme_sfo, f_nlme_sfo_tc, f_nlme_dfop, f_nlme_dfop_tc) print(f_nlme_dfop_tc) } #> Kinetic nonlinear mixed-effects model fit by maximum likelihood #> #> Structural model: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * #> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) #> * parent #> #> Data: #> 90 observations of 1 variable(s) grouped in 5 datasets #> #> Log-likelihood: -238.4 #> #> Fixed effects: #> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) #> parent_0 log_k1 log_k2 g_qlogis #> 94.04774 -1.82340 -4.16716 0.05685 #> #> Random effects: #> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) #> Level: ds #> Structure: Diagonal #> parent_0 log_k1 log_k2 g_qlogis Residual #> StdDev: 2.474 0.85 1.337 0.4659 1 #> #> Variance function: #> Structure: Constant plus proportion of variance covariate #> Formula: ~fitted(.) #> Parameter estimates: #> const prop #> 2.23222933 0.01262399 f_2_obs <- update(f_2, error_model = \"obs\") f_nlme_sfo_sfo_obs <- nlme(f_2_obs[\"SFO-SFO\", ]) print(f_nlme_sfo_sfo_obs) #> Kinetic nonlinear mixed-effects model fit by maximum likelihood #> #> Structural model: #> d_parent/dt = - k_parent_sink * parent - k_parent_A1 * parent #> d_A1/dt = + k_parent_A1 * parent - k_A1_sink * A1 #> #> Data: #> 170 observations of 2 variable(s) grouped in 5 datasets #> #> Log-likelihood: -473 #> #> Fixed effects: #> list(parent_0 ~ 1, log_k_parent_sink ~ 1, log_k_parent_A1 ~ 1, log_k_A1_sink ~ 1) #> parent_0 log_k_parent_sink log_k_parent_A1 log_k_A1_sink #> 87.976 -3.670 -4.164 -4.645 #> #> Random effects: #> Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1, log_k_parent_A1 ~ 1, log_k_A1_sink ~ 1) #> Level: ds #> Structure: Diagonal #> parent_0 log_k_parent_sink log_k_parent_A1 log_k_A1_sink Residual #> StdDev: 3.992 1.777 1.055 0.4821 6.483 #> #> Variance function: #> Structure: Different standard deviations per stratum #> Formula: ~1 | name #> Parameter estimates: #> parent A1 #> 1.0000000 0.2050005 f_nlme_dfop_sfo_obs <- nlme(f_2_obs[\"DFOP-SFO\", ], control = list(pnlsMaxIter = 120, tolerance = 5e-4)) f_2_tc <- update(f_2, error_model = \"tc\") # f_nlme_sfo_sfo_tc <- nlme(f_2_tc[\"SFO-SFO\", ]) # No convergence with 50 iterations # f_nlme_dfop_sfo_tc <- nlme(f_2_tc[\"DFOP-SFO\", ], # control = list(pnlsMaxIter = 120, tolerance = 5e-4)) # Error in X[, fmap[[nm]]] <- gradnm anova(f_nlme_dfop_sfo, f_nlme_dfop_sfo_obs) #> Model df AIC BIC logLik Test L.Ratio p-value #> f_nlme_dfop_sfo 1 13 843.8547 884.620 -408.9273 #> f_nlme_dfop_sfo_obs 2 14 817.5338 861.435 -394.7669 1 vs 2 28.32084 <.0001 # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/nobs.mkinfit.html","id":null,"dir":"Reference","previous_headings":"","what":"Number of observations on which an mkinfit object was fitted — nobs.mkinfit","title":"Number of observations on which an mkinfit object was fitted — nobs.mkinfit","text":"Number observations mkinfit object fitted","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/nobs.mkinfit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Number of observations on which an mkinfit object was fitted — nobs.mkinfit","text":"","code":"# S3 method for mkinfit nobs(object, ...)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/nobs.mkinfit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Number of observations on which an mkinfit object was fitted — nobs.mkinfit","text":"object mkinfit object ... compatibility generic method","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/nobs.mkinfit.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Number of observations on which an mkinfit object was fitted — nobs.mkinfit","text":"number rows data included mkinfit object","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/parms.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract model parameters — parms","title":"Extract model parameters — parms","text":"function returns degradation model parameters well error model parameters per default, order avoid working fitted model without considering error structure assumed fit.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/parms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract model parameters — parms","text":"","code":"parms(object, ...) # S3 method for mkinfit parms(object, transformed = FALSE, errparms = TRUE, ...) # S3 method for mmkin parms(object, transformed = FALSE, errparms = TRUE, ...) # S3 method for multistart parms(object, exclude_failed = TRUE, ...) # S3 method for saem.mmkin parms(object, ci = FALSE, covariates = NULL, ...)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/parms.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract model parameters — parms","text":"object fitted model object. ... used transformed parameters returned used internally optimisation? errparms error model parameters returned addition degradation parameters? exclude_failed multistart objects, rows failed fits removed returned parameter matrix? ci matrix estimates confidence interval boundaries returned? FALSE (default), vector estimates returned covariates given, otherwise matrix estimates returned, column corresponding row data frame holding covariates covariates data frame holding covariate values return parameter values. effect 'ci' FALSE.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/parms.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Extract model parameters — parms","text":"Depending object, numeric vector fitted model parameters, matrix (e.g. mmkin row objects), list matrices (e.g. mmkin objects one row).","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/reference/parms.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extract model parameters — parms","text":"","code":"# mkinfit objects fit <- mkinfit(\"SFO\", FOCUS_2006_C, quiet = TRUE) parms(fit) #> parent_0 k_parent sigma #> 82.4921598 0.3060633 4.6730124 parms(fit, transformed = TRUE) #> parent_0 log_k_parent sigma #> 82.492160 -1.183963 4.673012 # mmkin objects ds <- lapply(experimental_data_for_UBA_2019[6:10], function(x) subset(x$data[c(\"name\", \"time\", \"value\")])) names(ds) <- paste(\"Dataset\", 6:10) # \\dontrun{ fits <- mmkin(c(\"SFO\", \"FOMC\", \"DFOP\"), ds, quiet = TRUE, cores = 1) parms(fits[\"SFO\", ]) #> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 #> parent_0 88.52275400 82.666781678 86.8547308 91.7779306 82.14809450 #> k_parent 0.05794659 0.009647805 0.2102974 0.1232258 0.00720421 #> sigma 5.15274487 7.040168584 3.6769645 6.4669234 6.50457673 parms(fits[, 2]) #> $SFO #> Dataset 7 #> parent_0 82.666781678 #> k_parent 0.009647805 #> sigma 7.040168584 #> #> $FOMC #> Dataset 7 #> parent_0 92.6837649 #> alpha 0.4967832 #> beta 14.1451255 #> sigma 1.9167519 #> #> $DFOP #> Dataset 7 #> parent_0 91.058971584 #> k1 0.044946770 #> k2 0.002868336 #> g 0.526942414 #> sigma 2.221302196 #> parms(fits) #> $SFO #> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 #> parent_0 88.52275400 82.666781678 86.8547308 91.7779306 82.14809450 #> k_parent 0.05794659 0.009647805 0.2102974 0.1232258 0.00720421 #> sigma 5.15274487 7.040168584 3.6769645 6.4669234 6.50457673 #> #> $FOMC #> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 #> parent_0 95.558575 92.6837649 90.719787 98.383939 94.8481458 #> alpha 1.338667 0.4967832 1.639099 1.074460 0.2805272 #> beta 13.033315 14.1451255 5.007077 4.397126 6.9052224 #> sigma 1.847671 1.9167519 1.066063 3.146056 1.6222778 #> #> $DFOP #> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 #> parent_0 96.55213663 91.058971584 90.34509493 98.14858820 94.311323735 #> k1 0.21954588 0.044946770 0.41232288 0.31697588 0.080663857 #> k2 0.02957934 0.002868336 0.07581766 0.03260384 0.003425417 #> g 0.44845068 0.526942414 0.66091967 0.65322767 0.342652880 #> sigma 1.35690468 2.221302196 1.34169076 2.87159846 1.942067831 #> parms(fits, transformed = TRUE) #> $SFO #> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 #> parent_0 88.522754 82.666782 86.854731 91.777931 82.148095 #> log_k_parent -2.848234 -4.641025 -1.559232 -2.093737 -4.933090 #> sigma 5.152745 7.040169 3.676964 6.466923 6.504577 #> #> $FOMC #> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 #> parent_0 95.5585751 92.6837649 90.7197870 98.38393898 94.848146 #> log_alpha 0.2916741 -0.6996015 0.4941466 0.07181816 -1.271085 #> log_beta 2.5675088 2.6493701 1.6108523 1.48095106 1.932278 #> sigma 1.8476712 1.9167519 1.0660627 3.14605557 1.622278 #> #> $DFOP #> Dataset 6 Dataset 7 Dataset 8 Dataset 9 Dataset 10 #> parent_0 96.5521366 91.0589716 90.3450949 98.1485882 94.3113237 #> log_k1 -1.5161940 -3.1022764 -0.8859486 -1.1489296 -2.5174647 #> log_k2 -3.5206791 -5.8540232 -2.5794240 -3.4233253 -5.6765322 #> g_qlogis -0.2069326 0.1078741 0.6673953 0.6332573 -0.6514943 #> sigma 1.3569047 2.2213022 1.3416908 2.8715985 1.9420678 #> # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/parplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot parameter variability of multistart objects — parplot","title":"Plot parameter variability of multistart objects — parplot","text":"Produces boxplot parameters multiple runs, scaled either parameters run highest likelihood, medians proposed paper Duchesne et al. (2021).","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/parplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot parameter variability of multistart objects — parplot","text":"","code":"parplot(object, ...) # S3 method for multistart.saem.mmkin parplot( object, llmin = -Inf, llquant = NA, scale = c(\"best\", \"median\"), lpos = \"bottomleft\", main = \"\", ... )"},{"path":"https://pkgdown.jrwb.de/mkin/reference/parplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot parameter variability of multistart objects — parplot","text":"object multistart object ... Passed boxplot llmin minimum likelihood objects shown llquant Fractional value selecting fits higher likelihoods. Overrides 'llmin'. scale default, scale parameters using best available fit. 'median', parameters scaled using median parameters fits. lpos Positioning legend. main Title plot","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/parplot.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Plot parameter variability of multistart objects — parplot","text":"Starting values degradation model parameters error model parameters shown green circles. results obtained original run shown red circles.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/parplot.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Plot parameter variability of multistart objects — parplot","text":"Duchesne R, Guillemin , Gandrillon O, Crauste F. Practical identifiability frame nonlinear mixed effects models: example vitro erythropoiesis. BMC Bioinformatics. 2021 Oct 4;22(1):478. doi: 10.1186/s12859-021-04373-4.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/reference/plot.mixed.mmkin.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object — plot.mixed.mmkin","title":"Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object — plot.mixed.mmkin","text":"Plot predictions fitted nonlinear mixed model obtained via mmkin row object","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/plot.mixed.mmkin.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object — plot.mixed.mmkin","text":"","code":"# S3 method for mixed.mmkin plot( x, i = 1:ncol(x$mmkin), obs_vars = names(x$mkinmod$map), standardized = TRUE, covariates = NULL, covariate_quantiles = c(0.5, 0.05, 0.95), xlab = \"Time\", xlim = range(x$data$time), resplot = c(\"predicted\", \"time\"), pop_curves = \"auto\", pred_over = NULL, test_log_parms = FALSE, conf.level = 0.6, default_log_parms = NA, ymax = \"auto\", maxabs = \"auto\", ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)), nrow.legend = ceiling((length(i) + 1)/ncol.legend), rel.height.legend = 0.02 + 0.07 * nrow.legend, rel.height.bottom = 1.1, pch_ds = 1:length(i), col_ds = pch_ds + 1, lty_ds = col_ds, frame = TRUE, ... )"},{"path":"https://pkgdown.jrwb.de/mkin/reference/plot.mixed.mmkin.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object — plot.mixed.mmkin","text":"x object class mixed.mmkin, saem.mmkin nlme.mmkin numeric index select datasets plot individual predictions, case plots get large obs_vars character vector names observed variables data model plotted. Defauls observed variables model. standardized residuals standardized? takes effect resplot = \"time\". covariates Data frame covariate values variables covariate models object. given, overrides 'covariate_quantiles'. line data frame result line drawn population. Rownames used legend label lines. covariate_quantiles argument effect fitted object covariate models. , default show three population curves, 5th percentile, 50th percentile 95th percentile covariate values used fitting model. xlab Label x axis. xlim Plot range x direction. resplot residuals plotted time predicted values? pop_curves Per default, one population curve drawn case population parameters fitted model, e.g. saem objects. case covariate model, behaviour depends value 'covariates' pred_over Named list alternative predictions obtained mkinpredict compatible mkinmod. test_log_parms Passed mean_degparms case mixed.mmkin object conf.level Passed mean_degparms case mixed.mmkin object default_log_parms Passed mean_degparms case mixed.mmkin object ymax Vector maximum y axis values maxabs Maximum absolute value residuals. used scaling y axis defaults \"auto\". ncol.legend Number columns use legend nrow.legend Number rows use legend rel.height.legend relative height legend shown top rel.height.bottom relative height bottom plot row pch_ds Symbols used plotting data. col_ds Colors used plotting observed data corresponding model prediction lines different datasets. lty_ds Line types used model predictions. frame frame drawn around plots? ... arguments passed plot.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/plot.mixed.mmkin.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object — plot.mixed.mmkin","text":"function called side effect.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/plot.mixed.mmkin.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object — plot.mixed.mmkin","text":"Covariate models currently supported saem.mmkin objects.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/plot.mixed.mmkin.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object — plot.mixed.mmkin","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/plot.mixed.mmkin.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object — plot.mixed.mmkin","text":"","code":"ds <- lapply(experimental_data_for_UBA_2019[6:10], function(x) x$data[c(\"name\", \"time\", \"value\")]) names(ds) <- paste0(\"ds \", 6:10) dfop_sfo <- mkinmod(parent = mkinsub(\"DFOP\", \"A1\"), A1 = mkinsub(\"SFO\"), quiet = TRUE) # \\dontrun{ f <- mmkin(list(\"DFOP-SFO\" = dfop_sfo), ds, quiet = TRUE) plot(f[, 3:4], standardized = TRUE) # For this fit we need to increase pnlsMaxiter, and we increase the # tolerance in order to speed up the fit for this example evaluation # It still takes 20 seconds to run f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-3)) plot(f_nlme) f_saem <- saem(f, transformations = \"saemix\") plot(f_saem) f_obs <- mmkin(list(\"DFOP-SFO\" = dfop_sfo), ds, quiet = TRUE, error_model = \"obs\") f_nlmix <- nlmix(f_obs) #> Error in nlmix(f_obs): could not find function \"nlmix\" plot(f_nlmix) #> Error in eval(expr, envir, enclos): object 'f_nlmix' not found # We can overlay the two variants if we generate predictions pred_nlme <- mkinpredict(dfop_sfo, f_nlme$bparms.optim[-1], c(parent = f_nlme$bparms.optim[[1]], A1 = 0), seq(0, 180, by = 0.2)) plot(f_saem, pred_over = list(nlme = pred_nlme)) # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/plot.mkinfit.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit","title":"Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit","text":"Solves differential equations optimised fixed parameters previous successful call mkinfit plots observed data together solution fitted model.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/plot.mkinfit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit","text":"","code":"# S3 method for mkinfit plot( x, fit = x, obs_vars = names(fit$mkinmod$map), xlab = \"Time\", ylab = \"Residue\", xlim = range(fit$data$time), ylim = \"default\", col_obs = 1:length(obs_vars), pch_obs = col_obs, lty_obs = rep(1, length(obs_vars)), add = FALSE, legend = !add, show_residuals = FALSE, show_errplot = FALSE, maxabs = \"auto\", sep_obs = FALSE, rel.height.middle = 0.9, row_layout = FALSE, lpos = \"topright\", inset = c(0.05, 0.05), show_errmin = FALSE, errmin_digits = 3, frame = TRUE, ... ) plot_sep( fit, show_errmin = TRUE, show_residuals = ifelse(identical(fit$err_mod, \"const\"), TRUE, \"standardized\"), ... ) plot_res( fit, sep_obs = FALSE, show_errmin = sep_obs, standardized = ifelse(identical(fit$err_mod, \"const\"), FALSE, TRUE), ... ) plot_err(fit, sep_obs = FALSE, show_errmin = sep_obs, ...)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/plot.mkinfit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit","text":"x Alias fit introduced compatibility generic S3 method. fit object class mkinfit. obs_vars character vector names observed variables data model plotted. Defauls observed variables model. xlab Label x axis. ylab Label y axis. xlim Plot range x direction. ylim Plot range y direction. given list, plot ranges different plot rows can given row layout. col_obs Colors used plotting observed data corresponding model prediction lines. pch_obs Symbols used plotting data. lty_obs Line types used model predictions. add plot added existing plot? legend legend added plot? show_residuals residuals shown? one plot fits shown, residual plot lower third plot. Otherwise, .e. \"sep_obs\" given, residual plots located right plots fitted curves. set 'standardized', plot residuals divided standard deviation given fitted error model shown. show_errplot squared residuals error model shown? one plot fits shown, plot lower third plot. Otherwise, .e. \"sep_obs\" given, residual plots located right plots fitted curves. maxabs Maximum absolute value residuals. used scaling y axis defaults \"auto\". sep_obs observed variables shown separate subplots? yes, residual plots requested \"show_residuals\" shown next , plot fits. rel.height.middle relative height middle plot, two rows plots shown. row_layout use row layout residual plot error model plot shown right? lpos Position(s) legend(s). Passed legend first argument. length one, length obs_var argument. inset Passed legend applicable. show_errmin FOCUS chi2 error value shown upper margin plot? errmin_digits number significant digits rounding FOCUS chi2 error percentage. frame frame drawn around plots? ... arguments passed plot. standardized calling 'plot_res', residuals standardized residual plot?","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/plot.mkinfit.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit","text":"function called side effect.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/plot.mkinfit.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit","text":"current plot device tikz device, latex used formatting chi2 error level, show_errmin = TRUE.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/plot.mkinfit.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/plot.mkinfit.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit","text":"","code":"# One parent compound, one metabolite, both single first order, path from # parent to sink included # \\dontrun{ SFO_SFO <- mkinmod(parent = mkinsub(\"SFO\", \"m1\", full = \"Parent\"), m1 = mkinsub(\"SFO\", full = \"Metabolite M1\" )) #> Temporary DLL for differentials generated and loaded fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE) #> Warning: Observations with value of zero were removed from the data fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, error_model = \"tc\") #> Warning: Observations with value of zero were removed from the data plot(fit) plot_res(fit) plot_res(fit, standardized = FALSE) plot_err(fit) # Show the observed variables separately, with residuals plot(fit, sep_obs = TRUE, show_residuals = TRUE, lpos = c(\"topright\", \"bottomright\"), show_errmin = TRUE) # The same can be obtained with less typing, using the convenience function plot_sep plot_sep(fit, lpos = c(\"topright\", \"bottomright\")) # Show the observed variables separately, with the error model plot(fit, sep_obs = TRUE, show_errplot = TRUE, lpos = c(\"topright\", \"bottomright\"), show_errmin = TRUE) # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/plot.mmkin.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot model fits (observed and fitted) and the residuals for a row or column\nof an mmkin object — plot.mmkin","title":"Plot model fits (observed and fitted) and the residuals for a row or column\nof an mmkin object — plot.mmkin","text":"x row selected mmkin object ([.mmkin), model fitted least one dataset shown. column, fit least one model dataset shown.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/plot.mmkin.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot model fits (observed and fitted) and the residuals for a row or column\nof an mmkin object — plot.mmkin","text":"","code":"# S3 method for mmkin plot( x, main = \"auto\", legends = 1, resplot = c(\"time\", \"errmod\"), ylab = \"Residue\", standardized = FALSE, show_errmin = TRUE, errmin_var = \"All data\", errmin_digits = 3, cex = 0.7, rel.height.middle = 0.9, ymax = \"auto\", ... )"},{"path":"https://pkgdown.jrwb.de/mkin/reference/plot.mmkin.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot model fits (observed and fitted) and the residuals for a row or column\nof an mmkin object — plot.mmkin","text":"x object class mmkin, either one row one column. main main title placed outer margin plot. legends index fits legends shown. resplot residuals plotted time, using mkinresplot, squared residuals predicted values, error model, using mkinerrplot. ylab Label y axis. standardized residuals standardized? option passed mkinresplot, takes effect resplot = \"time\". show_errmin chi2 error level shown top plots left? errmin_var variable FOCUS chi2 error value shown. errmin_digits number significant digits rounding FOCUS chi2 error percentage. cex Passed plot functions mtext. rel.height.middle relative height middle plot, two rows plots shown. ymax Maximum y axis value plot.mkinfit. ... arguments passed plot.mkinfit mkinresplot.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/plot.mmkin.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot model fits (observed and fitted) and the residuals for a row or column\nof an mmkin object — plot.mmkin","text":"function called side effect.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/plot.mmkin.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Plot model fits (observed and fitted) and the residuals for a row or column\nof an mmkin object — plot.mmkin","text":"current plot device tikz device, latex used formatting chi2 error level.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/plot.mmkin.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plot model fits (observed and fitted) and the residuals for a row or column\nof an mmkin object — plot.mmkin","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/plot.mmkin.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot model fits (observed and fitted) and the residuals for a row or column\nof an mmkin object — plot.mmkin","text":"","code":"# \\dontrun{ # Only use one core not to offend CRAN checks fits <- mmkin(c(\"FOMC\", \"HS\"), list(\"FOCUS B\" = FOCUS_2006_B, \"FOCUS C\" = FOCUS_2006_C), # named list for titles cores = 1, quiet = TRUE, error_model = \"tc\") #> Warning: Optimisation did not converge: #> iteration limit reached without convergence (10) plot(fits[, \"FOCUS C\"]) plot(fits[\"FOMC\", ]) plot(fits[\"FOMC\", ], show_errmin = FALSE) # We can also plot a single fit, if we like the way plot.mmkin works, but then the plot # height should be smaller than the plot width (this is not possible for the html pages # generated by pkgdown, as far as I know). plot(fits[\"FOMC\", \"FOCUS C\"]) # same as plot(fits[1, 2]) # Show the error models plot(fits[\"FOMC\", ], resplot = \"errmod\") # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/plot.nafta.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot the results of the three models used in the NAFTA scheme. — plot.nafta","title":"Plot the results of the three models used in the NAFTA scheme. — plot.nafta","text":"plots ordered increasing complexity model function (SFO, IORE, DFOP).","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/plot.nafta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot the results of the three models used in the NAFTA scheme. — plot.nafta","text":"","code":"# S3 method for nafta plot(x, legend = FALSE, main = \"auto\", ...)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/plot.nafta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot the results of the three models used in the NAFTA scheme. — plot.nafta","text":"x object class nafta. legend legend added? main Possibility override main title plot. ... arguments passed plot.mmkin.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/plot.nafta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot the results of the three models used in the NAFTA scheme. — plot.nafta","text":"function called side effect.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/plot.nafta.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Plot the results of the three models used in the NAFTA scheme. — plot.nafta","text":"Calls plot.mmkin.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/plot.nafta.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Plot the results of the three models used in the NAFTA scheme. — plot.nafta","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/read_spreadsheet.html","id":null,"dir":"Reference","previous_headings":"","what":"Read datasets and relevant meta information from a spreadsheet file — read_spreadsheet","title":"Read datasets and relevant meta information from a spreadsheet file — read_spreadsheet","text":"function imports one dataset sheet spreadsheet file. sheets selected based contents sheet 'Datasets', column called 'Dataset Number', containing numbers identifying dataset sheets read . second column must grouping variable, often named 'Soil'. Optionally, time normalization factors can given columns named 'Temperature' 'Moisture'.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/read_spreadsheet.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read datasets and relevant meta information from a spreadsheet file — read_spreadsheet","text":"","code":"read_spreadsheet( path, valid_datasets = \"all\", parent_only = FALSE, normalize = TRUE )"},{"path":"https://pkgdown.jrwb.de/mkin/reference/read_spreadsheet.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read datasets and relevant meta information from a spreadsheet file — read_spreadsheet","text":"path Absolute relative path spreadsheet file valid_datasets Optional numeric index valid datasets, default use datasets parent_only parent data used? normalize time scale normalized using temperature moisture normalisation factors sheet 'Datasets'?","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/read_spreadsheet.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Read datasets and relevant meta information from a spreadsheet file — read_spreadsheet","text":"must sheet 'Compounds', columns 'Name' 'Acronym'. first row read header read sheet assumed contain name acronym parent compound. dataset sheets named using dataset numbers read 'Datasets' sheet, .e. '1', '2', ... . dataset sheet, name observed variable (e.g. acronym parent compound one transformation products) first column, time values second colum, observed value third column. case relevant covariate data available, given sheet 'Covariates', containing one line value grouping variable specified 'Datasets'. values first column column must name second column 'Datasets'. Covariates read columns four higher. names preferably contain special characters like spaces, can easily used specifying covariate models. similar data structure defined R6 class mkindsg, probably complicated use.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/reexports.html","id":null,"dir":"Reference","previous_headings":"","what":"Objects exported from other packages — reexports","title":"Objects exported from other packages — reexports","text":"objects imported packages. Follow links see documentation. lmtest lrtest nlme intervals, nlme","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/residuals.mkinfit.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract residuals from an mkinfit model — residuals.mkinfit","title":"Extract residuals from an mkinfit model — residuals.mkinfit","text":"Extract residuals mkinfit model","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/residuals.mkinfit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract residuals from an mkinfit model — residuals.mkinfit","text":"","code":"# S3 method for mkinfit residuals(object, standardized = FALSE, ...)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/residuals.mkinfit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract residuals from an mkinfit model — residuals.mkinfit","text":"object mkinfit object standardized residuals standardized dividing standard deviation obtained fitted error model? ... used","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/residuals.mkinfit.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Extract residuals from an mkinfit model — residuals.mkinfit","text":"","code":"f <- mkinfit(\"DFOP\", FOCUS_2006_C, quiet = TRUE) residuals(f) #> [1] 0.09726374 -0.13912142 -0.15351210 0.73388322 -0.08657004 -0.93204702 #> [7] -0.03269080 1.45347823 -0.88423697 residuals(f, standardized = TRUE) #> [1] 0.13969917 -0.19981904 -0.22048826 1.05407091 -0.12433989 -1.33869208 #> [7] -0.04695355 2.08761977 -1.27002287"},{"path":"https://pkgdown.jrwb.de/mkin/reference/saem.html","id":null,"dir":"Reference","previous_headings":"","what":"Fit nonlinear mixed models with SAEM — saem","title":"Fit nonlinear mixed models with SAEM — saem","text":"function uses saemix::saemix() backend fitting nonlinear mixed effects models created mmkin row objects using Stochastic Approximation Expectation Maximisation algorithm (SAEM).","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/saem.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Fit nonlinear mixed models with SAEM — saem","text":"","code":"saem(object, ...) # S3 method for mmkin saem( object, transformations = c(\"mkin\", \"saemix\"), error_model = \"auto\", degparms_start = numeric(), test_log_parms = TRUE, conf.level = 0.6, solution_type = \"auto\", covariance.model = \"auto\", omega.init = \"auto\", covariates = NULL, covariate_models = NULL, no_random_effect = NULL, error.init = c(1, 1), nbiter.saemix = c(300, 100), control = list(displayProgress = FALSE, print = FALSE, nbiter.saemix = nbiter.saemix, save = FALSE, save.graphs = FALSE), verbose = FALSE, quiet = FALSE, ... ) # S3 method for saem.mmkin print(x, digits = max(3, getOption(\"digits\") - 3), ...) saemix_model( object, solution_type = \"auto\", transformations = c(\"mkin\", \"saemix\"), error_model = \"auto\", degparms_start = numeric(), covariance.model = \"auto\", no_random_effect = NULL, omega.init = \"auto\", covariates = NULL, covariate_models = NULL, error.init = numeric(), test_log_parms = FALSE, conf.level = 0.6, verbose = FALSE, ... ) saemix_data(object, covariates = NULL, verbose = FALSE, ...)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/saem.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Fit nonlinear mixed models with SAEM — saem","text":"object mmkin row object containing several fits mkinmod model different datasets ... parameters passed saemix::saemixModel. transformations Per default, parameter transformations done mkin. argument set 'saemix', parameter transformations done 'saemix' supported cases, .e. (version 1.1.2) SFO, FOMC, DFOP HS without fixing parent_0, SFO DFOP one SFO metabolite. error_model Possibility override error model used mmkin object degparms_start Parameter values given named numeric vector used override starting values obtained 'mmkin' object. test_log_parms TRUE, attempt made use robust starting values population parameters fitted log parameters mkin (like rate constants) considering rate constants pass t-test calculating mean degradation parameters using mean_degparms. conf.level Possibility adjust required confidence level parameter tested requested 'test_log_parms'. solution_type Possibility specify solution type case automatic choice desired covariance.model passed saemix::saemixModel(). Per default, uncorrelated random effects specified degradation parameters. omega.init passed saemix::saemixModel(). using mkin transformations default covariance model optionally excluded random effects, variances degradation parameters estimated using mean_degparms, testing untransformed log parameters significant difference zero. using mkin transformations custom covariance model, default initialisation saemix::saemixModel used omega.init. covariates data frame covariate data use 'covariate_models', dataset names row names. covariate_models list containing linear model formulas one explanatory variable, .e. type 'parameter ~ covariate'. Covariates must available 'covariates' data frame. no_random_effect Character vector degradation parameters variability groups. used covariance model explicitly specified. error.init passed saemix::saemixModel(). nbiter.saemix Convenience option increase number iterations control Passed saemix::saemix. verbose print information created objects type saemix::SaemixModel saemix::SaemixData? quiet suppress messages saemix prints beginning end optimisation process? x saem.mmkin object print digits Number digits use printing","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/saem.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Fit nonlinear mixed models with SAEM — saem","text":"S3 object class 'saem.mmkin', containing fitted saemix::SaemixObject list component named ''. object also inherits 'mixed.mmkin'. saemix::SaemixModel object. saemix::SaemixData object.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/saem.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Fit nonlinear mixed models with SAEM — saem","text":"mmkin row object essentially list mkinfit objects obtained fitting model list datasets using mkinfit. Starting values fixed effects (population mean parameters, argument psi0 saemix::saemixModel() mean values parameters found using mmkin.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/reference/saem.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Fit nonlinear mixed models with SAEM — saem","text":"","code":"# \\dontrun{ ds <- lapply(experimental_data_for_UBA_2019[6:10], function(x) subset(x$data[c(\"name\", \"time\", \"value\")])) names(ds) <- paste(\"Dataset\", 6:10) f_mmkin_parent_p0_fixed <- mmkin(\"FOMC\", ds, state.ini = c(parent = 100), fixed_initials = \"parent\", quiet = TRUE) f_saem_p0_fixed <- saem(f_mmkin_parent_p0_fixed) f_mmkin_parent <- mmkin(c(\"SFO\", \"FOMC\", \"DFOP\"), ds, quiet = TRUE) f_saem_sfo <- saem(f_mmkin_parent[\"SFO\", ]) f_saem_fomc <- saem(f_mmkin_parent[\"FOMC\", ]) f_saem_dfop <- saem(f_mmkin_parent[\"DFOP\", ]) anova(f_saem_sfo, f_saem_fomc, f_saem_dfop) #> Data: 90 observations of 1 variable(s) grouped in 5 datasets #> #> npar AIC BIC Lik #> f_saem_sfo 5 624.33 622.38 -307.17 #> f_saem_fomc 7 467.85 465.11 -226.92 #> f_saem_dfop 9 493.76 490.24 -237.88 anova(f_saem_sfo, f_saem_dfop, test = TRUE) #> Data: 90 observations of 1 variable(s) grouped in 5 datasets #> #> npar AIC BIC Lik Chisq Df Pr(>Chisq) #> f_saem_sfo 5 624.33 622.38 -307.17 #> f_saem_dfop 9 493.76 490.24 -237.88 138.57 4 < 2.2e-16 *** #> --- #> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 illparms(f_saem_dfop) #> [1] \"sd(g_qlogis)\" f_saem_dfop_red <- update(f_saem_dfop, no_random_effect = \"g_qlogis\") anova(f_saem_dfop, f_saem_dfop_red, test = TRUE) #> Data: 90 observations of 1 variable(s) grouped in 5 datasets #> #> npar AIC BIC Lik Chisq Df Pr(>Chisq) #> f_saem_dfop_red 8 488.68 485.55 -236.34 #> f_saem_dfop 9 493.76 490.24 -237.88 0 1 1 anova(f_saem_sfo, f_saem_fomc, f_saem_dfop) #> Data: 90 observations of 1 variable(s) grouped in 5 datasets #> #> npar AIC BIC Lik #> f_saem_sfo 5 624.33 622.38 -307.17 #> f_saem_fomc 7 467.85 465.11 -226.92 #> f_saem_dfop 9 493.76 490.24 -237.88 # The returned saem.mmkin object contains an SaemixObject, therefore we can use # functions from saemix library(saemix) #> Loading required package: npde #> Package saemix, version 3.2 #> please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr #> #> Attaching package: ‘saemix’ #> The following objects are masked from ‘package:npde’: #> #> kurtosis, skewness compare.saemix(f_saem_sfo$so, f_saem_fomc$so, f_saem_dfop$so) #> Likelihoods calculated by importance sampling #> AIC BIC #> 1 624.3316 622.3788 #> 2 467.8472 465.1132 #> 3 493.7592 490.2441 plot(f_saem_fomc$so, plot.type = \"convergence\") plot(f_saem_fomc$so, plot.type = \"individual.fit\") #> Simulating data using nsim = 1000 simulated datasets #> Computing WRES and npde . plot(f_saem_fomc$so, plot.type = \"npde\") #> Simulating data using nsim = 1000 simulated datasets #> Computing WRES and npde . #> Please use npdeSaemix to obtain VPC and npde plot(f_saem_fomc$so, plot.type = \"vpc\") f_mmkin_parent_tc <- update(f_mmkin_parent, error_model = \"tc\") f_saem_fomc_tc <- saem(f_mmkin_parent_tc[\"FOMC\", ]) anova(f_saem_fomc, f_saem_fomc_tc, test = TRUE) #> Data: 90 observations of 1 variable(s) grouped in 5 datasets #> #> npar AIC BIC Lik Chisq Df Pr(>Chisq) #> f_saem_fomc 7 467.85 465.11 -226.92 #> f_saem_fomc_tc 8 469.90 466.77 -226.95 0 1 1 sfo_sfo <- mkinmod(parent = mkinsub(\"SFO\", \"A1\"), A1 = mkinsub(\"SFO\")) #> Temporary DLL for differentials generated and loaded fomc_sfo <- mkinmod(parent = mkinsub(\"FOMC\", \"A1\"), A1 = mkinsub(\"SFO\")) #> Temporary DLL for differentials generated and loaded dfop_sfo <- mkinmod(parent = mkinsub(\"DFOP\", \"A1\"), A1 = mkinsub(\"SFO\")) #> Temporary DLL for differentials generated and loaded # The following fit uses analytical solutions for SFO-SFO and DFOP-SFO, # and compiled ODEs for FOMC that are much slower f_mmkin <- mmkin(list( \"SFO-SFO\" = sfo_sfo, \"FOMC-SFO\" = fomc_sfo, \"DFOP-SFO\" = dfop_sfo), ds, quiet = TRUE) # saem fits of SFO-SFO and DFOP-SFO to these data take about five seconds # each on this system, as we use analytical solutions written for saemix. # When using the analytical solutions written for mkin this took around # four minutes f_saem_sfo_sfo <- saem(f_mmkin[\"SFO-SFO\", ]) f_saem_dfop_sfo <- saem(f_mmkin[\"DFOP-SFO\", ]) # We can use print, plot and summary methods to check the results print(f_saem_dfop_sfo) #> Kinetic nonlinear mixed-effects model fit by SAEM #> Structural model: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * #> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) #> * parent #> d_A1/dt = + f_parent_to_A1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) #> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * #> exp(-k2 * time))) * parent - k_A1 * A1 #> #> Data: #> 170 observations of 2 variable(s) grouped in 5 datasets #> #> Likelihood computed by importance sampling #> AIC BIC logLik #> 839.2 834.1 -406.6 #> #> Fitted parameters: #> estimate lower upper #> parent_0 93.70402 91.04104 96.3670 #> log_k_A1 -5.83760 -7.66452 -4.0107 #> f_parent_qlogis -0.95718 -1.35955 -0.5548 #> log_k1 -2.35514 -3.39402 -1.3163 #> log_k2 -3.79634 -5.64009 -1.9526 #> g_qlogis -0.02108 -0.66463 0.6225 #> a.1 1.88191 1.66491 2.0989 #> SD.parent_0 2.81628 0.78922 4.8433 #> SD.log_k_A1 1.78751 0.42105 3.1540 #> SD.f_parent_qlogis 0.45016 0.16116 0.7391 #> SD.log_k1 1.06923 0.31676 1.8217 #> SD.log_k2 2.03768 0.70938 3.3660 #> SD.g_qlogis 0.44024 -0.09262 0.9731 plot(f_saem_dfop_sfo) summary(f_saem_dfop_sfo, data = TRUE) #> saemix version used for fitting: 3.2 #> mkin version used for pre-fitting: 1.2.6 #> R version used for fitting: 4.3.2 #> Date of fit: Thu Nov 16 04:17:34 2023 #> Date of summary: Thu Nov 16 04:17:34 2023 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * #> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) #> * parent #> d_A1/dt = + f_parent_to_A1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) #> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * #> exp(-k2 * time))) * parent - k_A1 * A1 #> #> Data: #> 170 observations of 2 variable(s) grouped in 5 datasets #> #> Model predictions using solution type analytical #> #> Fitted in 3.385 s #> Using 300, 100 iterations and 10 chains #> #> Variance model: Constant variance #> #> Starting values for degradation parameters: #> parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2 #> 93.8102 -5.3734 -0.9711 -1.8799 -4.2708 #> g_qlogis #> 0.1356 #> #> Fixed degradation parameter values: #> None #> #> Starting values for random effects (square root of initial entries in omega): #> parent_0 log_k_A1 f_parent_qlogis log_k1 log_k2 g_qlogis #> parent_0 4.941 0.000 0.0000 0.000 0.000 0.0000 #> log_k_A1 0.000 2.551 0.0000 0.000 0.000 0.0000 #> f_parent_qlogis 0.000 0.000 0.7251 0.000 0.000 0.0000 #> log_k1 0.000 0.000 0.0000 1.449 0.000 0.0000 #> log_k2 0.000 0.000 0.0000 0.000 2.228 0.0000 #> g_qlogis 0.000 0.000 0.0000 0.000 0.000 0.7814 #> #> Starting values for error model parameters: #> a.1 #> 1 #> #> Results: #> #> Likelihood computed by importance sampling #> AIC BIC logLik #> 839.2 834.1 -406.6 #> #> Optimised parameters: #> est. lower upper #> parent_0 93.70402 91.04104 96.3670 #> log_k_A1 -5.83760 -7.66452 -4.0107 #> f_parent_qlogis -0.95718 -1.35955 -0.5548 #> log_k1 -2.35514 -3.39402 -1.3163 #> log_k2 -3.79634 -5.64009 -1.9526 #> g_qlogis -0.02108 -0.66463 0.6225 #> a.1 1.88191 1.66491 2.0989 #> SD.parent_0 2.81628 0.78922 4.8433 #> SD.log_k_A1 1.78751 0.42105 3.1540 #> SD.f_parent_qlogis 0.45016 0.16116 0.7391 #> SD.log_k1 1.06923 0.31676 1.8217 #> SD.log_k2 2.03768 0.70938 3.3660 #> SD.g_qlogis 0.44024 -0.09262 0.9731 #> #> Correlation: #> parnt_0 lg_k_A1 f_prnt_ log_k1 log_k2 #> log_k_A1 -0.0147 #> f_parent_qlogis -0.0269 0.0573 #> log_k1 0.0263 -0.0011 -0.0040 #> log_k2 0.0020 0.0065 -0.0002 -0.0776 #> g_qlogis -0.0248 -0.0180 -0.0004 -0.0903 -0.0603 #> #> Random effects: #> est. lower upper #> SD.parent_0 2.8163 0.78922 4.8433 #> SD.log_k_A1 1.7875 0.42105 3.1540 #> SD.f_parent_qlogis 0.4502 0.16116 0.7391 #> SD.log_k1 1.0692 0.31676 1.8217 #> SD.log_k2 2.0377 0.70938 3.3660 #> SD.g_qlogis 0.4402 -0.09262 0.9731 #> #> Variance model: #> est. lower upper #> a.1 1.882 1.665 2.099 #> #> Backtransformed parameters: #> est. lower upper #> parent_0 93.704015 9.104e+01 96.36699 #> k_A1 0.002916 4.692e-04 0.01812 #> f_parent_to_A1 0.277443 2.043e-01 0.36475 #> k1 0.094880 3.357e-02 0.26813 #> k2 0.022453 3.553e-03 0.14191 #> g 0.494731 3.397e-01 0.65078 #> #> Resulting formation fractions: #> ff #> parent_A1 0.2774 #> parent_sink 0.7226 #> #> Estimated disappearance times: #> DT50 DT90 DT50back DT50_k1 DT50_k2 #> parent 14.0 72.38 21.79 7.306 30.87 #> A1 237.7 789.68 NA NA NA #> #> Data: #> ds name time observed predicted residual std standardized #> Dataset 6 parent 0 97.2 95.70025 1.49975 1.882 0.79693 #> Dataset 6 parent 0 96.4 95.70025 0.69975 1.882 0.37183 #> Dataset 6 parent 3 71.1 71.44670 -0.34670 1.882 -0.18423 #> Dataset 6 parent 3 69.2 71.44670 -2.24670 1.882 -1.19384 #> Dataset 6 parent 6 58.1 56.59283 1.50717 1.882 0.80087 #> Dataset 6 parent 6 56.6 56.59283 0.00717 1.882 0.00381 #> Dataset 6 parent 10 44.4 44.56648 -0.16648 1.882 -0.08847 #> Dataset 6 parent 10 43.4 44.56648 -1.16648 1.882 -0.61984 #> Dataset 6 parent 20 33.3 29.76020 3.53980 1.882 1.88096 #> Dataset 6 parent 20 29.2 29.76020 -0.56020 1.882 -0.29767 #> Dataset 6 parent 34 17.6 19.39208 -1.79208 1.882 -0.95226 #> Dataset 6 parent 34 18.0 19.39208 -1.39208 1.882 -0.73971 #> Dataset 6 parent 55 10.5 10.55761 -0.05761 1.882 -0.03061 #> Dataset 6 parent 55 9.3 10.55761 -1.25761 1.882 -0.66826 #> Dataset 6 parent 90 4.5 3.84742 0.65258 1.882 0.34676 #> Dataset 6 parent 90 4.7 3.84742 0.85258 1.882 0.45304 #> Dataset 6 parent 112 3.0 2.03997 0.96003 1.882 0.51013 #> Dataset 6 parent 112 3.4 2.03997 1.36003 1.882 0.72268 #> Dataset 6 parent 132 2.3 1.14585 1.15415 1.882 0.61328 #> Dataset 6 parent 132 2.7 1.14585 1.55415 1.882 0.82583 #> Dataset 6 A1 3 4.3 4.86054 -0.56054 1.882 -0.29786 #> Dataset 6 A1 3 4.6 4.86054 -0.26054 1.882 -0.13844 #> Dataset 6 A1 6 7.0 7.74179 -0.74179 1.882 -0.39417 #> Dataset 6 A1 6 7.2 7.74179 -0.54179 1.882 -0.28789 #> Dataset 6 A1 10 8.2 9.94048 -1.74048 1.882 -0.92485 #> Dataset 6 A1 10 8.0 9.94048 -1.94048 1.882 -1.03112 #> Dataset 6 A1 20 11.0 12.19109 -1.19109 1.882 -0.63291 #> Dataset 6 A1 20 13.7 12.19109 1.50891 1.882 0.80180 #> Dataset 6 A1 34 11.5 13.10706 -1.60706 1.882 -0.85395 #> Dataset 6 A1 34 12.7 13.10706 -0.40706 1.882 -0.21630 #> Dataset 6 A1 55 14.9 13.06131 1.83869 1.882 0.97703 #> Dataset 6 A1 55 14.5 13.06131 1.43869 1.882 0.76448 #> Dataset 6 A1 90 12.1 11.54495 0.55505 1.882 0.29494 #> Dataset 6 A1 90 12.3 11.54495 0.75505 1.882 0.40122 #> Dataset 6 A1 112 9.9 10.31533 -0.41533 1.882 -0.22070 #> Dataset 6 A1 112 10.2 10.31533 -0.11533 1.882 -0.06128 #> Dataset 6 A1 132 8.8 9.20222 -0.40222 1.882 -0.21373 #> Dataset 6 A1 132 7.8 9.20222 -1.40222 1.882 -0.74510 #> Dataset 7 parent 0 93.6 90.82357 2.77643 1.882 1.47532 #> Dataset 7 parent 0 92.3 90.82357 1.47643 1.882 0.78453 #> Dataset 7 parent 3 87.0 84.73448 2.26552 1.882 1.20384 #> Dataset 7 parent 3 82.2 84.73448 -2.53448 1.882 -1.34675 #> Dataset 7 parent 7 74.0 77.65013 -3.65013 1.882 -1.93958 #> Dataset 7 parent 7 73.9 77.65013 -3.75013 1.882 -1.99272 #> Dataset 7 parent 14 64.2 67.60639 -3.40639 1.882 -1.81007 #> Dataset 7 parent 14 69.5 67.60639 1.89361 1.882 1.00621 #> Dataset 7 parent 30 54.0 52.53663 1.46337 1.882 0.77760 #> Dataset 7 parent 30 54.6 52.53663 2.06337 1.882 1.09642 #> Dataset 7 parent 60 41.1 39.42728 1.67272 1.882 0.88884 #> Dataset 7 parent 60 38.4 39.42728 -1.02728 1.882 -0.54587 #> Dataset 7 parent 90 32.5 33.76360 -1.26360 1.882 -0.67144 #> Dataset 7 parent 90 35.5 33.76360 1.73640 1.882 0.92268 #> Dataset 7 parent 120 28.1 30.39975 -2.29975 1.882 -1.22203 #> Dataset 7 parent 120 29.0 30.39975 -1.39975 1.882 -0.74379 #> Dataset 7 parent 180 26.5 25.62379 0.87621 1.882 0.46559 #> Dataset 7 parent 180 27.6 25.62379 1.97621 1.882 1.05010 #> Dataset 7 A1 3 3.9 2.70005 1.19995 1.882 0.63762 #> Dataset 7 A1 3 3.1 2.70005 0.39995 1.882 0.21252 #> Dataset 7 A1 7 6.9 5.83475 1.06525 1.882 0.56605 #> Dataset 7 A1 7 6.6 5.83475 0.76525 1.882 0.40663 #> Dataset 7 A1 14 10.4 10.26142 0.13858 1.882 0.07364 #> Dataset 7 A1 14 8.3 10.26142 -1.96142 1.882 -1.04225 #> Dataset 7 A1 30 14.4 16.82999 -2.42999 1.882 -1.29123 #> Dataset 7 A1 30 13.7 16.82999 -3.12999 1.882 -1.66319 #> Dataset 7 A1 60 22.1 22.32486 -0.22486 1.882 -0.11949 #> Dataset 7 A1 60 22.3 22.32486 -0.02486 1.882 -0.01321 #> Dataset 7 A1 90 27.5 24.45927 3.04073 1.882 1.61576 #> Dataset 7 A1 90 25.4 24.45927 0.94073 1.882 0.49988 #> Dataset 7 A1 120 28.0 25.54862 2.45138 1.882 1.30260 #> Dataset 7 A1 120 26.6 25.54862 1.05138 1.882 0.55868 #> Dataset 7 A1 180 25.8 26.82277 -1.02277 1.882 -0.54347 #> Dataset 7 A1 180 25.3 26.82277 -1.52277 1.882 -0.80916 #> Dataset 8 parent 0 91.9 91.16791 0.73209 1.882 0.38901 #> Dataset 8 parent 0 90.8 91.16791 -0.36791 1.882 -0.19550 #> Dataset 8 parent 1 64.9 67.58358 -2.68358 1.882 -1.42598 #> Dataset 8 parent 1 66.2 67.58358 -1.38358 1.882 -0.73520 #> Dataset 8 parent 3 43.5 41.62086 1.87914 1.882 0.99853 #> Dataset 8 parent 3 44.1 41.62086 2.47914 1.882 1.31735 #> Dataset 8 parent 8 18.3 19.60116 -1.30116 1.882 -0.69140 #> Dataset 8 parent 8 18.1 19.60116 -1.50116 1.882 -0.79768 #> Dataset 8 parent 14 10.2 10.63101 -0.43101 1.882 -0.22903 #> Dataset 8 parent 14 10.8 10.63101 0.16899 1.882 0.08980 #> Dataset 8 parent 27 4.9 3.12435 1.77565 1.882 0.94354 #> Dataset 8 parent 27 3.3 3.12435 0.17565 1.882 0.09334 #> Dataset 8 parent 48 1.6 0.43578 1.16422 1.882 0.61864 #> Dataset 8 parent 48 1.5 0.43578 1.06422 1.882 0.56550 #> Dataset 8 parent 70 1.1 0.05534 1.04466 1.882 0.55510 #> Dataset 8 parent 70 0.9 0.05534 0.84466 1.882 0.44883 #> Dataset 8 A1 1 9.6 7.63450 1.96550 1.882 1.04442 #> Dataset 8 A1 1 7.7 7.63450 0.06550 1.882 0.03481 #> Dataset 8 A1 3 15.0 15.52593 -0.52593 1.882 -0.27947 #> Dataset 8 A1 3 15.1 15.52593 -0.42593 1.882 -0.22633 #> Dataset 8 A1 8 21.2 20.32192 0.87808 1.882 0.46659 #> Dataset 8 A1 8 21.1 20.32192 0.77808 1.882 0.41345 #> Dataset 8 A1 14 19.7 20.09721 -0.39721 1.882 -0.21107 #> Dataset 8 A1 14 18.9 20.09721 -1.19721 1.882 -0.63617 #> Dataset 8 A1 27 17.5 16.37477 1.12523 1.882 0.59792 #> Dataset 8 A1 27 15.9 16.37477 -0.47477 1.882 -0.25228 #> Dataset 8 A1 48 9.5 10.13141 -0.63141 1.882 -0.33551 #> Dataset 8 A1 48 9.8 10.13141 -0.33141 1.882 -0.17610 #> Dataset 8 A1 70 6.2 5.81827 0.38173 1.882 0.20284 #> Dataset 8 A1 70 6.1 5.81827 0.28173 1.882 0.14970 #> Dataset 9 parent 0 99.8 97.48728 2.31272 1.882 1.22892 #> Dataset 9 parent 0 98.3 97.48728 0.81272 1.882 0.43186 #> Dataset 9 parent 1 77.1 79.29476 -2.19476 1.882 -1.16624 #> Dataset 9 parent 1 77.2 79.29476 -2.09476 1.882 -1.11310 #> Dataset 9 parent 3 59.0 55.67060 3.32940 1.882 1.76915 #> Dataset 9 parent 3 58.1 55.67060 2.42940 1.882 1.29092 #> Dataset 9 parent 8 27.4 31.57871 -4.17871 1.882 -2.22046 #> Dataset 9 parent 8 29.2 31.57871 -2.37871 1.882 -1.26398 #> Dataset 9 parent 14 19.1 22.51546 -3.41546 1.882 -1.81489 #> Dataset 9 parent 14 29.6 22.51546 7.08454 1.882 3.76454 #> Dataset 9 parent 27 10.1 14.09074 -3.99074 1.882 -2.12057 #> Dataset 9 parent 27 18.2 14.09074 4.10926 1.882 2.18355 #> Dataset 9 parent 48 4.5 6.95747 -2.45747 1.882 -1.30584 #> Dataset 9 parent 48 9.1 6.95747 2.14253 1.882 1.13848 #> Dataset 9 parent 70 2.3 3.32472 -1.02472 1.882 -0.54451 #> Dataset 9 parent 70 2.9 3.32472 -0.42472 1.882 -0.22569 #> Dataset 9 parent 91 2.0 1.64300 0.35700 1.882 0.18970 #> Dataset 9 parent 91 1.8 1.64300 0.15700 1.882 0.08343 #> Dataset 9 parent 120 2.0 0.62073 1.37927 1.882 0.73291 #> Dataset 9 parent 120 2.2 0.62073 1.57927 1.882 0.83918 #> Dataset 9 A1 1 4.2 3.64568 0.55432 1.882 0.29455 #> Dataset 9 A1 1 3.9 3.64568 0.25432 1.882 0.13514 #> Dataset 9 A1 3 7.4 8.30173 -0.90173 1.882 -0.47916 #> Dataset 9 A1 3 7.9 8.30173 -0.40173 1.882 -0.21347 #> Dataset 9 A1 8 14.5 12.71589 1.78411 1.882 0.94803 #> Dataset 9 A1 8 13.7 12.71589 0.98411 1.882 0.52293 #> Dataset 9 A1 14 14.2 13.90452 0.29548 1.882 0.15701 #> Dataset 9 A1 14 12.2 13.90452 -1.70452 1.882 -0.90574 #> Dataset 9 A1 27 13.7 14.15523 -0.45523 1.882 -0.24190 #> Dataset 9 A1 27 13.2 14.15523 -0.95523 1.882 -0.50759 #> Dataset 9 A1 48 13.6 13.31038 0.28962 1.882 0.15389 #> Dataset 9 A1 48 15.4 13.31038 2.08962 1.882 1.11037 #> Dataset 9 A1 70 10.4 11.85965 -1.45965 1.882 -0.77562 #> Dataset 9 A1 70 11.6 11.85965 -0.25965 1.882 -0.13797 #> Dataset 9 A1 91 10.0 10.36294 -0.36294 1.882 -0.19286 #> Dataset 9 A1 91 9.5 10.36294 -0.86294 1.882 -0.45855 #> Dataset 9 A1 120 9.1 8.43003 0.66997 1.882 0.35601 #> Dataset 9 A1 120 9.0 8.43003 0.56997 1.882 0.30287 #> Dataset 10 parent 0 96.1 93.95603 2.14397 1.882 1.13925 #> Dataset 10 parent 0 94.3 93.95603 0.34397 1.882 0.18278 #> Dataset 10 parent 8 73.9 77.70592 -3.80592 1.882 -2.02237 #> Dataset 10 parent 8 73.9 77.70592 -3.80592 1.882 -2.02237 #> Dataset 10 parent 14 69.4 70.04570 -0.64570 1.882 -0.34311 #> Dataset 10 parent 14 73.1 70.04570 3.05430 1.882 1.62298 #> Dataset 10 parent 21 65.6 64.01710 1.58290 1.882 0.84111 #> Dataset 10 parent 21 65.3 64.01710 1.28290 1.882 0.68170 #> Dataset 10 parent 41 55.9 54.98434 0.91566 1.882 0.48656 #> Dataset 10 parent 41 54.4 54.98434 -0.58434 1.882 -0.31050 #> Dataset 10 parent 63 47.0 49.87137 -2.87137 1.882 -1.52577 #> Dataset 10 parent 63 49.3 49.87137 -0.57137 1.882 -0.30361 #> Dataset 10 parent 91 44.7 45.06727 -0.36727 1.882 -0.19516 #> Dataset 10 parent 91 46.7 45.06727 1.63273 1.882 0.86759 #> Dataset 10 parent 120 42.1 40.76402 1.33598 1.882 0.70991 #> Dataset 10 parent 120 41.3 40.76402 0.53598 1.882 0.28481 #> Dataset 10 A1 8 3.3 4.14599 -0.84599 1.882 -0.44954 #> Dataset 10 A1 8 3.4 4.14599 -0.74599 1.882 -0.39640 #> Dataset 10 A1 14 3.9 6.08478 -2.18478 1.882 -1.16093 #> Dataset 10 A1 14 2.9 6.08478 -3.18478 1.882 -1.69231 #> Dataset 10 A1 21 6.4 7.59411 -1.19411 1.882 -0.63452 #> Dataset 10 A1 21 7.2 7.59411 -0.39411 1.882 -0.20942 #> Dataset 10 A1 41 9.1 9.78292 -0.68292 1.882 -0.36289 #> Dataset 10 A1 41 8.5 9.78292 -1.28292 1.882 -0.68171 #> Dataset 10 A1 63 11.7 10.93274 0.76726 1.882 0.40770 #> Dataset 10 A1 63 12.0 10.93274 1.06726 1.882 0.56711 #> Dataset 10 A1 91 13.3 11.93986 1.36014 1.882 0.72274 #> Dataset 10 A1 91 13.2 11.93986 1.26014 1.882 0.66961 #> Dataset 10 A1 120 14.3 12.79238 1.50762 1.882 0.80111 #> Dataset 10 A1 120 12.1 12.79238 -0.69238 1.882 -0.36791 # The following takes about 6 minutes f_saem_dfop_sfo_deSolve <- saem(f_mmkin[\"DFOP-SFO\", ], solution_type = \"deSolve\", nbiter.saemix = c(200, 80)) #> DINTDY- T (=R1) illegal #> In above message, R1 = 70 #> #> T not in interval TCUR - HU (= R1) to TCUR (=R2) #> In above message, R1 = 53.1042, R2 = 56.6326 #> #> DINTDY- T (=R1) illegal #> In above message, R1 = 91 #> #> T not in interval TCUR - HU (= R1) to TCUR (=R2) #> In above message, R1 = 53.1042, R2 = 56.6326 #> #> DLSODA- Trouble in DINTDY. ITASK = I1, TOUT = R1 #> In above message, I1 = 1 #> #> In above message, R1 = 91 #> #> Error in deSolve::lsoda(y = odeini, times = outtimes, func = lsoda_func, : #> illegal input detected before taking any integration steps - see written message #anova( # f_saem_dfop_sfo, # f_saem_dfop_sfo_deSolve)) # If the model supports it, we can also use eigenvalue based solutions, which # take a similar amount of time #f_saem_sfo_sfo_eigen <- saem(f_mmkin[\"SFO-SFO\", ], solution_type = \"eigen\", # control = list(nbiter.saemix = c(200, 80), nbdisplay = 10)) # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/schaefer07_complex_case.html","id":null,"dir":"Reference","previous_headings":"","what":"Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case","title":"Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case","text":"dataset used comparison KinGUI ModelMaker check software quality KinGUI original publication (Schäfer et al., 2007). results fitting also included.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/schaefer07_complex_case.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case","text":"","code":"schaefer07_complex_case"},{"path":"https://pkgdown.jrwb.de/mkin/reference/schaefer07_complex_case.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case","text":"data set data frame 8 observations following 6 variables. time numeric vector parent numeric vector A1 numeric vector B1 numeric vector C1 numeric vector A2 numeric vector results data frame 14 results different parameter values","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/schaefer07_complex_case.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case","text":"Schäfer D, Mikolasch B, Rainbird P Harvey B (2007). KinGUI: new kinetic software tool evaluations according FOCUS degradation kinetics. : Del Re AAM, Capri E, Fragoulis G Trevisan M (Eds.). Proceedings XIII Symposium Pesticide Chemistry, Piacenza, 2007, p. 916-923.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/schaefer07_complex_case.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case","text":"","code":"data <- mkin_wide_to_long(schaefer07_complex_case, time = \"time\") model <- mkinmod( parent = list(type = \"SFO\", to = c(\"A1\", \"B1\", \"C1\"), sink = FALSE), A1 = list(type = \"SFO\", to = \"A2\"), B1 = list(type = \"SFO\"), C1 = list(type = \"SFO\"), A2 = list(type = \"SFO\"), use_of_ff = \"max\") #> Temporary DLL for differentials generated and loaded # \\dontrun{ fit <- mkinfit(model, data, quiet = TRUE) plot(fit) endpoints(fit) #> $ff #> parent_A1 parent_B1 parent_C1 parent_sink A1_A2 A1_sink #> 0.3809618 0.1954668 0.4235714 0.0000000 0.4479540 0.5520460 #> #> $distimes #> DT50 DT90 #> parent 13.95078 46.34349 #> A1 49.75347 165.27745 #> B1 37.26905 123.80511 #> C1 11.23129 37.30955 #> A2 28.50690 94.69789 #> # } # Compare with the results obtained in the original publication print(schaefer07_complex_results) #> compound parameter KinGUI ModelMaker deviation #> 1 parent degradation rate 0.0496 0.0506 2.0 #> 2 parent DT50 13.9900 13.6900 2.2 #> 3 metabolite A1 formation fraction 0.3803 0.3696 2.9 #> 4 metabolite A1 degradation rate 0.0139 0.0136 2.2 #> 5 metabolite A1 DT50 49.9600 50.8900 1.8 #> 6 metabolite B1 formation fraction 0.1866 0.1818 2.6 #> 7 metabolite B1 degradation rate 0.0175 0.0172 1.7 #> 8 metabolite B1 DT50 39.6100 40.2400 1.6 #> 9 metabolite C1 formation fraction 0.4331 0.4486 3.5 #> 10 metabolite C1 degradation rate 0.0638 0.0700 8.9 #> 11 metabolite C1 DT50 10.8700 9.9000 9.8 #> 12 metabolite A2 formation fraction 0.4529 0.4559 0.7 #> 13 metabolite A2 degradation rate 0.0245 0.0244 0.4 #> 14 metabolite A2 DT50 28.2400 28.4500 0.7"},{"path":"https://pkgdown.jrwb.de/mkin/reference/set_nd_nq.html","id":null,"dir":"Reference","previous_headings":"","what":"Set non-detects and unquantified values in residue series without replicates — set_nd_nq","title":"Set non-detects and unquantified values in residue series without replicates — set_nd_nq","text":"function automates replacing unquantified values residue time depth series. time series, function performs part residue processing proposed FOCUS kinetics guidance parent compounds metabolites. two-dimensional residue series time depth, automates proposal Boesten et al (2015).","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/set_nd_nq.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set non-detects and unquantified values in residue series without replicates — set_nd_nq","text":"","code":"set_nd_nq(res_raw, lod, loq = NA, time_zero_presence = FALSE) set_nd_nq_focus( res_raw, lod, loq = NA, set_first_sample_nd = TRUE, first_sample_nd_value = 0, ignore_below_loq_after_first_nd = TRUE )"},{"path":"https://pkgdown.jrwb.de/mkin/reference/set_nd_nq.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set non-detects and unquantified values in residue series without replicates — set_nd_nq","text":"res_raw Character vector residue time series, matrix residue values rows representing depth profiles specific sampling time, columns representing time series residues depth. Values limit detection (lod) coded \"nd\", values limit detection limit quantification, , coded \"nq\". Samples analysed coded \"na\". values \"na\", \"nd\" \"nq\" coercible numeric lod Limit detection (numeric) loq Limit quantification(numeric). Must specified FOCUS rule stop first non-detection applied time_zero_presence assume residues occur time zero? affects samples first sampling time reported \"nd\" (detected). set_first_sample_nd first sample set \"first_sample_nd_value\" case non-detection? first_sample_nd_value Value used first sample non-detection ignore_below_loq_after_first_nd ignore values LOQ first non-detection occurs quantified values?","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/set_nd_nq.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set non-detects and unquantified values in residue series without replicates — set_nd_nq","text":"numeric vector, vector supplied, numeric matrix otherwise","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/set_nd_nq.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Set non-detects and unquantified values in residue series without replicates — set_nd_nq","text":"set_nd_nq_focus(): Set non-detects residue time series according FOCUS rules","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/set_nd_nq.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Set non-detects and unquantified values in residue series without replicates — set_nd_nq","text":"Boesten, J. J. T. ., van der Linden, . M. ., Beltman, W. H. J. Pol, J. W. (2015). Leaching plant protection products transformation products; Proposals improving assessment leaching groundwater Netherlands — Version 2. Alterra report 2630, Alterra Wageningen UR (University & Research centre) FOCUS (2014) Generic Guidance Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration, Version 1.1, 18 December 2014, p. 251","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/set_nd_nq.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set non-detects and unquantified values in residue series without replicates — set_nd_nq","text":"","code":"# FOCUS (2014) p. 75/76 and 131/132 parent_1 <- c(.12, .09, .05, .03, \"nd\", \"nd\", \"nd\", \"nd\", \"nd\", \"nd\") set_nd_nq(parent_1, 0.02) #> [1] 0.12 0.09 0.05 0.03 0.01 NA NA NA NA NA parent_2 <- c(.12, .09, .05, .03, \"nd\", \"nd\", .03, \"nd\", \"nd\", \"nd\") set_nd_nq(parent_2, 0.02) #> [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.03 0.01 NA NA set_nd_nq_focus(parent_2, 0.02, loq = 0.05) #> [1] 0.12 0.09 0.05 0.03 0.01 NA NA NA NA NA parent_3 <- c(.12, .09, .05, .03, \"nd\", \"nd\", .06, \"nd\", \"nd\", \"nd\") set_nd_nq(parent_3, 0.02) #> [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.06 0.01 NA NA set_nd_nq_focus(parent_3, 0.02, loq = 0.05) #> [1] 0.12 0.09 0.05 0.03 0.01 0.01 0.06 0.01 NA NA metabolite <- c(\"nd\", \"nd\", \"nd\", 0.03, 0.06, 0.10, 0.11, 0.10, 0.09, 0.05, 0.03, \"nd\", \"nd\") set_nd_nq(metabolite, 0.02) #> [1] NA NA 0.01 0.03 0.06 0.10 0.11 0.10 0.09 0.05 0.03 0.01 NA set_nd_nq_focus(metabolite, 0.02, 0.05) #> [1] 0.00 NA 0.01 0.03 0.06 0.10 0.11 0.10 0.09 0.05 0.03 0.01 NA # # Boesten et al. (2015), p. 57/58 table_8 <- matrix( c(10, 10, rep(\"nd\", 4), 10, 10, rep(\"nq\", 2), rep(\"nd\", 2), 10, 10, 10, \"nq\", \"nd\", \"nd\", \"nq\", 10, \"nq\", rep(\"nd\", 3), \"nd\", \"nq\", \"nq\", rep(\"nd\", 3), rep(\"nd\", 6), rep(\"nd\", 6)), ncol = 6, byrow = TRUE) set_nd_nq(table_8, 0.5, 1.5, time_zero_presence = TRUE) #> [,1] [,2] [,3] [,4] [,5] [,6] #> [1,] 10.00 10.00 0.25 0.25 NA NA #> [2,] 10.00 10.00 1.00 1.00 0.25 NA #> [3,] 10.00 10.00 10.00 1.00 0.25 NA #> [4,] 1.00 10.00 1.00 0.25 NA NA #> [5,] 0.25 1.00 1.00 0.25 NA NA #> [6,] NA 0.25 0.25 NA NA NA #> [7,] NA NA NA NA NA NA table_10 <- matrix( c(10, 10, rep(\"nd\", 4), 10, 10, rep(\"nd\", 4), 10, 10, 10, rep(\"nd\", 3), \"nd\", 10, rep(\"nd\", 4), rep(\"nd\", 18)), ncol = 6, byrow = TRUE) set_nd_nq(table_10, 0.5, time_zero_presence = TRUE) #> [,1] [,2] [,3] [,4] [,5] [,6] #> [1,] 10.00 10.00 0.25 NA NA NA #> [2,] 10.00 10.00 0.25 NA NA NA #> [3,] 10.00 10.00 10.00 0.25 NA NA #> [4,] 0.25 10.00 0.25 NA NA NA #> [5,] NA 0.25 NA NA NA NA #> [6,] NA NA NA NA NA NA #> [7,] NA NA NA NA NA NA"},{"path":"https://pkgdown.jrwb.de/mkin/reference/sigma_twocomp.html","id":null,"dir":"Reference","previous_headings":"","what":"Two-component error model — sigma_twocomp","title":"Two-component error model — sigma_twocomp","text":"Function describing standard deviation measurement error dependence measured value \\(y\\):","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/sigma_twocomp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Two-component error model — sigma_twocomp","text":"","code":"sigma_twocomp(y, sigma_low, rsd_high)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/sigma_twocomp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Two-component error model — sigma_twocomp","text":"y magnitude observed value sigma_low asymptotic minimum standard deviation low observed values rsd_high coefficient describing increase standard deviation magnitude observed value","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/sigma_twocomp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Two-component error model — sigma_twocomp","text":"standard deviation response variable.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/sigma_twocomp.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Two-component error model — sigma_twocomp","text":"$$\\sigma = \\sqrt{ \\sigma_{low}^2 + y^2 * {rsd}_{high}^2}$$ sigma = sqrt(sigma_low^2 + y^2 * rsd_high^2) error model used example Werner et al. (1978). model proposed Rocke Lorenzato (1995) can written form well, assumes approximate lognormal distribution errors high values y.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/sigma_twocomp.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Two-component error model — sigma_twocomp","text":"Werner, Mario, Brooks, Samuel H., Knott, Lancaster B. (1978) Additive, Multiplicative, Mixed Analytical Errors. Clinical Chemistry 24(11), 1895-1898. Rocke, David M. Lorenzato, Stefan (1995) two-component model measurement error analytical chemistry. Technometrics 37(2), 176-184. Ranke J Meinecke S (2019) Error Models Kinetic Evaluation Chemical Degradation Data. Environments 6(12) 124 doi:10.3390/environments6120124 .","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/sigma_twocomp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Two-component error model — sigma_twocomp","text":"","code":"times <- c(0, 1, 3, 7, 14, 28, 60, 90, 120) d_pred <- data.frame(time = times, parent = 100 * exp(- 0.03 * times)) set.seed(123456) d_syn <- add_err(d_pred, function(y) sigma_twocomp(y, 1, 0.07), reps = 2, n = 1)[[1]] f_nls <- nls(value ~ SSasymp(time, 0, parent_0, lrc), data = d_syn, start = list(parent_0 = 100, lrc = -3)) library(nlme) f_gnls <- gnls(value ~ SSasymp(time, 0, parent_0, lrc), data = d_syn, na.action = na.omit, start = list(parent_0 = 100, lrc = -3)) if (length(findFunction(\"varConstProp\")) > 0) { f_gnls_tc <- update(f_gnls, weights = varConstProp()) f_gnls_tc_sf <- update(f_gnls_tc, control = list(sigma = 1)) } f_mkin <- mkinfit(\"SFO\", d_syn, error_model = \"const\", quiet = TRUE) f_mkin_tc <- mkinfit(\"SFO\", d_syn, error_model = \"tc\", quiet = TRUE) plot_res(f_mkin_tc, standardized = TRUE) AIC(f_nls, f_gnls, f_gnls_tc, f_gnls_tc_sf, f_mkin, f_mkin_tc) #> df AIC #> f_nls 3 114.4817 #> f_gnls 3 114.4817 #> f_gnls_tc 5 103.6447 #> f_gnls_tc_sf 4 101.6447 #> f_mkin 3 114.4817 #> f_mkin_tc 4 101.6446"},{"path":"https://pkgdown.jrwb.de/mkin/reference/status.html","id":null,"dir":"Reference","previous_headings":"","what":"Method to get status information for fit array objects — status","title":"Method to get status information for fit array objects — status","text":"Method get status information fit array objects","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/status.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Method to get status information for fit array objects — status","text":"","code":"status(object, ...) # S3 method for mmkin status(object, ...) # S3 method for status.mmkin print(x, ...) # S3 method for mhmkin status(object, ...) # S3 method for status.mhmkin print(x, ...)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/status.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Method to get status information for fit array objects — status","text":"object object investigate ... potential future extensions x object printed","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/status.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Method to get status information for fit array objects — status","text":"object dimensions fit array suitable printing method.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/status.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Method to get status information for fit array objects — status","text":"","code":"# \\dontrun{ fits <- mmkin( c(\"SFO\", \"FOMC\"), list(\"FOCUS A\" = FOCUS_2006_A, \"FOCUS B\" = FOCUS_2006_C), quiet = TRUE) status(fits) #> dataset #> model FOCUS A FOCUS B #> SFO OK OK #> FOMC C OK #> #> C: Optimisation did not converge: #> false convergence (8) #> OK: No warnings # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/summary.mkinfit.html","id":null,"dir":"Reference","previous_headings":"","what":"Summary method for class ","title":"Summary method for class ","text":"Lists model equations, initial parameter values, optimised parameters uncertainty statistics, chi2 error levels calculated according FOCUS guidance (2006) defined therein, formation fractions, DT50 values optionally data, consisting observed, predicted residual values.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/summary.mkinfit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summary method for class ","text":"","code":"# S3 method for mkinfit summary(object, data = TRUE, distimes = TRUE, alpha = 0.05, ...) # S3 method for summary.mkinfit print(x, digits = max(3, getOption(\"digits\") - 3), ...)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/summary.mkinfit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summary method for class ","text":"object object class mkinfit. data logical, indicating whether data included summary. distimes logical, indicating whether DT50 DT90 values included. alpha error level confidence interval estimation t distribution ... optional arguments passed methods like print. x object class summary.mkinfit. digits Number digits use printing","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/summary.mkinfit.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summary method for class ","text":"summary function returns list components, among others version, Rversion mkin R versions used date.fit, date.summary dates fit summary produced diffs differential equations used model use_of_ff maximum minimum use made formation fractions bpar Optimised backtransformed parameters data data (see Description ). start starting values bounds, applicable, optimised parameters. fixed values fixed parameters. errmin chi2 error levels observed variable. bparms.ode backtransformed ODE parameters, use starting parameters related models. errparms Error model parameters. ff estimated formation fractions derived fitted model. distimes DT50 DT90 values observed variable. SFORB applicable, eigenvalues fractional eigenvector component g SFORB systems model. print method called side effect, .e. printing summary.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/summary.mkinfit.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Summary method for class ","text":"FOCUS (2006) “Guidance Document Estimating Persistence Degradation Kinetics Environmental Fate Studies Pesticides EU Registration” Report FOCUS Work Group Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/summary.mkinfit.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Summary method for class ","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/summary.mkinfit.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summary method for class ","text":"","code":"summary(mkinfit(\"SFO\", FOCUS_2006_A, quiet = TRUE)) #> mkin version used for fitting: 1.2.6 #> R version used for fitting: 4.3.2 #> Date of fit: Thu Nov 16 04:19:39 2023 #> Date of summary: Thu Nov 16 04:19:39 2023 #> #> Equations: #> d_parent/dt = - k_parent * parent #> #> Model predictions using solution type analytical #> #> Fitted using 131 model solutions performed in 0.009 s #> #> Error model: Constant variance #> #> Error model algorithm: OLS #> #> Starting values for parameters to be optimised: #> value type #> parent_0 101.24 state #> k_parent 0.10 deparm #> #> Starting values for the transformed parameters actually optimised: #> value lower upper #> parent_0 101.240000 -Inf Inf #> log_k_parent -2.302585 -Inf Inf #> #> Fixed parameter values: #> None #> #> Results: #> #> AIC BIC logLik #> 55.28197 55.5203 -24.64099 #> #> Optimised, transformed parameters with symmetric confidence intervals: #> Estimate Std. Error Lower Upper #> parent_0 109.200 3.70400 99.630 118.700 #> log_k_parent -3.291 0.09176 -3.527 -3.055 #> sigma 5.266 1.31600 1.882 8.649 #> #> Parameter correlation: #> parent_0 log_k_parent sigma #> parent_0 1.000e+00 5.428e-01 1.642e-07 #> log_k_parent 5.428e-01 1.000e+00 2.507e-07 #> sigma 1.642e-07 2.507e-07 1.000e+00 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. #> t-test (unrealistically) based on the assumption of normal distribution #> for estimators of untransformed parameters. #> Estimate t value Pr(>t) Lower Upper #> parent_0 109.20000 29.47 4.218e-07 99.6300 118.70000 #> k_parent 0.03722 10.90 5.650e-05 0.0294 0.04712 #> sigma 5.26600 4.00 5.162e-03 1.8820 8.64900 #> #> FOCUS Chi2 error levels in percent: #> err.min n.optim df #> All data 8.385 2 6 #> parent 8.385 2 6 #> #> Estimated disappearance times: #> DT50 DT90 #> parent 18.62 61.87 #> #> Data: #> time variable observed predicted residual #> 0 parent 101.24 109.153 -7.9132 #> 3 parent 99.27 97.622 1.6484 #> 7 parent 90.11 84.119 5.9913 #> 14 parent 72.19 64.826 7.3641 #> 30 parent 29.71 35.738 -6.0283 #> 62 parent 5.98 10.862 -4.8818 #> 90 parent 1.54 3.831 -2.2911 #> 118 parent 0.39 1.351 -0.9613"},{"path":"https://pkgdown.jrwb.de/mkin/reference/summary.mmkin.html","id":null,"dir":"Reference","previous_headings":"","what":"Summary method for class ","title":"Summary method for class ","text":"Shows status information mkinfit objects contained object gives overview ill-defined parameters calculated illparms.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/summary.mmkin.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summary method for class ","text":"","code":"# S3 method for mmkin summary(object, conf.level = 0.95, ...) # S3 method for summary.mmkin print(x, digits = max(3, getOption(\"digits\") - 3), ...)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/summary.mmkin.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summary method for class ","text":"object object class mmkin conf.level confidence level testing parameters ... optional arguments passed methods like print. x object class summary.mmkin. digits number digits use printing","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/summary.mmkin.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summary method for class ","text":"","code":"fits <- mmkin( c(\"SFO\", \"FOMC\"), list(\"FOCUS A\" = FOCUS_2006_A, \"FOCUS C\" = FOCUS_2006_C), quiet = TRUE, cores = 1) #> Warning: Optimisation did not converge: #> false convergence (8) summary(fits) #> Error model: Constant variance #> Fitted in 0.454 s #> #> Status: #> dataset #> model FOCUS A FOCUS C #> SFO OK OK #> FOMC C OK #> #> C: Optimisation did not converge: #> false convergence (8) #> OK: No warnings #> #> Ill-defined parameters: #> dataset #> model FOCUS A FOCUS C #> SFO #> FOMC parent_0, alpha, beta, sigma"},{"path":"https://pkgdown.jrwb.de/mkin/reference/summary.nlme.mmkin.html","id":null,"dir":"Reference","previous_headings":"","what":"Summary method for class ","title":"Summary method for class ","text":"Lists model equations, initial parameter values, optimised parameters fixed effects (population), random effects (deviations population mean) residual error model, well resulting endpoints formation fractions DT50 values. Optionally (default FALSE), data listed full.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/summary.nlme.mmkin.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summary method for class ","text":"","code":"# S3 method for nlme.mmkin summary( object, data = FALSE, verbose = FALSE, distimes = TRUE, alpha = 0.05, ... ) # S3 method for summary.nlme.mmkin print(x, digits = max(3, getOption(\"digits\") - 3), verbose = x$verbose, ...)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/summary.nlme.mmkin.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summary method for class ","text":"object object class nlme.mmkin data logical, indicating whether full data included summary. verbose summary verbose? distimes logical, indicating whether DT50 DT90 values included. alpha error level confidence interval estimation t distribution ... optional arguments passed methods like print. x object class summary.nlme.mmkin digits Number digits use printing","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/summary.nlme.mmkin.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summary method for class ","text":"summary function returns list based nlme object obtained fit, least following additional components nlmeversion, mkinversion, Rversion nlme, mkin R versions used date.fit, date.summary dates fit summary produced diffs differential equations used degradation model use_of_ff maximum minimum use made formation fractions data data confint_trans Transformed parameters used optimisation, confidence intervals confint_back Backtransformed parameters, confidence intervals available ff estimated formation fractions derived fitted model. distimes DT50 DT90 values observed variable. SFORB applicable, eigenvalues SFORB components model. print method called side effect, .e. printing summary.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/summary.nlme.mmkin.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Summary method for class ","text":"Johannes Ranke mkin specific parts José Pinheiro Douglas Bates components inherited nlme","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/summary.nlme.mmkin.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summary method for class ","text":"","code":"# Generate five datasets following SFO kinetics sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) dt50_sfo_in_pop <- 50 k_in_pop <- log(2) / dt50_sfo_in_pop set.seed(1234) k_in <- rlnorm(5, log(k_in_pop), 0.5) SFO <- mkinmod(parent = mkinsub(\"SFO\")) pred_sfo <- function(k) { mkinpredict(SFO, c(k_parent = k), c(parent = 100), sampling_times) } ds_sfo_mean <- lapply(k_in, pred_sfo) names(ds_sfo_mean) <- paste(\"ds\", 1:5) set.seed(12345) ds_sfo_syn <- lapply(ds_sfo_mean, function(ds) { add_err(ds, sdfunc = function(value) sqrt(1^2 + value^2 * 0.07^2), n = 1)[[1]] }) # \\dontrun{ # Evaluate using mmkin and nlme library(nlme) f_mmkin <- mmkin(\"SFO\", ds_sfo_syn, quiet = TRUE, error_model = \"tc\", cores = 1) #> Warning: Optimisation did not converge: #> iteration limit reached without convergence (10) f_nlme <- nlme(f_mmkin) summary(f_nlme, data = TRUE) #> nlme version used for fitting: 3.1.163 #> mkin version used for pre-fitting: 1.2.6 #> R version used for fitting: 4.3.2 #> Date of fit: Thu Nov 16 04:19:41 2023 #> Date of summary: Thu Nov 16 04:19:41 2023 #> #> Equations: #> d_parent/dt = - k_parent * parent #> #> Data: #> 90 observations of 1 variable(s) grouped in 5 datasets #> #> Model predictions using solution type analytical #> #> Fitted in 0.182 s using 4 iterations #> #> Variance model: Two-component variance function #> #> Mean of starting values for individual parameters: #> parent_0 log_k_parent #> 101.569 -4.454 #> #> Fixed degradation parameter values: #> None #> #> Results: #> #> AIC BIC logLik #> 584.5 599.5 -286.2 #> #> Optimised, transformed parameters with symmetric confidence intervals: #> lower est. upper #> parent_0 99.371 101.592 103.814 #> log_k_parent -4.973 -4.449 -3.926 #> #> Correlation: #> parnt_0 #> log_k_parent 0.0507 #> #> Random effects: #> Formula: list(parent_0 ~ 1, log_k_parent ~ 1) #> Level: ds #> Structure: Diagonal #> parent_0 log_k_parent Residual #> StdDev: 6.921e-05 0.5863 1 #> #> Variance function: #> Structure: Constant plus proportion of variance covariate #> Formula: ~fitted(.) #> Parameter estimates: #> const prop #> 0.0001208313 0.0789967985 #> #> Backtransformed parameters with asymmetric confidence intervals: #> lower est. upper #> parent_0 99.370882 101.59243 103.81398 #> k_parent 0.006923 0.01168 0.01972 #> #> Estimated disappearance times: #> DT50 DT90 #> parent 59.32 197.1 #> #> Data: #> ds name time observed predicted residual std standardized #> ds 1 parent 0 104.1 101.592 2.50757 8.0255 0.312451 #> ds 1 parent 0 105.0 101.592 3.40757 8.0255 0.424594 #> ds 1 parent 1 98.5 100.796 -2.29571 7.9625 -0.288313 #> ds 1 parent 1 96.1 100.796 -4.69571 7.9625 -0.589725 #> ds 1 parent 3 101.9 99.221 2.67904 7.8381 0.341796 #> ds 1 parent 3 85.2 99.221 -14.02096 7.8381 -1.788812 #> ds 1 parent 7 99.1 96.145 2.95512 7.5951 0.389081 #> ds 1 parent 7 93.0 96.145 -3.14488 7.5951 -0.414065 #> ds 1 parent 14 88.1 90.989 -2.88944 7.1879 -0.401987 #> ds 1 parent 14 84.1 90.989 -6.88944 7.1879 -0.958480 #> ds 1 parent 28 80.2 81.493 -1.29305 6.4377 -0.200857 #> ds 1 parent 28 91.3 81.493 9.80695 6.4377 1.523364 #> ds 1 parent 60 65.1 63.344 1.75642 5.0039 0.351008 #> ds 1 parent 60 65.8 63.344 2.45642 5.0039 0.490898 #> ds 1 parent 90 47.8 50.018 -2.21764 3.9512 -0.561252 #> ds 1 parent 90 53.5 50.018 3.48236 3.9512 0.881335 #> ds 1 parent 120 37.6 39.495 -1.89515 3.1200 -0.607423 #> ds 1 parent 120 39.3 39.495 -0.19515 3.1200 -0.062549 #> ds 2 parent 0 107.9 101.592 6.30757 8.0255 0.785943 #> ds 2 parent 0 102.1 101.592 0.50757 8.0255 0.063245 #> ds 2 parent 1 103.8 100.058 3.74159 7.9043 0.473361 #> ds 2 parent 1 108.6 100.058 8.54159 7.9043 1.080626 #> ds 2 parent 3 91.0 97.060 -6.05952 7.6674 -0.790297 #> ds 2 parent 3 84.9 97.060 -12.15952 7.6674 -1.585874 #> ds 2 parent 7 79.3 91.329 -12.02867 7.2147 -1.667251 #> ds 2 parent 7 100.9 91.329 9.57133 7.2147 1.326647 #> ds 2 parent 14 77.3 82.102 -4.80185 6.4858 -0.740366 #> ds 2 parent 14 83.5 82.102 1.39815 6.4858 0.215571 #> ds 2 parent 28 66.8 66.351 0.44945 5.2415 0.085748 #> ds 2 parent 28 63.3 66.351 -3.05055 5.2415 -0.582002 #> ds 2 parent 60 40.8 40.775 0.02474 3.2211 0.007679 #> ds 2 parent 60 44.8 40.775 4.02474 3.2211 1.249485 #> ds 2 parent 90 27.8 25.832 1.96762 2.0407 0.964198 #> ds 2 parent 90 27.0 25.832 1.16762 2.0407 0.572171 #> ds 2 parent 120 15.2 16.366 -1.16561 1.2928 -0.901595 #> ds 2 parent 120 15.5 16.366 -0.86561 1.2928 -0.669547 #> ds 3 parent 0 97.7 101.592 -3.89243 8.0255 -0.485009 #> ds 3 parent 0 88.2 101.592 -13.39243 8.0255 -1.668740 #> ds 3 parent 1 109.9 99.218 10.68196 7.8379 1.362858 #> ds 3 parent 1 97.8 99.218 -1.41804 7.8379 -0.180921 #> ds 3 parent 3 100.5 94.634 5.86555 7.4758 0.784603 #> ds 3 parent 3 77.4 94.634 -17.23445 7.4758 -2.305360 #> ds 3 parent 7 78.3 86.093 -7.79273 6.8011 -1.145813 #> ds 3 parent 7 90.3 86.093 4.20727 6.8011 0.618620 #> ds 3 parent 14 76.0 72.958 3.04222 5.7634 0.527848 #> ds 3 parent 14 79.1 72.958 6.14222 5.7634 1.065722 #> ds 3 parent 28 46.0 52.394 -6.39404 4.1390 -1.544842 #> ds 3 parent 28 53.4 52.394 1.00596 4.1390 0.243046 #> ds 3 parent 60 25.1 24.582 0.51786 1.9419 0.266676 #> ds 3 parent 60 21.4 24.582 -3.18214 1.9419 -1.638664 #> ds 3 parent 90 11.0 12.092 -1.09202 0.9552 -1.143199 #> ds 3 parent 90 14.2 12.092 2.10798 0.9552 2.206777 #> ds 3 parent 120 5.8 5.948 -0.14810 0.4699 -0.315178 #> ds 3 parent 120 6.1 5.948 0.15190 0.4699 0.323282 #> ds 4 parent 0 95.3 101.592 -6.29243 8.0255 -0.784057 #> ds 4 parent 0 102.0 101.592 0.40757 8.0255 0.050784 #> ds 4 parent 1 104.4 101.125 3.27549 7.9885 0.410025 #> ds 4 parent 1 105.4 101.125 4.27549 7.9885 0.535205 #> ds 4 parent 3 113.7 100.195 13.50487 7.9151 1.706218 #> ds 4 parent 3 82.3 100.195 -17.89513 7.9151 -2.260886 #> ds 4 parent 7 98.1 98.362 -0.26190 7.7703 -0.033706 #> ds 4 parent 7 87.8 98.362 -10.56190 7.7703 -1.359270 #> ds 4 parent 14 97.9 95.234 2.66590 7.5232 0.354357 #> ds 4 parent 14 104.8 95.234 9.56590 7.5232 1.271521 #> ds 4 parent 28 85.0 89.274 -4.27372 7.0523 -0.606001 #> ds 4 parent 28 77.2 89.274 -12.07372 7.0523 -1.712017 #> ds 4 parent 60 82.2 77.013 5.18661 6.0838 0.852526 #> ds 4 parent 60 86.1 77.013 9.08661 6.0838 1.493571 #> ds 4 parent 90 70.5 67.053 3.44692 5.2970 0.650733 #> ds 4 parent 90 61.7 67.053 -5.35308 5.2970 -1.010591 #> ds 4 parent 120 60.0 58.381 1.61905 4.6119 0.351058 #> ds 4 parent 120 56.4 58.381 -1.98095 4.6119 -0.429530 #> ds 5 parent 0 92.6 101.592 -8.99243 8.0255 -1.120485 #> ds 5 parent 0 116.5 101.592 14.90757 8.0255 1.857531 #> ds 5 parent 1 108.0 99.914 8.08560 7.8929 1.024413 #> ds 5 parent 1 104.9 99.914 4.98560 7.8929 0.631655 #> ds 5 parent 3 100.5 96.641 3.85898 7.6343 0.505477 #> ds 5 parent 3 89.5 96.641 -7.14102 7.6343 -0.935383 #> ds 5 parent 7 91.7 90.412 1.28752 7.1423 0.180267 #> ds 5 parent 7 95.1 90.412 4.68752 7.1423 0.656304 #> ds 5 parent 14 82.2 80.463 1.73715 6.3563 0.273295 #> ds 5 parent 14 84.5 80.463 4.03715 6.3563 0.635141 #> ds 5 parent 28 60.5 63.728 -3.22788 5.0343 -0.641178 #> ds 5 parent 28 72.8 63.728 9.07212 5.0343 1.802062 #> ds 5 parent 60 38.3 37.399 0.90061 2.9544 0.304835 #> ds 5 parent 60 40.7 37.399 3.30061 2.9544 1.117174 #> ds 5 parent 90 22.5 22.692 -0.19165 1.7926 -0.106913 #> ds 5 parent 90 20.8 22.692 -1.89165 1.7926 -1.055273 #> ds 5 parent 120 13.4 13.768 -0.36790 1.0876 -0.338259 #> ds 5 parent 120 13.8 13.768 0.03210 1.0876 0.029517 # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/summary.saem.mmkin.html","id":null,"dir":"Reference","previous_headings":"","what":"Summary method for class ","title":"Summary method for class ","text":"Lists model equations, initial parameter values, optimised parameters fixed effects (population), random effects (deviations population mean) residual error model, well resulting endpoints formation fractions DT50 values. Optionally (default FALSE), data listed full.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/summary.saem.mmkin.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Summary method for class ","text":"","code":"# S3 method for saem.mmkin summary( object, data = FALSE, verbose = FALSE, covariates = NULL, covariate_quantile = 0.5, distimes = TRUE, ... ) # S3 method for summary.saem.mmkin print(x, digits = max(3, getOption(\"digits\") - 3), verbose = x$verbose, ...)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/summary.saem.mmkin.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Summary method for class ","text":"object object class saem.mmkin data logical, indicating whether full data included summary. verbose summary verbose? covariates Numeric vector covariate values variables covariate models object. given, overrides 'covariate_quantile'. covariate_quantile argument effect fitted object covariate models. , default show endpoints median covariate values (50th percentile). distimes logical, indicating whether DT50 DT90 values included. ... optional arguments passed methods like print. x object class summary.saem.mmkin digits Number digits use printing","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/summary.saem.mmkin.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Summary method for class ","text":"summary function returns list based saemix::SaemixObject obtained fit, least following additional components saemixversion, mkinversion, Rversion saemix, mkin R versions used date.fit, date.summary dates fit summary produced diffs differential equations used degradation model use_of_ff maximum minimum use made formation fractions data data confint_trans Transformed parameters used optimisation, confidence intervals confint_back Backtransformed parameters, confidence intervals available confint_errmod Error model parameters confidence intervals ff estimated formation fractions derived fitted model. distimes DT50 DT90 values observed variable. SFORB applicable, eigenvalues SFORB components model. print method called side effect, .e. printing summary.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/summary.saem.mmkin.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Summary method for class ","text":"Johannes Ranke mkin specific parts saemix authors parts inherited saemix.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/summary.saem.mmkin.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Summary method for class ","text":"","code":"# Generate five datasets following DFOP-SFO kinetics sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) dfop_sfo <- mkinmod(parent = mkinsub(\"DFOP\", \"m1\"), m1 = mkinsub(\"SFO\"), quiet = TRUE) set.seed(1234) k1_in <- rlnorm(5, log(0.1), 0.3) k2_in <- rlnorm(5, log(0.02), 0.3) g_in <- plogis(rnorm(5, qlogis(0.5), 0.3)) f_parent_to_m1_in <- plogis(rnorm(5, qlogis(0.3), 0.3)) k_m1_in <- rlnorm(5, log(0.02), 0.3) pred_dfop_sfo <- function(k1, k2, g, f_parent_to_m1, k_m1) { mkinpredict(dfop_sfo, c(k1 = k1, k2 = k2, g = g, f_parent_to_m1 = f_parent_to_m1, k_m1 = k_m1), c(parent = 100, m1 = 0), sampling_times) } ds_mean_dfop_sfo <- lapply(1:5, function(i) { mkinpredict(dfop_sfo, c(k1 = k1_in[i], k2 = k2_in[i], g = g_in[i], f_parent_to_m1 = f_parent_to_m1_in[i], k_m1 = k_m1_in[i]), c(parent = 100, m1 = 0), sampling_times) }) names(ds_mean_dfop_sfo) <- paste(\"ds\", 1:5) ds_syn_dfop_sfo <- lapply(ds_mean_dfop_sfo, function(ds) { add_err(ds, sdfunc = function(value) sqrt(1^2 + value^2 * 0.07^2), n = 1)[[1]] }) # \\dontrun{ # Evaluate using mmkin and saem f_mmkin_dfop_sfo <- mmkin(list(dfop_sfo), ds_syn_dfop_sfo, quiet = TRUE, error_model = \"tc\", cores = 5) f_saem_dfop_sfo <- saem(f_mmkin_dfop_sfo) print(f_saem_dfop_sfo) #> Kinetic nonlinear mixed-effects model fit by SAEM #> Structural model: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * #> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) #> * parent #> d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) #> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * #> exp(-k2 * time))) * parent - k_m1 * m1 #> #> Data: #> 171 observations of 2 variable(s) grouped in 5 datasets #> #> Likelihood computed by importance sampling #> AIC BIC logLik #> 810.8 805.4 -391.4 #> #> Fitted parameters: #> estimate lower upper #> parent_0 100.966822 97.90584 104.0278 #> log_k_m1 -4.076164 -4.17485 -3.9775 #> f_parent_qlogis -0.940902 -1.35358 -0.5282 #> log_k1 -2.363988 -2.71690 -2.0111 #> log_k2 -4.060016 -4.21743 -3.9026 #> g_qlogis -0.029999 -0.44766 0.3877 #> a.1 0.876272 0.67308 1.0795 #> b.1 0.079594 0.06399 0.0952 #> SD.parent_0 0.076322 -76.47330 76.6259 #> SD.log_k_m1 0.005052 -1.09071 1.1008 #> SD.f_parent_qlogis 0.446968 0.16577 0.7282 #> SD.log_k1 0.348786 0.09502 0.6025 #> SD.log_k2 0.147456 0.03111 0.2638 #> SD.g_qlogis 0.348244 0.02794 0.6686 illparms(f_saem_dfop_sfo) #> [1] \"sd(parent_0)\" \"sd(log_k_m1)\" f_saem_dfop_sfo_2 <- update(f_saem_dfop_sfo, no_random_effect = c(\"parent_0\", \"log_k_m1\")) illparms(f_saem_dfop_sfo_2) intervals(f_saem_dfop_sfo_2) #> Approximate 95% confidence intervals #> #> Fixed effects: #> lower est. upper #> parent_0 98.04247057 101.09950884 104.15654711 #> k_m1 0.01528983 0.01687734 0.01862969 #> f_parent_to_m1 0.20447650 0.27932896 0.36887691 #> k1 0.06779844 0.09638524 0.13702550 #> k2 0.01495629 0.01741775 0.02028431 #> g 0.37669311 0.48368409 0.59219202 #> #> Random effects: #> lower est. upper #> sd(f_parent_qlogis) 0.16515100 0.4448330 0.7245149 #> sd(log_k1) 0.08982372 0.3447403 0.5996568 #> sd(log_k2) 0.02806589 0.1419560 0.2558462 #> sd(g_qlogis) 0.04908160 0.3801993 0.7113170 #> #> #> lower est. upper #> a.1 0.67539922 0.87630147 1.07720371 #> b.1 0.06401324 0.07920531 0.09439739 summary(f_saem_dfop_sfo_2, data = TRUE) #> saemix version used for fitting: 3.2 #> mkin version used for pre-fitting: 1.2.6 #> R version used for fitting: 4.3.2 #> Date of fit: Thu Nov 16 04:19:57 2023 #> Date of summary: Thu Nov 16 04:19:57 2023 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * #> time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) #> * parent #> d_m1/dt = + f_parent_to_m1 * ((k1 * g * exp(-k1 * time) + k2 * (1 - g) #> * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * #> exp(-k2 * time))) * parent - k_m1 * m1 #> #> Data: #> 171 observations of 2 variable(s) grouped in 5 datasets #> #> Model predictions using solution type analytical #> #> Fitted in 9.193 s #> Using 300, 100 iterations and 10 chains #> #> Variance model: Two-component variance function #> #> Starting values for degradation parameters: #> parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 #> 101.65645 -4.05368 -0.94311 -2.35943 -4.07006 #> g_qlogis #> -0.01133 #> #> Fixed degradation parameter values: #> None #> #> Starting values for random effects (square root of initial entries in omega): #> parent_0 log_k_m1 f_parent_qlogis log_k1 log_k2 g_qlogis #> parent_0 6.742 0.0000 0.0000 0.0000 0.0000 0.000 #> log_k_m1 0.000 0.2236 0.0000 0.0000 0.0000 0.000 #> f_parent_qlogis 0.000 0.0000 0.5572 0.0000 0.0000 0.000 #> log_k1 0.000 0.0000 0.0000 0.8031 0.0000 0.000 #> log_k2 0.000 0.0000 0.0000 0.0000 0.2931 0.000 #> g_qlogis 0.000 0.0000 0.0000 0.0000 0.0000 0.807 #> #> Starting values for error model parameters: #> a.1 b.1 #> 1 1 #> #> Results: #> #> Likelihood computed by importance sampling #> AIC BIC logLik #> 806.9 802.2 -391.5 #> #> Optimised parameters: #> est. lower upper #> parent_0 101.09951 98.04247 104.1565 #> log_k_m1 -4.08178 -4.18057 -3.9830 #> f_parent_qlogis -0.94779 -1.35855 -0.5370 #> log_k1 -2.33940 -2.69122 -1.9876 #> log_k2 -4.05027 -4.20262 -3.8979 #> g_qlogis -0.06529 -0.50361 0.3730 #> a.1 0.87630 0.67540 1.0772 #> b.1 0.07921 0.06401 0.0944 #> SD.f_parent_qlogis 0.44483 0.16515 0.7245 #> SD.log_k1 0.34474 0.08982 0.5997 #> SD.log_k2 0.14196 0.02807 0.2558 #> SD.g_qlogis 0.38020 0.04908 0.7113 #> #> Correlation: #> parnt_0 lg_k_m1 f_prnt_ log_k1 log_k2 #> log_k_m1 -0.4716 #> f_parent_qlogis -0.2394 0.2617 #> log_k1 0.1677 -0.1566 -0.0659 #> log_k2 0.0165 0.0638 0.0045 0.2013 #> g_qlogis 0.1118 -0.1118 -0.0340 -0.2324 -0.3419 #> #> Random effects: #> est. lower upper #> SD.f_parent_qlogis 0.4448 0.16515 0.7245 #> SD.log_k1 0.3447 0.08982 0.5997 #> SD.log_k2 0.1420 0.02807 0.2558 #> SD.g_qlogis 0.3802 0.04908 0.7113 #> #> Variance model: #> est. lower upper #> a.1 0.87630 0.67540 1.0772 #> b.1 0.07921 0.06401 0.0944 #> #> Backtransformed parameters: #> est. lower upper #> parent_0 101.09951 98.04247 104.15655 #> k_m1 0.01688 0.01529 0.01863 #> f_parent_to_m1 0.27933 0.20448 0.36888 #> k1 0.09639 0.06780 0.13703 #> k2 0.01742 0.01496 0.02028 #> g 0.48368 0.37669 0.59219 #> #> Resulting formation fractions: #> ff #> parent_m1 0.2793 #> parent_sink 0.7207 #> #> Estimated disappearance times: #> DT50 DT90 DT50back DT50_k1 DT50_k2 #> parent 15.66 94.28 28.38 7.191 39.8 #> m1 41.07 136.43 NA NA NA #> #> Data: #> ds name time observed predicted residual std standardized #> ds 1 parent 0 89.8 1.011e+02 -11.29951 8.0554 -1.402721 #> ds 1 parent 0 104.1 1.011e+02 3.00049 8.0554 0.372481 #> ds 1 parent 1 88.7 9.624e+01 -7.53600 7.6726 -0.982195 #> ds 1 parent 1 95.5 9.624e+01 -0.73600 7.6726 -0.095925 #> ds 1 parent 3 81.8 8.736e+01 -5.55672 6.9744 -0.796732 #> ds 1 parent 3 94.5 8.736e+01 7.14328 6.9744 1.024217 #> ds 1 parent 7 71.5 7.251e+01 -1.00511 5.8093 -0.173019 #> ds 1 parent 7 70.3 7.251e+01 -2.20511 5.8093 -0.379585 #> ds 1 parent 14 54.2 5.356e+01 0.63921 4.3319 0.147560 #> ds 1 parent 14 49.6 5.356e+01 -3.96079 4.3319 -0.914340 #> ds 1 parent 28 31.5 3.175e+01 -0.25429 2.6634 -0.095475 #> ds 1 parent 28 28.8 3.175e+01 -2.95429 2.6634 -1.109218 #> ds 1 parent 60 12.1 1.281e+01 -0.71388 1.3409 -0.532390 #> ds 1 parent 60 13.6 1.281e+01 0.78612 1.3409 0.586271 #> ds 1 parent 90 6.2 6.405e+00 -0.20462 1.0125 -0.202083 #> ds 1 parent 90 8.3 6.405e+00 1.89538 1.0125 1.871910 #> ds 1 parent 120 2.2 3.329e+00 -1.12941 0.9151 -1.234165 #> ds 1 parent 120 2.4 3.329e+00 -0.92941 0.9151 -1.015615 #> ds 1 m1 1 0.3 1.177e+00 -0.87699 0.8812 -0.995168 #> ds 1 m1 1 0.2 1.177e+00 -0.97699 0.8812 -1.108644 #> ds 1 m1 3 2.2 3.268e+00 -1.06821 0.9137 -1.169063 #> ds 1 m1 3 3.0 3.268e+00 -0.26821 0.9137 -0.293536 #> ds 1 m1 7 6.5 6.555e+00 -0.05539 1.0186 -0.054377 #> ds 1 m1 7 5.0 6.555e+00 -1.55539 1.0186 -1.527022 #> ds 1 m1 14 10.2 1.017e+01 0.03108 1.1902 0.026117 #> ds 1 m1 14 9.5 1.017e+01 -0.66892 1.1902 -0.562010 #> ds 1 m1 28 12.2 1.270e+01 -0.50262 1.3342 -0.376708 #> ds 1 m1 28 13.4 1.270e+01 0.69738 1.3342 0.522686 #> ds 1 m1 60 11.8 1.078e+01 1.01734 1.2236 0.831403 #> ds 1 m1 60 13.2 1.078e+01 2.41734 1.2236 1.975530 #> ds 1 m1 90 6.6 7.686e+00 -1.08586 1.0670 -1.017675 #> ds 1 m1 90 9.3 7.686e+00 1.61414 1.0670 1.512779 #> ds 1 m1 120 3.5 5.205e+00 -1.70467 0.9684 -1.760250 #> ds 1 m1 120 5.4 5.205e+00 0.19533 0.9684 0.201701 #> ds 2 parent 0 118.0 1.011e+02 16.90049 8.0554 2.098026 #> ds 2 parent 0 99.8 1.011e+02 -1.29951 8.0554 -0.161321 #> ds 2 parent 1 90.2 9.574e+01 -5.53784 7.6334 -0.725473 #> ds 2 parent 1 94.6 9.574e+01 -1.13784 7.6334 -0.149060 #> ds 2 parent 3 96.1 8.638e+01 9.72233 6.8975 1.409551 #> ds 2 parent 3 78.4 8.638e+01 -7.97767 6.8975 -1.156610 #> ds 2 parent 7 77.9 7.194e+01 5.95854 5.7651 1.033547 #> ds 2 parent 7 77.7 7.194e+01 5.75854 5.7651 0.998856 #> ds 2 parent 14 56.0 5.558e+01 0.42141 4.4885 0.093888 #> ds 2 parent 14 54.7 5.558e+01 -0.87859 4.4885 -0.195742 #> ds 2 parent 28 36.6 3.852e+01 -1.92382 3.1746 -0.605999 #> ds 2 parent 28 36.8 3.852e+01 -1.72382 3.1746 -0.543000 #> ds 2 parent 60 22.1 2.108e+01 1.02043 1.8856 0.541168 #> ds 2 parent 60 24.7 2.108e+01 3.62043 1.8856 1.920034 #> ds 2 parent 90 12.4 1.250e+01 -0.09675 1.3220 -0.073184 #> ds 2 parent 90 10.8 1.250e+01 -1.69675 1.3220 -1.283492 #> ds 2 parent 120 6.8 7.426e+00 -0.62587 1.0554 -0.593027 #> ds 2 parent 120 7.9 7.426e+00 0.47413 1.0554 0.449242 #> ds 2 m1 1 1.3 1.417e+00 -0.11735 0.8835 -0.132825 #> ds 2 m1 3 3.7 3.823e+00 -0.12301 0.9271 -0.132673 #> ds 2 m1 3 4.7 3.823e+00 0.87699 0.9271 0.945909 #> ds 2 m1 7 8.1 7.288e+00 0.81180 1.0494 0.773619 #> ds 2 m1 7 7.9 7.288e+00 0.61180 1.0494 0.583025 #> ds 2 m1 14 10.1 1.057e+01 -0.46957 1.2119 -0.387459 #> ds 2 m1 14 10.3 1.057e+01 -0.26957 1.2119 -0.222432 #> ds 2 m1 28 10.7 1.234e+01 -1.63555 1.3124 -1.246185 #> ds 2 m1 28 12.2 1.234e+01 -0.13555 1.3124 -0.103281 #> ds 2 m1 60 10.7 1.065e+01 0.04641 1.2165 0.038151 #> ds 2 m1 60 12.5 1.065e+01 1.84641 1.2165 1.517773 #> ds 2 m1 90 9.1 8.177e+00 0.92337 1.0896 0.847403 #> ds 2 m1 90 7.4 8.177e+00 -0.77663 1.0896 -0.712734 #> ds 2 m1 120 6.1 5.966e+00 0.13404 0.9956 0.134631 #> ds 2 m1 120 4.5 5.966e+00 -1.46596 0.9956 -1.472460 #> ds 3 parent 0 106.2 1.011e+02 5.10049 8.0554 0.633175 #> ds 3 parent 0 106.9 1.011e+02 5.80049 8.0554 0.720073 #> ds 3 parent 1 107.4 9.365e+01 13.74627 7.4695 1.840332 #> ds 3 parent 1 96.1 9.365e+01 2.44627 7.4695 0.327504 #> ds 3 parent 3 79.4 8.139e+01 -1.99118 6.5059 -0.306058 #> ds 3 parent 3 82.6 8.139e+01 1.20882 6.5059 0.185803 #> ds 3 parent 7 63.9 6.445e+01 -0.54666 5.1792 -0.105549 #> ds 3 parent 7 62.4 6.445e+01 -2.04666 5.1792 -0.395170 #> ds 3 parent 14 51.0 4.830e+01 2.69944 3.9247 0.687800 #> ds 3 parent 14 47.1 4.830e+01 -1.20056 3.9247 -0.305896 #> ds 3 parent 28 36.1 3.426e+01 1.83885 2.8516 0.644839 #> ds 3 parent 28 36.6 3.426e+01 2.33885 2.8516 0.820177 #> ds 3 parent 60 20.1 1.968e+01 0.42208 1.7881 0.236053 #> ds 3 parent 60 19.8 1.968e+01 0.12208 1.7881 0.068273 #> ds 3 parent 90 11.3 1.194e+01 -0.64013 1.2893 -0.496496 #> ds 3 parent 90 10.7 1.194e+01 -1.24013 1.2893 -0.961865 #> ds 3 parent 120 8.2 7.247e+00 0.95264 1.0476 0.909381 #> ds 3 parent 120 7.3 7.247e+00 0.05264 1.0476 0.050254 #> ds 3 m1 0 0.8 -2.956e-12 0.80000 0.8763 0.912928 #> ds 3 m1 1 1.8 1.757e+00 0.04318 0.8873 0.048666 #> ds 3 m1 1 2.3 1.757e+00 0.54318 0.8873 0.612186 #> ds 3 m1 3 4.2 4.566e+00 -0.36607 0.9480 -0.386149 #> ds 3 m1 3 4.1 4.566e+00 -0.46607 0.9480 -0.491634 #> ds 3 m1 7 6.8 8.157e+00 -1.35680 1.0887 -1.246241 #> ds 3 m1 7 10.1 8.157e+00 1.94320 1.0887 1.784855 #> ds 3 m1 14 11.4 1.085e+01 0.55367 1.2272 0.451182 #> ds 3 m1 14 12.8 1.085e+01 1.95367 1.2272 1.592023 #> ds 3 m1 28 11.5 1.149e+01 0.01098 1.2633 0.008689 #> ds 3 m1 28 10.6 1.149e+01 -0.88902 1.2633 -0.703717 #> ds 3 m1 60 7.5 9.295e+00 -1.79500 1.1445 -1.568351 #> ds 3 m1 60 8.6 9.295e+00 -0.69500 1.1445 -0.607245 #> ds 3 m1 90 7.3 7.017e+00 0.28305 1.0377 0.272775 #> ds 3 m1 90 8.1 7.017e+00 1.08305 1.0377 1.043720 #> ds 3 m1 120 5.3 5.087e+00 0.21272 0.9645 0.220547 #> ds 3 m1 120 3.8 5.087e+00 -1.28728 0.9645 -1.334660 #> ds 4 parent 0 104.7 1.011e+02 3.60049 8.0554 0.446965 #> ds 4 parent 0 88.3 1.011e+02 -12.79951 8.0554 -1.588930 #> ds 4 parent 1 94.2 9.755e+01 -3.35176 7.7762 -0.431030 #> ds 4 parent 1 94.6 9.755e+01 -2.95176 7.7762 -0.379591 #> ds 4 parent 3 78.1 9.095e+01 -12.85198 7.2570 -1.770981 #> ds 4 parent 3 96.5 9.095e+01 5.54802 7.2570 0.764508 #> ds 4 parent 7 76.2 7.949e+01 -3.29267 6.3569 -0.517966 #> ds 4 parent 7 77.8 7.949e+01 -1.69267 6.3569 -0.266272 #> ds 4 parent 14 70.8 6.384e+01 6.95621 5.1321 1.355423 #> ds 4 parent 14 67.3 6.384e+01 3.45621 5.1321 0.673445 #> ds 4 parent 28 43.1 4.345e+01 -0.35291 3.5515 -0.099370 #> ds 4 parent 28 45.1 4.345e+01 1.64709 3.5515 0.463771 #> ds 4 parent 60 21.3 2.137e+01 -0.07478 1.9063 -0.039229 #> ds 4 parent 60 23.5 2.137e+01 2.12522 1.9063 1.114813 #> ds 4 parent 90 11.8 1.205e+01 -0.24925 1.2957 -0.192375 #> ds 4 parent 90 12.1 1.205e+01 0.05075 1.2957 0.039168 #> ds 4 parent 120 7.0 6.967e+00 0.03315 1.0356 0.032013 #> ds 4 parent 120 6.2 6.967e+00 -0.76685 1.0356 -0.740510 #> ds 4 m1 0 1.6 1.421e-13 1.60000 0.8763 1.825856 #> ds 4 m1 1 0.9 7.250e-01 0.17503 0.8782 0.199310 #> ds 4 m1 3 3.7 2.038e+00 1.66201 0.8910 1.865236 #> ds 4 m1 3 2.0 2.038e+00 -0.03799 0.8910 -0.042637 #> ds 4 m1 7 3.6 4.186e+00 -0.58623 0.9369 -0.625692 #> ds 4 m1 7 3.8 4.186e+00 -0.38623 0.9369 -0.412230 #> ds 4 m1 14 7.1 6.752e+00 0.34768 1.0266 0.338666 #> ds 4 m1 14 6.6 6.752e+00 -0.15232 1.0266 -0.148372 #> ds 4 m1 28 9.5 9.034e+00 0.46628 1.1313 0.412159 #> ds 4 m1 28 9.3 9.034e+00 0.26628 1.1313 0.235373 #> ds 4 m1 60 8.3 8.634e+00 -0.33359 1.1115 -0.300112 #> ds 4 m1 60 9.0 8.634e+00 0.36641 1.1115 0.329645 #> ds 4 m1 90 6.6 6.671e+00 -0.07091 1.0233 -0.069295 #> ds 4 m1 90 7.7 6.671e+00 1.02909 1.0233 1.005691 #> ds 4 m1 120 3.7 4.823e+00 -1.12301 0.9559 -1.174763 #> ds 4 m1 120 3.5 4.823e+00 -1.32301 0.9559 -1.383979 #> ds 5 parent 0 110.4 1.011e+02 9.30049 8.0554 1.154563 #> ds 5 parent 0 112.1 1.011e+02 11.00049 8.0554 1.365601 #> ds 5 parent 1 93.5 9.440e+01 -0.90098 7.5282 -0.119681 #> ds 5 parent 1 91.0 9.440e+01 -3.40098 7.5282 -0.451764 #> ds 5 parent 3 71.0 8.287e+01 -11.86698 6.6217 -1.792122 #> ds 5 parent 3 89.7 8.287e+01 6.83302 6.6217 1.031907 #> ds 5 parent 7 60.4 6.562e+01 -5.22329 5.2711 -0.990936 #> ds 5 parent 7 59.1 6.562e+01 -6.52329 5.2711 -1.237566 #> ds 5 parent 14 56.5 4.739e+01 9.10588 3.8548 2.362225 #> ds 5 parent 14 47.0 4.739e+01 -0.39412 3.8548 -0.102240 #> ds 5 parent 28 30.2 3.118e+01 -0.98128 2.6206 -0.374451 #> ds 5 parent 28 23.9 3.118e+01 -7.28128 2.6206 -2.778500 #> ds 5 parent 60 17.0 1.804e+01 -1.03959 1.6761 -0.620224 #> ds 5 parent 60 18.7 1.804e+01 0.66041 1.6761 0.394008 #> ds 5 parent 90 11.3 1.165e+01 -0.35248 1.2727 -0.276958 #> ds 5 parent 90 11.9 1.165e+01 0.24752 1.2727 0.194488 #> ds 5 parent 120 9.0 7.556e+00 1.44368 1.0612 1.360449 #> ds 5 parent 120 8.1 7.556e+00 0.54368 1.0612 0.512338 #> ds 5 m1 0 0.7 -1.421e-14 0.70000 0.8763 0.798812 #> ds 5 m1 1 3.0 3.160e+00 -0.15979 0.9113 -0.175340 #> ds 5 m1 1 2.6 3.160e+00 -0.55979 0.9113 -0.614254 #> ds 5 m1 3 5.1 8.448e+00 -3.34789 1.1026 -3.036487 #> ds 5 m1 3 7.5 8.448e+00 -0.94789 1.1026 -0.859720 #> ds 5 m1 7 16.5 1.581e+01 0.68760 1.5286 0.449839 #> ds 5 m1 7 19.0 1.581e+01 3.18760 1.5286 2.085373 #> ds 5 m1 14 22.9 2.218e+01 0.71983 1.9632 0.366658 #> ds 5 m1 14 23.2 2.218e+01 1.01983 1.9632 0.519469 #> ds 5 m1 28 22.2 2.425e+01 -2.05105 2.1113 -0.971479 #> ds 5 m1 28 24.4 2.425e+01 0.14895 2.1113 0.070552 #> ds 5 m1 60 15.5 1.876e+01 -3.25968 1.7250 -1.889646 #> ds 5 m1 60 19.8 1.876e+01 1.04032 1.7250 0.603074 #> ds 5 m1 90 14.9 1.365e+01 1.25477 1.3914 0.901806 #> ds 5 m1 90 14.2 1.365e+01 0.55477 1.3914 0.398714 #> ds 5 m1 120 10.9 9.726e+00 1.17443 1.1667 1.006587 #> ds 5 m1 120 10.4 9.726e+00 0.67443 1.1667 0.578044 # Add a correlation between random effects of g and k2 cov_model_3 <- f_saem_dfop_sfo_2$so@model@covariance.model cov_model_3[\"log_k2\", \"g_qlogis\"] <- 1 cov_model_3[\"g_qlogis\", \"log_k2\"] <- 1 f_saem_dfop_sfo_3 <- update(f_saem_dfop_sfo, covariance.model = cov_model_3) intervals(f_saem_dfop_sfo_3) #> Approximate 95% confidence intervals #> #> Fixed effects: #> lower est. upper #> parent_0 98.42519529 101.51623115 104.60726702 #> k_m1 0.01505059 0.01662123 0.01835577 #> f_parent_to_m1 0.20100222 0.27477835 0.36332008 #> k1 0.07347479 0.10139028 0.13991179 #> k2 0.01469861 0.01771120 0.02134125 #> g 0.35506898 0.46263682 0.57379888 #> #> Random effects: #> lower est. upper #> sd(f_parent_qlogis) 0.3827416 0.4435866 0.5044315 #> sd(log_k1) 0.1226277 0.2981783 0.4737289 #> sd(log_k2) -0.5457764 0.1912531 0.9282825 #> sd(g_qlogis) 0.1483976 0.3997298 0.6510619 #> corr(log_k2,g_qlogis) -0.8537145 -0.5845703 -0.3154261 #> #> #> lower est. upper #> a.1 0.6732869 0.87421677 1.0751467 #> b.1 0.0640392 0.07925135 0.0944635 # The correlation does not improve the fit judged by AIC and BIC, although # the likelihood is higher with the additional parameter anova(f_saem_dfop_sfo, f_saem_dfop_sfo_2, f_saem_dfop_sfo_3) #> Data: 171 observations of 2 variable(s) grouped in 5 datasets #> #> npar AIC BIC Lik #> f_saem_dfop_sfo_2 12 806.91 802.23 -391.46 #> f_saem_dfop_sfo_3 13 807.96 802.88 -390.98 #> f_saem_dfop_sfo 14 810.83 805.36 -391.41 # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/summary_listing.html","id":null,"dir":"Reference","previous_headings":"","what":"Display the output of a summary function according to the output format — summary_listing","title":"Display the output of a summary function according to the output format — summary_listing","text":"function intended use R markdown code chunk chunk option results = \"asis\".","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/summary_listing.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Display the output of a summary function according to the output format — summary_listing","text":"","code":"summary_listing(object, caption = NULL, label = NULL, clearpage = TRUE) tex_listing(object, caption = NULL, label = NULL, clearpage = TRUE) html_listing(object, caption = NULL)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/summary_listing.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Display the output of a summary function according to the output format — summary_listing","text":"object object summary listed caption optional caption label optional label, ignored html output clearpage new page started listing? Ignored html output","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/synthetic_data_for_UBA_2014.html","id":null,"dir":"Reference","previous_headings":"","what":"Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014","title":"Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014","text":"12 datasets generated using four different models three different variance components. four models either SFO DFOP model either two sequential two parallel metabolites. Variance component '' based normal distribution standard deviation 3, Variance component 'b' also based normal distribution, standard deviation 7. Variance component 'c' based error model Rocke Lorenzato (1995), minimum standard deviation (small y values) 0.5, proportionality constant 0.07 increase standard deviation y. Note simplified version error model proposed Rocke Lorenzato (1995), model error measured values approximates lognormal distribution high values, whereas using normally distributed error components along. Initial concentrations metabolites values adding variance component resulted value assumed limit detection 0.1 set NA. example, first dataset title SFO_lin_a based SFO model two sequential metabolites (linear pathway), added variance component ''. Compare also code example section see degradation models.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/synthetic_data_for_UBA_2014.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014","text":"","code":"synthetic_data_for_UBA_2014"},{"path":"https://pkgdown.jrwb.de/mkin/reference/synthetic_data_for_UBA_2014.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014","text":"list containing twelve datasets R6 class defined mkinds, containing, among others, following components title name dataset, e.g. SFO_lin_a data data frame data form expected mkinfit","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/synthetic_data_for_UBA_2014.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014","text":"Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452 Rocke, David M. und Lorenzato, Stefan (1995) two-component model measurement error analytical chemistry. Technometrics 37(2), 176-184.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/synthetic_data_for_UBA_2014.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014","text":"","code":"# \\dontrun{ # The data have been generated using the following kinetic models m_synth_SFO_lin <- mkinmod(parent = list(type = \"SFO\", to = \"M1\"), M1 = list(type = \"SFO\", to = \"M2\"), M2 = list(type = \"SFO\"), use_of_ff = \"max\") #> Temporary DLL for differentials generated and loaded m_synth_SFO_par <- mkinmod(parent = list(type = \"SFO\", to = c(\"M1\", \"M2\"), sink = FALSE), M1 = list(type = \"SFO\"), M2 = list(type = \"SFO\"), use_of_ff = \"max\") #> Temporary DLL for differentials generated and loaded m_synth_DFOP_lin <- mkinmod(parent = list(type = \"DFOP\", to = \"M1\"), M1 = list(type = \"SFO\", to = \"M2\"), M2 = list(type = \"SFO\"), use_of_ff = \"max\") #> Temporary DLL for differentials generated and loaded m_synth_DFOP_par <- mkinmod(parent = list(type = \"DFOP\", to = c(\"M1\", \"M2\"), sink = FALSE), M1 = list(type = \"SFO\"), M2 = list(type = \"SFO\"), use_of_ff = \"max\") #> Temporary DLL for differentials generated and loaded # The model predictions without intentional error were generated as follows sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) d_synth_SFO_lin <- mkinpredict(m_synth_SFO_lin, c(k_parent = 0.7, f_parent_to_M1 = 0.8, k_M1 = 0.3, f_M1_to_M2 = 0.7, k_M2 = 0.02), c(parent = 100, M1 = 0, M2 = 0), sampling_times) d_synth_DFOP_lin <- mkinpredict(m_synth_DFOP_lin, c(k1 = 0.2, k2 = 0.02, g = 0.5, f_parent_to_M1 = 0.5, k_M1 = 0.3, f_M1_to_M2 = 0.7, k_M2 = 0.02), c(parent = 100, M1 = 0, M2 = 0), sampling_times) d_synth_SFO_par <- mkinpredict(m_synth_SFO_par, c(k_parent = 0.2, f_parent_to_M1 = 0.8, k_M1 = 0.01, f_parent_to_M2 = 0.2, k_M2 = 0.02), c(parent = 100, M1 = 0, M2 = 0), sampling_times) d_synth_DFOP_par <- mkinpredict(m_synth_DFOP_par, c(k1 = 0.3, k2 = 0.02, g = 0.7, f_parent_to_M1 = 0.6, k_M1 = 0.04, f_parent_to_M2 = 0.4, k_M2 = 0.01), c(parent = 100, M1 = 0, M2 = 0), sampling_times) # Construct names for datasets with errors d_synth_names = paste0(\"d_synth_\", c(\"SFO_lin\", \"SFO_par\", \"DFOP_lin\", \"DFOP_par\")) # Original function used or adding errors. The add_err function now published # with this package is a slightly generalised version where the names of # secondary compartments that should have an initial value of zero (M1 and M2 # in this case) are not hardcoded any more. # add_err = function(d, sdfunc, LOD = 0.1, reps = 2, seed = 123456789) # { # set.seed(seed) # d_long = mkin_wide_to_long(d, time = \"time\") # d_rep = data.frame(lapply(d_long, rep, each = 2)) # d_rep$value = rnorm(length(d_rep$value), d_rep$value, sdfunc(d_rep$value)) # # d_rep[d_rep$time == 0 & d_rep$name %in% c(\"M1\", \"M2\"), \"value\"] <- 0 # d_NA <- transform(d_rep, value = ifelse(value < LOD, NA, value)) # d_NA$value <- round(d_NA$value, 1) # return(d_NA) # } # The following is the simplified version of the two-component model of Rocke # and Lorenzato (1995) sdfunc_twocomp = function(value, sd_low, rsd_high) { sqrt(sd_low^2 + value^2 * rsd_high^2) } # Add the errors. for (d_synth_name in d_synth_names) { d_synth = get(d_synth_name) assign(paste0(d_synth_name, \"_a\"), add_err(d_synth, function(value) 3)) assign(paste0(d_synth_name, \"_b\"), add_err(d_synth, function(value) 7)) assign(paste0(d_synth_name, \"_c\"), add_err(d_synth, function(value) sdfunc_twocomp(value, 0.5, 0.07))) } d_synth_err_names = c( paste(rep(d_synth_names, each = 3), letters[1:3], sep = \"_\") ) # This is just one example of an evaluation using the kinetic model used for # the generation of the data fit <- mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data, quiet = TRUE) plot_sep(fit) summary(fit) #> mkin version used for fitting: 1.2.6 #> R version used for fitting: 4.3.2 #> Date of fit: Thu Nov 16 04:20:07 2023 #> Date of summary: Thu Nov 16 04:20:07 2023 #> #> Equations: #> d_parent/dt = - k_parent * parent #> d_M1/dt = + f_parent_to_M1 * k_parent * parent - k_M1 * M1 #> d_M2/dt = + f_M1_to_M2 * k_M1 * M1 - k_M2 * M2 #> #> Model predictions using solution type deSolve #> #> Fitted using 848 model solutions performed in 0.166 s #> #> Error model: Constant variance #> #> Error model algorithm: OLS #> #> Starting values for parameters to be optimised: #> value type #> parent_0 101.3500 state #> k_parent 0.1000 deparm #> k_M1 0.1001 deparm #> k_M2 0.1002 deparm #> f_parent_to_M1 0.5000 deparm #> f_M1_to_M2 0.5000 deparm #> #> Starting values for the transformed parameters actually optimised: #> value lower upper #> parent_0 101.350000 -Inf Inf #> log_k_parent -2.302585 -Inf Inf #> log_k_M1 -2.301586 -Inf Inf #> log_k_M2 -2.300587 -Inf Inf #> f_parent_qlogis 0.000000 -Inf Inf #> f_M1_qlogis 0.000000 -Inf Inf #> #> Fixed parameter values: #> value type #> M1_0 0 state #> M2_0 0 state #> #> Results: #> #> AIC BIC logLik #> 188.7274 200.3723 -87.36368 #> #> Optimised, transformed parameters with symmetric confidence intervals: #> Estimate Std. Error Lower Upper #> parent_0 102.1000 1.57000 98.8600 105.3000 #> log_k_parent -0.3020 0.03885 -0.3812 -0.2229 #> log_k_M1 -1.2070 0.07123 -1.3520 -1.0620 #> log_k_M2 -3.9010 0.06571 -4.0350 -3.7670 #> f_parent_qlogis 1.2010 0.23530 0.7216 1.6800 #> f_M1_qlogis 0.9589 0.24890 0.4520 1.4660 #> sigma 2.2730 0.25740 1.7490 2.7970 #> #> Parameter correlation: #> parent_0 log_k_parent log_k_M1 log_k_M2 f_parent_qlogis #> parent_0 1.000e+00 3.933e-01 -1.605e-01 2.819e-02 -4.624e-01 #> log_k_parent 3.933e-01 1.000e+00 -4.082e-01 7.166e-02 -5.682e-01 #> log_k_M1 -1.605e-01 -4.082e-01 1.000e+00 -3.929e-01 7.478e-01 #> log_k_M2 2.819e-02 7.166e-02 -3.929e-01 1.000e+00 -2.658e-01 #> f_parent_qlogis -4.624e-01 -5.682e-01 7.478e-01 -2.658e-01 1.000e+00 #> f_M1_qlogis 1.614e-01 4.102e-01 -8.109e-01 5.419e-01 -8.605e-01 #> sigma -1.377e-08 7.536e-10 1.089e-08 -4.422e-08 7.124e-09 #> f_M1_qlogis sigma #> parent_0 1.614e-01 -1.377e-08 #> log_k_parent 4.102e-01 7.536e-10 #> log_k_M1 -8.109e-01 1.089e-08 #> log_k_M2 5.419e-01 -4.422e-08 #> f_parent_qlogis -8.605e-01 7.124e-09 #> f_M1_qlogis 1.000e+00 -2.685e-08 #> sigma -2.685e-08 1.000e+00 #> #> Backtransformed parameters: #> Confidence intervals for internally transformed parameters are asymmetric. #> t-test (unrealistically) based on the assumption of normal distribution #> for estimators of untransformed parameters. #> Estimate t value Pr(>t) Lower Upper #> parent_0 102.10000 65.000 7.281e-36 98.86000 105.30000 #> k_parent 0.73930 25.740 2.948e-23 0.68310 0.80020 #> k_M1 0.29920 14.040 1.577e-15 0.25880 0.34590 #> k_M2 0.02023 15.220 1.653e-16 0.01769 0.02312 #> f_parent_to_M1 0.76870 18.370 7.295e-19 0.67300 0.84290 #> f_M1_to_M2 0.72290 14.500 6.418e-16 0.61110 0.81240 #> sigma 2.27300 8.832 2.161e-10 1.74900 2.79700 #> #> FOCUS Chi2 error levels in percent: #> err.min n.optim df #> All data 8.454 6 17 #> parent 8.660 2 6 #> M1 10.583 2 5 #> M2 3.586 2 6 #> #> Resulting formation fractions: #> ff #> parent_M1 0.7687 #> parent_sink 0.2313 #> M1_M2 0.7229 #> M1_sink 0.2771 #> #> Estimated disappearance times: #> DT50 DT90 #> parent 0.9376 3.114 #> M1 2.3170 7.697 #> M2 34.2689 113.839 #> #> Data: #> time variable observed predicted residual #> 0 parent 101.5 1.021e+02 -0.56248 #> 0 parent 101.2 1.021e+02 -0.86248 #> 1 parent 53.9 4.873e+01 5.17118 #> 1 parent 47.5 4.873e+01 -1.22882 #> 3 parent 10.4 1.111e+01 -0.70773 #> 3 parent 7.6 1.111e+01 -3.50773 #> 7 parent 1.1 5.772e-01 0.52283 #> 7 parent 0.3 5.772e-01 -0.27717 #> 14 parent 3.5 3.264e-03 3.49674 #> 28 parent 3.2 1.045e-07 3.20000 #> 90 parent 0.6 9.532e-10 0.60000 #> 120 parent 3.5 -5.940e-10 3.50000 #> 1 M1 36.4 3.479e+01 1.61088 #> 1 M1 37.4 3.479e+01 2.61088 #> 3 M1 34.3 3.937e+01 -5.07027 #> 3 M1 39.8 3.937e+01 0.42973 #> 7 M1 15.1 1.549e+01 -0.38715 #> 7 M1 17.8 1.549e+01 2.31285 #> 14 M1 5.8 1.995e+00 3.80469 #> 14 M1 1.2 1.995e+00 -0.79531 #> 60 M1 0.5 2.111e-06 0.50000 #> 90 M1 3.2 -9.672e-10 3.20000 #> 120 M1 1.5 7.670e-10 1.50000 #> 120 M1 0.6 7.670e-10 0.60000 #> 1 M2 4.8 4.455e+00 0.34517 #> 3 M2 20.9 2.153e+01 -0.62527 #> 3 M2 19.3 2.153e+01 -2.22527 #> 7 M2 42.0 4.192e+01 0.07941 #> 7 M2 43.1 4.192e+01 1.17941 #> 14 M2 49.4 4.557e+01 3.83353 #> 14 M2 44.3 4.557e+01 -1.26647 #> 28 M2 34.6 3.547e+01 -0.87275 #> 28 M2 33.0 3.547e+01 -2.47275 #> 60 M2 18.8 1.858e+01 0.21837 #> 60 M2 17.6 1.858e+01 -0.98163 #> 90 M2 10.6 1.013e+01 0.47130 #> 90 M2 10.8 1.013e+01 0.67130 #> 120 M2 9.8 5.521e+00 4.27893 #> 120 M2 3.3 5.521e+00 -2.22107 # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/test_data_from_UBA_2014.html","id":null,"dir":"Reference","previous_headings":"","what":"Three experimental datasets from two water sediment systems and one soil — test_data_from_UBA_2014","title":"Three experimental datasets from two water sediment systems and one soil — test_data_from_UBA_2014","text":"datasets used comparative validation several kinetic evaluation software packages (Ranke, 2014).","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/test_data_from_UBA_2014.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Three experimental datasets from two water sediment systems and one soil — test_data_from_UBA_2014","text":"","code":"test_data_from_UBA_2014"},{"path":"https://pkgdown.jrwb.de/mkin/reference/test_data_from_UBA_2014.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Three experimental datasets from two water sediment systems and one soil — test_data_from_UBA_2014","text":"list containing three datasets R6 class defined mkinds. dataset , among others, following components title name dataset, e.g. UBA_2014_WS_river data data frame data form expected mkinfit","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/test_data_from_UBA_2014.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Three experimental datasets from two water sediment systems and one soil — test_data_from_UBA_2014","text":"Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/test_data_from_UBA_2014.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Three experimental datasets from two water sediment systems and one soil — test_data_from_UBA_2014","text":"","code":"# \\dontrun{ # This is a level P-II evaluation of the dataset according to the FOCUS kinetics # guidance. Due to the strong correlation of the parameter estimates, the # covariance matrix is not returned. Note that level P-II evaluations are # generally considered deprecated due to the frequent occurrence of such # large parameter correlations, among other reasons (e.g. the adequacy of the # model). m_ws <- mkinmod(parent_w = mkinsub(\"SFO\", \"parent_s\"), parent_s = mkinsub(\"SFO\", \"parent_w\")) #> Temporary DLL for differentials generated and loaded f_river <- mkinfit(m_ws, test_data_from_UBA_2014[[1]]$data, quiet = TRUE) #> Warning: Observations with value of zero were removed from the data plot_sep(f_river) summary(f_river)$bpar #> Warning: Could not calculate correlation; no covariance matrix #> Estimate se_notrans t value Pr(>t) Lower Upper #> parent_w_0 95.91998118 NA NA NA NA NA #> k_parent_w 0.41145375 NA NA NA NA NA #> k_parent_s 0.04663944 NA NA NA NA NA #> f_parent_w_to_parent_s 0.12467894 NA NA NA NA NA #> f_parent_s_to_parent_w 0.50000000 NA NA NA NA NA #> sigma 3.13612618 NA NA NA NA NA mkinerrmin(f_river) #> err.min n.optim df #> All data 0.1090929 5 6 #> parent_w 0.0817436 3 3 #> parent_s 0.1619965 2 3 # This is the evaluation used for the validation of software packages # in the expertise from 2014 m_soil <- mkinmod(parent = mkinsub(\"SFO\", c(\"M1\", \"M2\")), M1 = mkinsub(\"SFO\", \"M3\"), M2 = mkinsub(\"SFO\", \"M3\"), M3 = mkinsub(\"SFO\"), use_of_ff = \"max\") #> Temporary DLL for differentials generated and loaded f_soil <- mkinfit(m_soil, test_data_from_UBA_2014[[3]]$data, quiet = TRUE) #> Warning: Observations with value of zero were removed from the data plot_sep(f_soil, lpos = c(\"topright\", \"topright\", \"topright\", \"bottomright\")) summary(f_soil)$bpar #> Estimate se_notrans t value Pr(>t) Lower #> parent_0 76.55425650 0.859186398 89.1008711 1.113861e-26 74.755959420 #> k_parent 0.12081956 0.004601918 26.2541722 1.077359e-16 0.111561575 #> k_M1 0.84258615 0.806159719 1.0451851 1.545266e-01 0.113779564 #> k_M2 0.04210880 0.017083034 2.4649483 1.170188e-02 0.018013857 #> k_M3 0.01122918 0.007245855 1.5497385 6.885051e-02 0.002909431 #> f_parent_to_M1 0.32240200 0.240783878 1.3389684 9.819070e-02 NA #> f_parent_to_M2 0.16099855 0.033691952 4.7785463 6.531136e-05 NA #> f_M1_to_M3 0.27921507 0.269423709 1.0363419 1.565266e-01 0.022978202 #> f_M2_to_M3 0.55641252 0.595119937 0.9349586 1.807707e-01 0.008002509 #> sigma 1.14005399 0.149696423 7.6157731 1.727024e-07 0.826735778 #> Upper #> parent_0 78.35255358 #> k_parent 0.13084582 #> k_M1 6.23970946 #> k_M2 0.09843260 #> k_M3 0.04333992 #> f_parent_to_M1 NA #> f_parent_to_M2 NA #> f_M1_to_M3 0.86450778 #> f_M2_to_M3 0.99489895 #> sigma 1.45337221 mkinerrmin(f_soil) #> err.min n.optim df #> All data 0.09649963 9 20 #> parent 0.04721283 2 6 #> M1 0.26551208 2 5 #> M2 0.20327575 2 5 #> M3 0.05196550 3 4 # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/transform_odeparms.html","id":null,"dir":"Reference","previous_headings":"","what":"Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms","title":"Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms","text":"transformations intended map parameters take restricted values full scale real numbers. kinetic rate constants parameters can take positive values, simple log transformation used. compositional parameters, formations fractions always sum 1 can negative, ilr transformation used.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/transform_odeparms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms","text":"","code":"transform_odeparms( parms, mkinmod, transform_rates = TRUE, transform_fractions = TRUE ) backtransform_odeparms( transparms, mkinmod, transform_rates = TRUE, transform_fractions = TRUE )"},{"path":"https://pkgdown.jrwb.de/mkin/reference/transform_odeparms.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms","text":"parms Parameters kinetic models used differential equations. mkinmod kinetic model class mkinmod, containing names model variables needed grouping formation fractions ilr transformation, parameter names information pathway sink included model. transform_rates Boolean specifying kinetic rate constants transformed model specification used fitting better compliance assumption normal distribution estimator. TRUE, also alpha beta parameters FOMC model log-transformed, well k1 k2 rate constants DFOP HS models break point tb HS model. transform_fractions Boolean specifying formation fractions constants transformed model specification used fitting better compliance assumption normal distribution estimator. default (TRUE) transformations. g parameter DFOP model also seen fraction. single fraction transformed (g parameter DFOP single target variable e.g. single metabolite plus pathway sink), logistic transformation used stats::qlogis(). cases, .e. two formation fractions need transformed whose sum exceed one, ilr transformation used. transparms Transformed parameters kinetic models used fitting procedure.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/transform_odeparms.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms","text":"vector transformed backtransformed parameters","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/transform_odeparms.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms","text":"transformation sets formation fractions fragile, supposes ordering components forward backward transformation. problem internal use mkinfit.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/transform_odeparms.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms","text":"Johannes Ranke","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/transform_odeparms.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms","text":"","code":"SFO_SFO <- mkinmod( parent = list(type = \"SFO\", to = \"m1\", sink = TRUE), m1 = list(type = \"SFO\"), use_of_ff = \"min\") #> Temporary DLL for differentials generated and loaded # Fit the model to the FOCUS example dataset D using defaults FOCUS_D <- subset(FOCUS_2006_D, value != 0) # remove zero values to avoid warning fit <- mkinfit(SFO_SFO, FOCUS_D, quiet = TRUE) fit.s <- summary(fit) # Transformed and backtransformed parameters print(fit.s$par, 3) #> Estimate Std. Error Lower Upper #> parent_0 99.60 1.5702 96.40 102.79 #> log_k_parent_sink -3.04 0.0763 -3.19 -2.88 #> log_k_parent_m1 -2.98 0.0403 -3.06 -2.90 #> log_k_m1_sink -5.25 0.1332 -5.52 -4.98 #> sigma 3.13 0.3585 2.40 3.85 print(fit.s$bpar, 3) #> Estimate se_notrans t value Pr(>t) Lower Upper #> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 102.7931 #> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04103 0.0560 #> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04678 0.0551 #> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069 #> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549 # \\dontrun{ # Compare to the version without transforming rate parameters (does not work # with analytical solution, we get NA values for m1 in predictions) fit.2 <- mkinfit(SFO_SFO, FOCUS_D, transform_rates = FALSE, solution_type = \"deSolve\", quiet = TRUE) fit.2.s <- summary(fit.2) print(fit.2.s$par, 3) #> Estimate Std. Error Lower Upper #> parent_0 99.59848 1.57022 96.40384 1.03e+02 #> k_parent_sink 0.04792 0.00365 0.04049 5.54e-02 #> k_parent_m1 0.05078 0.00205 0.04661 5.49e-02 #> k_m1_sink 0.00526 0.00070 0.00384 6.69e-03 #> sigma 3.12550 0.35852 2.39609 3.85e+00 print(fit.2.s$bpar, 3) #> Estimate se_notrans t value Pr(>t) Lower Upper #> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40384 1.03e+02 #> k_parent_sink 0.04792 0.00365 13.11 6.13e-15 0.04049 5.54e-02 #> k_parent_m1 0.05078 0.00205 24.80 3.27e-23 0.04661 5.49e-02 #> k_m1_sink 0.00526 0.00070 7.51 6.16e-09 0.00384 6.69e-03 #> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.85e+00 # } initials <- fit$start$value names(initials) <- rownames(fit$start) transformed <- fit$start_transformed$value names(transformed) <- rownames(fit$start_transformed) transform_odeparms(initials, SFO_SFO) #> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 100.750000 -2.302585 -2.301586 -2.300587 backtransform_odeparms(transformed, SFO_SFO) #> parent_0 k_parent_sink k_parent_m1 k_m1_sink #> 100.7500 0.1000 0.1001 0.1002 # \\dontrun{ # The case of formation fractions (this is now the default) SFO_SFO.ff <- mkinmod( parent = list(type = \"SFO\", to = \"m1\", sink = TRUE), m1 = list(type = \"SFO\"), use_of_ff = \"max\") #> Temporary DLL for differentials generated and loaded fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_D, quiet = TRUE) fit.ff.s <- summary(fit.ff) print(fit.ff.s$par, 3) #> Estimate Std. Error Lower Upper #> parent_0 99.5985 1.5702 96.404 102.79 #> log_k_parent -2.3157 0.0409 -2.399 -2.23 #> log_k_m1 -5.2475 0.1332 -5.518 -4.98 #> f_parent_qlogis 0.0579 0.0893 -0.124 0.24 #> sigma 3.1255 0.3585 2.396 3.85 print(fit.ff.s$bpar, 3) #> Estimate se_notrans t value Pr(>t) Lower Upper #> parent_0 99.59848 1.57022 63.43 2.30e-36 96.40383 102.7931 #> k_parent 0.09870 0.00403 24.47 4.96e-23 0.09082 0.1073 #> k_m1 0.00526 0.00070 7.51 6.16e-09 0.00401 0.0069 #> f_parent_to_m1 0.51448 0.02230 23.07 3.10e-22 0.46912 0.5596 #> sigma 3.12550 0.35852 8.72 2.24e-10 2.39609 3.8549 initials <- c(\"f_parent_to_m1\" = 0.5) transformed <- transform_odeparms(initials, SFO_SFO.ff) backtransform_odeparms(transformed, SFO_SFO.ff) #> f_parent_to_m1 #> 0.5 # And without sink SFO_SFO.ff.2 <- mkinmod( parent = list(type = \"SFO\", to = \"m1\", sink = FALSE), m1 = list(type = \"SFO\"), use_of_ff = \"max\") #> Temporary DLL for differentials generated and loaded fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_D, quiet = TRUE) fit.ff.2.s <- summary(fit.ff.2) print(fit.ff.2.s$par, 3) #> Estimate Std. Error Lower Upper #> parent_0 84.79 3.012 78.67 90.91 #> log_k_parent -2.76 0.082 -2.92 -2.59 #> log_k_m1 -4.21 0.123 -4.46 -3.96 #> sigma 8.22 0.943 6.31 10.14 print(fit.ff.2.s$bpar, 3) #> Estimate se_notrans t value Pr(>t) Lower Upper #> parent_0 84.7916 3.01203 28.15 1.92e-25 78.6704 90.913 #> k_parent 0.0635 0.00521 12.19 2.91e-14 0.0538 0.075 #> k_m1 0.0148 0.00182 8.13 8.81e-10 0.0115 0.019 #> sigma 8.2229 0.94323 8.72 1.73e-10 6.3060 10.140 # }"},{"path":"https://pkgdown.jrwb.de/mkin/reference/update.mkinfit.html","id":null,"dir":"Reference","previous_headings":"","what":"Update an mkinfit model with different arguments — update.mkinfit","title":"Update an mkinfit model with different arguments — update.mkinfit","text":"function return updated mkinfit object. fitted degradation model parameters old fit used starting values updated fit. Values specified 'parms.ini' /'state.ini' override starting values.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/update.mkinfit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update an mkinfit model with different arguments — update.mkinfit","text":"","code":"# S3 method for mkinfit update(object, ..., evaluate = TRUE)"},{"path":"https://pkgdown.jrwb.de/mkin/reference/update.mkinfit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update an mkinfit model with different arguments — update.mkinfit","text":"object mkinfit object updated ... Arguments mkinfit replace arguments original call. Arguments set NULL remove arguments given original call evaluate call evaluated returned call","code":""},{"path":"https://pkgdown.jrwb.de/mkin/reference/update.mkinfit.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update an mkinfit model with different arguments — update.mkinfit","text":"","code":"# \\dontrun{ fit <- mkinfit(\"SFO\", subset(FOCUS_2006_D, value != 0), quiet = TRUE) parms(fit) #> parent_0 k_parent sigma #> 99.44423885 0.09793574 3.39632469 plot_err(fit) fit_2 <- update(fit, error_model = \"tc\") parms(fit_2) #> parent_0 k_parent sigma_low rsd_high #> 1.008549e+02 1.005665e-01 3.752222e-03 6.763434e-02 plot_err(fit_2) # }"},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-126","dir":"Changelog","previous_headings":"","what":"mkin 1.2.6","title":"mkin 1.2.6","text":"‘inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd’: Fix erroneous call ‘endpoints()’ function","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-125-2023-08-09","dir":"Changelog","previous_headings":"","what":"mkin 1.2.5 (2023-08-09)","title":"mkin 1.2.5 (2023-08-09)","text":"‘vignettes/mesotrione_parent_2023.rnw’: Prebuilt vignette showing covariate modelling can done relevant parent degradation models. ‘inst/testdata/mesotrione_soil_efsa_2016}.xlsx’: Another example spreadsheets use ‘read_spreadsheet()’, featuring pH dependent degradation R/illparms.R: Fix detection ill-defined slope error model parameters case estimate negative","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-124-2023-05-19","dir":"Changelog","previous_headings":"","what":"mkin 1.2.4 (2023-05-19)","title":"mkin 1.2.4 (2023-05-19)","text":"R/endpoints.R: Fix calculation endpoints user specified covariate values","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-1231-unreleased","dir":"Changelog","previous_headings":"","what":"mkin 1.2.3.1 (unreleased)","title":"mkin 1.2.3.1 (unreleased)","text":"Small fixes get online docs right (example code R/hierarchical_kinetics, cluster setup cyantraniliprole dmta pathway vignettes, graphics model comparison multistart vignette), rebuild online docs","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-123-2023-04-17","dir":"Changelog","previous_headings":"","what":"mkin 1.2.3 (2023-04-17)","title":"mkin 1.2.3 (2023-04-17)","text":"‘R/{endpoints,parms,plot.mixed.mmkin,summary.saem.mmkin}.R’: Calculate parameters endpoints plot population curves specific covariate values, specific percentiles covariate values used saem fits. Depend current deSolve version possibility avoid resolving symbols shared library (compiled models) , thanks Thomas Petzoldt. ‘inst/rmarkdown/templates/hierarchical_kinetics/skeleton/skeleton.Rmd’: Start new cluster creating model stored user specified location, otherwise symbols found worker processes. ‘tests/testthat/test_compiled_symbols.R’: new tests control problems may introduced possibility use pre-resolved symbols. ‘R/mkinerrmin.R’: Fix typo subset (use = instead ==), thanks Sebastian Meyer spotting work R 4.3.0.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-122-unreleased","dir":"Changelog","previous_headings":"","what":"mkin 1.2.2 (unreleased)","title":"mkin 1.2.2 (unreleased)","text":"‘inst/rmarkdown/templates/hierarchical_kinetics’: R markdown template facilitate application hierarchical kinetic models. ‘inst/testdata/{cyantraniliprole_soil_efsa_2014,lambda-cyhalothrin_soil_efsa_2014}.xlsx’: Example spreadsheets use ‘read_spreadsheet()’. ‘R/mhmkin.R’: Allow ‘illparms.mhmkin’ object list suitable dimensions value argument ‘no_random_effects’, making possible exclude random effects ill-defined simpler variants set degradation models. Remove possibility exclude random effects based separate fits, work well. ‘R/summary.saem.mmkin.R’: List initial parameter values summary, including random effects error model parameters. Avoid redundant warnings occurred calculation correlations fixed effects case Fisher information matrix inverted. List correlations random effects specified user covariance model. ‘R/parplot.R’: Possibility select top ‘llquant’ fraction fits parameter plots, improved legend text. ‘R/illparms.R’: Also check confidence intervals slope parameters covariate models include zero. implemented fits obtained saemix backend. ‘R/parplot.R’: Make function work also case multistart runs failed. ‘R/intervals.R’: Include correlations random effects model case .","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-121-2022-11-19","dir":"Changelog","previous_headings":"","what":"mkin 1.2.1 (2022-11-19)","title":"mkin 1.2.1 (2022-11-19)","text":"‘{data,R}/ds_mixed.rda’: Include test data package instead generating ‘tests/testthat/setup_script.R’. Refactor generating code make consistent update tests. ‘tests/testthat/setup_script.R’: Excluded another ill-defined random effect DFOP fit ‘saem’, attempt avoid platform dependence surfaced Fedora systems CRAN check farm ‘tests/testthat/test_mixed.R’: Round parameters found saemix two significant digits printing, also help avoid platform dependence tests ‘R/saem.R’: Fix bug prevented ‘error.ini’ passed ‘saemix_model’, set default c(1, 1) avoid changing test results ‘R/parplot.R’: Show initial values error model parameters ‘R/loglik.mkinfit.R’: Add ‘nobs’ attribute resulting ‘logLik’ object, order make test_AIC.R succeed current R-devel","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-120-2022-11-17","dir":"Changelog","previous_headings":"","what":"mkin 1.2.0 (2022-11-17)","title":"mkin 1.2.0 (2022-11-17)","text":"‘R/saem.R’: ‘logLik’, ‘update’ ‘anova’ methods ‘saem.mmkin’ objects. ‘R/saem.R’: Automatic estimation start parameters random effects case mkin transformations, nicely improving convergence reducing problems iterative ODE solutions. ‘R/status.R’: New generic show status information fit array objects methods ‘mmkin’, ‘mhmkin’ ‘multistart’ objects. ‘R/mhmkin.R’: New method performing multiple hierarchical mkin fits one function call, optionally parallel. ‘R/mhmkin.R’: ‘anova.mhmkin’ conveniently comparing resulting fits. ‘R/illparms.R’: New generic show ill-defined parameters methods ‘mkinfit’, ‘mmkin’, ‘saem.mmkin’ ‘mhmkin’ objects. ‘R/multistart.R’: New method testing multiple start parameters hierarchical model fits, function ‘llhist’ new generic ‘parplot’ diagnostics, new generics ‘.best’ ‘best’ extracting fit highest likelihood ‘R/summary.mmkin.R’: Summary method mmkin objects. ‘R/saem.R’: Implement test saemix transformations FOMC HS. Also, error saemix transformations requested supported. ‘R/read_spreadsheet.R’: Conveniently read data spreadsheet file. ‘R/tex_listings.R’: Conveniently include summaries fit objects R markdown documents compiled LaTeX.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-111-2022-07-12","dir":"Changelog","previous_headings":"","what":"mkin 1.1.1 (2022-07-12)","title":"mkin 1.1.1 (2022-07-12)","text":"’R/{mkinmod,mkinpredict}.R: Store DLL information mkinmod objects use information mkinpredict avoid performance regression brought bugfix R 4.2.x. Thanks Tomas Kalibera analysis problem r-package-devel list suggestion fix . ‘vignettes/FOCUS_L.rmd’: Remove outdated note referring failure calculate covariance matrix DFOP L2 dataset. Since 0.9.45.5 covariance matrix available ‘vignettes/web_only/benchmarks.rmd’: Add first benchmark data using laptop system, therefore add CPU showing benchmark results. ‘dimethenamid_2018’: Update example code use saemix ‘CAKE_export’: Check validity map argument, updates ‘saem()’: Slightly improve speed case analytical solution saemix implemented, activate test respective code ‘mean_degparms’: New argument ‘default_log_parms’ makes possible supply surrogate value (default) log parameters fail t-test ‘plot.mixed.mmkin’: Pass frame argument also residual plots, take ‘default_log_parms’ argument ‘mean_degparms’ used constructing approximate population curves, plot population curve last avoid covered data ‘plot.mkinfit’: Respect argument ‘maxabs’ residual plots, make possible give ylim list, row layouts","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mixed-effects-models-1-1-0","dir":"Changelog","previous_headings":"","what":"Mixed-effects models","title":"mkin 1.1.0 (2022-03-14)","text":"Reintroduce interface saemix version 3.0 (now CRAN), particular generic function ‘saem’ generator ‘saem.mmkin’, currently using ‘saemix_model’ ‘saemix_data’, summary plot methods ‘mean_degparms’: New argument ‘test_log_parms’ makes function consider log-transformed parameters untransformed parameters pass t-test certain confidence level. can used obtain plausible starting parameters different mixed-effects model backends ‘plot.mixed.mmkin’: Gains arguments ‘test_log_parms’ ‘conf.level’ ‘vignettes/web_only/dimethenamid_2018.rmd’: Example evaluations dimethenamid data. ‘intervals’: Provide method nlme function ‘saem.mmkin’ objects.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-105-2021-09-15","dir":"Changelog","previous_headings":"","what":"mkin 1.0.5 (2021-09-15)","title":"mkin 1.0.5 (2021-09-15)","text":"‘dimethenamid_2018’: Correct data Borstel soil. five observations Staudenmaier (2013) previously stored “Borstel 2” actually just subset 16 observations “Borstel 1” now simply “Borstel”","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-104-2021-04-20","dir":"Changelog","previous_headings":"","what":"mkin 1.0.4 (2021-04-20)","title":"mkin 1.0.4 (2021-04-20)","text":"plotting functions setting graphical parameters: Use .exit() resetting graphical parameters ‘plot.mkinfit’: Use xlab xlim residual plot show_residuals TRUE ‘mmkin’: Use cores = 1 per default Windows make easier first time users","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-103-2021-02-15","dir":"Changelog","previous_headings":"","what":"mkin 1.0.3 (2021-02-15)","title":"mkin 1.0.3 (2021-02-15)","text":"Review update README, ‘Introduction mkin’ vignette help pages","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-102-unreleased","dir":"Changelog","previous_headings":"","what":"mkin 1.0.2 (Unreleased)","title":"mkin 1.0.2 (Unreleased)","text":"‘mkinfit’: Keep model names stored ‘mkinmod’ objects, avoiding loss ‘gmkin’","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-101-2021-02-10","dir":"Changelog","previous_headings":"","what":"mkin 1.0.1 (2021-02-10)","title":"mkin 1.0.1 (2021-02-10)","text":"‘confint.mmkin’, ‘nlme.mmkin’, ‘transform_odeparms’: Fix example code dontrun sections failed current defaults ‘logLik.mkinfit’: Improve example code avoid warnings show convenient syntax ‘mkinresplot’: Re-add Katrin Lindenberger coauthor accidentally removed long ago Remove tests relying non-convergence FOMC fit FOCUS dataset platform dependent (revealed new additional tests CRAN, thanks!) Increase test tolerance parameter comparisons also proved platform dependent","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"general-1-0-0","dir":"Changelog","previous_headings":"","what":"General","title":"mkin 1.0.0 (2021-02-03)","text":"‘mkinmod’ models gain arguments ‘name’ ‘dll_dir’ , conjunction current version ‘inline’ package, make possible still use DLL used fast ODE solutions ‘deSolve’ saving restoring ‘mkinmod’ object. ‘mkindsg’ R6 class groups ‘mkinds’ datasets metadata ‘f_norm_temp_focus’ generic function normalise time intervals using FOCUS method, methods numeric vectors ‘mkindsg’ objects ‘D24_2014’ ‘dimethenamid_2018’ datasets ‘focus_soil_moisture’ FOCUS default soil moisture data ‘update’ method ‘mmkin’ objects ‘transform_odeparms’, ‘backtransform_odeparms’: Use logit transformation solitary fractions like g parameter DFOP model, formation fractions pathway one target variable ‘plot.mmkin’: Add ylab argument, making possible customize y axis label panels left without affecting residual plots. Reduce legend size vertical distance panels ‘plot.mkinfit’: Change default ylab “Observed” “Residue”. Pass xlab residual plot show_residuals TRUE.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mixed-effects-models-1-0-0","dir":"Changelog","previous_headings":"","what":"Mixed-effects models","title":"mkin 1.0.0 (2021-02-03)","text":"‘mixed.mmkin’ New container mmkin objects plotting ‘plot.mixed.mmkin’ method ‘plot.mixed.mmkin’ method used ‘nlme.mmkin’ inheriting ‘mixed.mmkin’ (currently virtual) ‘plot’, ‘summary’ ‘print’ methods ‘nlme.mmkin’ objects","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-09503-2020-10-08","dir":"Changelog","previous_headings":"","what":"mkin 0.9.50.3 (2020-10-08)","title":"mkin 0.9.50.3 (2020-10-08)","text":"‘parms’: Add method mmkin objects ‘mmkin’ ‘confint(method = ’profile’): Use cores detected parallel::detectCores() per default ‘confint(method = ’profile’): Choose accuracy based ‘rel_tol’ argument, relative bounds obtained quadratic approximation ‘mkinfit’: Make ‘use_of_ff’ = “max” also default models specified using short names like “SFO” “FOMC” ‘mkinfit’: Run ‘stats::shapiro.test()’ standardized residuals warn p < 0.05 ‘mkinfit’: ‘error_model_algorithm’ = ‘d_3’ fail direct fitting fails, reports results threestep algorithm returned ‘mmkin’: fail one fits fails, assign try-error respective position mmkin object ‘mkinfit’: Ignore components state.ini correspond state variables model ‘endpoints’: Back-calculate DT50 value DT90 also biphasic models DFOP, HS SFORB","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-09502-2020-05-12","dir":"Changelog","previous_headings":"","what":"mkin 0.9.50.2 (2020-05-12)","title":"mkin 0.9.50.2 (2020-05-12)","text":"Increase tolerance platform specific test results Solaris test machine CRAN Updates corrections (using spelling package) documentation","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-09501-2020-05-11","dir":"Changelog","previous_headings":"","what":"mkin 0.9.50.1 (2020-05-11)","title":"mkin 0.9.50.1 (2020-05-11)","text":"Support SFORB formation fractions ‘mkinmod’: Make ‘use_of_ff’ = “max” default Improve performance ) avoiding expensive calls cost function like merge() data.frame(), b) implementing analytical solutions SFO-SFO DFOP-SFO","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-094911-2020-04-20","dir":"Changelog","previous_headings":"","what":"mkin 0.9.49.11 (2020-04-20)","title":"mkin 0.9.49.11 (2020-04-20)","text":"Increase test tolerance make pass CRAN check machines","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-094910-2020-04-18","dir":"Changelog","previous_headings":"","what":"mkin 0.9.49.10 (2020-04-18)","title":"mkin 0.9.49.10 (2020-04-18)","text":"‘nlme.mmkin’: nlme method mmkin row objects associated S3 class print, plot, anova endpoint methods ‘mean_degparms, nlme_data, nlme_function’: Three new functions facilitate building nlme models mmkin row objects ‘endpoints’: Don’t return SFORB list component ’s empty. reduces distraction complies documentation Article compiled models: Add platform specific code suppress warnings zero values removed FOCUS D dataset ‘plot.mmkin’: Add argument ‘standardized’ avoid warnings occurred passed part additional arguments captured dots (…) ‘summary.mkinfit’: Add AIC, BIC log likelihood summary","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-09499-2020-03-31","dir":"Changelog","previous_headings":"","what":"mkin 0.9.49.9 (2020-03-31)","title":"mkin 0.9.49.9 (2020-03-31)","text":"‘mkinmod’: Use pkgbuild::has_compiler instead Sys.(‘gcc’), latter often fail even Rtools installed ‘mkinds’: Use roxygen documenting fields methods R6 class","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-09498-2020-01-09","dir":"Changelog","previous_headings":"","what":"mkin 0.9.49.8 (2020-01-09)","title":"mkin 0.9.49.8 (2020-01-09)","text":"‘aw’: Generic function calculating Akaike weights, methods mkinfit objects mmkin columns ‘loftest’: Add lack--fit test ‘plot_res’, ‘plot_sep’ ‘mkinerrplot’: Add possibility show standardized residuals make default fits error models ‘const’ ‘lrtest.mkinfit’: Improve naming compared fits case fixed parameters ‘confint.mkinfit’: Make quadratic approximation default, likelihood profiling takes lot time, especially fit three parameters","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-09497-2019-11-01","dir":"Changelog","previous_headings":"","what":"mkin 0.9.49.7 (2019-11-01)","title":"mkin 0.9.49.7 (2019-11-01)","text":"Fix bug introduced 0.9.49.6 occurred direct optimisation yielded higher likelihood three-step optimisation d_3 algorithm, caused fitted parameters three-step optimisation returned instead parameters direct optimisation Add ‘nobs’ method mkinfit objects, enabling default ‘BIC’ method stats package. Also, add ‘BIC’ method mmkin column objects.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-09496-2019-10-31","dir":"Changelog","previous_headings":"","what":"mkin 0.9.49.6 (2019-10-31)","title":"mkin 0.9.49.6 (2019-10-31)","text":"Implement likelihood ratio test method ‘lrtest’ lmtest package Add ‘update’ method mkinfit objects remembers fitted parameters appropriate Add ‘residuals’ method mkinfit objects supports scaling based error model Fix bug ‘mkinfit’ prevented summaries objects fitted fixed parameters generated Add ‘parms’ ‘confint’ methods mkinfit objects. Confidence intervals based quadratic approximation summary, based profile likelihood Move long-running tests tests/testthat/slow separate test log. currently take around 7 minutes system ‘mkinfit’: Clean code return functions calculate log-likelihood sum squared residuals Vignette ‘twa.html’: Add maximum time weighted average formulas hockey stick model Support frameless plots (‘frame = FALSE’) Support suppress chi2 error level (‘show_errmin = FALSE’) ‘plot.mmkin’ Update README introductory vignette Report ‘OLS’ error_model_algorithm summary case default error_model (‘const’) used Support summarizing ‘mkinfit’ objects generated versions < 0.9.49.5","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-09495-2019-07-04","dir":"Changelog","previous_headings":"","what":"mkin 0.9.49.5 (2019-07-04)","title":"mkin 0.9.49.5 (2019-07-04)","text":"Several algorithms minimization negative log-likelihood non-constant error models (two-component variance variable). case error model constant variance, least squares used stable. default algorithm ‘d_3’ tries direct minimization three-step procedure, returns model highest likelihood. argument ‘reweight.method’ mkinfit mmkin now obsolete, use ‘error_model’ ‘error_model_algorithm’ instead Add test checks get best known AIC parent fits 12 test datasets. Add test datasets purpose. New function ‘mkinerrplot’. function also used residual plots ‘plot.mmkin’ argument ‘resplot = “errmod”’ given, ‘plot.mkinfit’ ‘show_errplot’ set TRUE. Remove dependency FME, use nlminb optimisation (‘Port’ algorithm). remember cases one optimisation algorithms preferable, except sometime used Levenberg-Marquardt speed cases expect get trapped local minimum. Use numDeriv package calculate hessians. results slightly different confidence intervals, takes bit longer, apparently robust Add simple benchmark vignette document impact performance. code manual weighting removed. functionality might get added later time. time , please use earlier version, e.g. 0.9.48.1 want manual weighting. fitting time reported summary now includes time used calculation hessians Adapt tests Fix error FOCUS chi2 error level calculations occurred parameters specified parms.ini model. warning already issued, fitting parallel via mmkin go unnoticed. Add example datasets obtained risk assessment reports published European Food Safety Agency.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-09481-2019-03-04","dir":"Changelog","previous_headings":"","what":"mkin 0.9.48.1 (2019-03-04)","title":"mkin 0.9.48.1 (2019-03-04)","text":"Add function ‘logLik.mkinfit’ makes possible calculate AIC mkinfit objects Add function ‘AIC.mmkin’ make easy compare columns mmkin objects ‘add_err’: Respect argument giving number replicates synthetic dataset ‘max_twa_parent’: Support maximum time weighted average concentration calculations hockey stick (HS) model ‘mkinpredict’: Make function generic create method mkinfit objects ‘mkinfit’: Improve correctness fitted two component error model fitting mean absolute deviance observation observed values, weighting current two-component error model ‘tests/testthat/test_irls.R’: Test components error model used generate data can reproduced moderate accuracy Add function ‘CAKE_export’ facilitate cross-checking results Implement logistic model (tested parent fits) ‘nafta’: Add evaluations according NAFTA guidance","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-09475-2018-09-14","dir":"Changelog","previous_headings":"","what":"mkin 0.9.47.5 (2018-09-14)","title":"mkin 0.9.47.5 (2018-09-14)","text":"Make two-component error model stop cases inadequate avoid nls crashes windows Move two vignettes location built CRAN (avoid NOTES long execution times) Exclude example code testing CRAN avoid NOTES long execution times","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-09473","dir":"Changelog","previous_headings":"","what":"mkin 0.9.47.3","title":"mkin 0.9.47.3","text":"‘mkinfit’: Improve fitting error model reweight.method = ‘tc’. Add ‘manual’ possible arguments ‘weight’ Test FOCUS_2006_C can evaluated DFOP reweight.method = ‘tc’","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-09472-2018-07-19","dir":"Changelog","previous_headings":"","what":"mkin 0.9.47.2 (2018-07-19)","title":"mkin 0.9.47.2 (2018-07-19)","text":"‘sigma_twocomp’: Rename ‘sigma_rl’ ‘sigma_twocomp’ Rocke Lorenzato model assumes lognormal distribution large y. Correct references Rocke Lorenzato model accordingly. ‘mkinfit’: Use 1.1 starting value N parameter IORE models obtain convergence difficult cases. Show parameter names ‘trace_parms’ ‘TRUE’.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-09471-2018-02-06","dir":"Changelog","previous_headings":"","what":"mkin 0.9.47.1 (2018-02-06)","title":"mkin 0.9.47.1 (2018-02-06)","text":"Skip tests CRAN winbuilder avoid timeouts ‘test_data_from_UBA_2014’: Added list datasets containing experimental data used expertise 2014 ‘mkinfit’: Added iterative reweighting method ‘tc’ using two-component error model Rocke Lorenzato. NA values data returned . ‘mkinfit’: Work around bug current FME version prevented convergence message returned case non-convergence. ‘summary.mkinfit’: Improved output regarding weighting method. predictions returned NA values model (see ). ‘summary.mkinfit’: Show versions mkin R used fitting (ones used summary) fit generated mkin >= 0.9.47.1","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-09463-2017-11-16","dir":"Changelog","previous_headings":"","what":"mkin 0.9.46.3 (2017-11-16)","title":"mkin 0.9.46.3 (2017-11-16)","text":"README.md, vignettes/mkin.Rmd: URLs updated synthetic_data_for_UBA: Add code used generate data interest reproducibility","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-09462-2017-10-10","dir":"Changelog","previous_headings":"","what":"mkin 0.9.46.2 (2017-10-10)","title":"mkin 0.9.46.2 (2017-10-10)","text":"Converted vignette FOCUS_Z tex/pdf markdown/html DESCRIPTION: Add ORCID","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-09461-2017-09-14","dir":"Changelog","previous_headings":"","what":"mkin 0.9.46.1 (2017-09-14)","title":"mkin 0.9.46.1 (2017-09-14)","text":"plot.mkinfit: Fix scaling residual plots case separate plots observed variable plot.mkinfit: Use data points fitted curve y axis scaling case separate plots observed variable Documentation updates","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-0946-2017-07-24","dir":"Changelog","previous_headings":"","what":"mkin 0.9.46 (2017-07-24)","title":"mkin 0.9.46 (2017-07-24)","text":"Remove test_FOMC_ill-defined.R platform dependent","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-09452-2017-07-24","dir":"Changelog","previous_headings":"","what":"mkin 0.9.45.2 (2017-07-24)","title":"mkin 0.9.45.2 (2017-07-24)","text":"Rename twa max_twa_parent avoid conflict twa pfm package Update URLs documentation Limit test code one core pass windows Switch microbenchmark rbenchmark former supported platforms","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"new-features-0-9-45-1","dir":"Changelog","previous_headings":"","what":"New features","title":"mkin 0.9.45.1 (2016-12-20)","text":"twa function, calculating maximum time weighted average concentrations parent (SFO, FOMC DFOP).","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"minor-changes-0-9-45","dir":"Changelog","previous_headings":"","what":"Minor changes","title":"mkin 0.9.45 (2016-12-08)","text":"plot.mkinfit plot.mmkin: plotting device tikz, LaTeX markup used chi2 error graphs. Use pkgdown, successor staticdocs generating static HTML documentation. Include example output graphs also dontrun sections. plot.mkinfit: Plotting fail compiled model available, e.g. removed temporary directory. case, uncompiled model now used plotting","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"bug-fixes-0-9-44","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"mkin 0.9.44 (2016-06-29)","text":"test test_FOMC_ill-defined failed several architectures, test now skipped","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"major-changes-0-9-43","dir":"Changelog","previous_headings":"","what":"Major changes","title":"mkin 0.9.43 (2016-06-28)","text":"title changed Kinetic evaluations chemical degradation data plot.mkinfit: Add possibility show fits (residual plots requested) separately observed variables plot.mkinfit: Add possibility show chi2 error levels plot, similar way shown plot.mmkin plot_sep: Add function convenience wrapper plotting observed variables mkinfit objects separately, chi2 error values residual plots. Vignettes: main vignette mkin converted R markdown updated. vignettes also updated show current improved functionality. function add_err added package, making easy generate simulated data using error model based normal distribution","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"minor-changes-0-9-43","dir":"Changelog","previous_headings":"","what":"Minor changes","title":"mkin 0.9.43 (2016-06-28)","text":"Remove outdated reference inline package compiled_models vignette mkinfit: error cases fit converges, Jacobian untransformed model cost can estimated. Give warning instead return NA t-test results. summary.mkinfit: Give warning message covariance matrix can obtained. test added containing corresponding edge case check warnings correctly issued fit terminate. plot.mmkin: Round chi2 error value three significant digits, instead two decimal digits. mkinfit: Return err values used weighted fits column named err. Also include inverse weights column value observed data used, returned observed data component mkinfit object.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"bug-fixes-0-9-43","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"mkin 0.9.43 (2016-06-28)","text":"endpoints: name substance degrading metabolite (e.g. parent compound) used model formulation ended letter f, rate parameters listed formation fractions mixed names. also appear summary. mkinfit: Check observed variables checking user tried fix formation fractions fitting using ilr transformation. plot.mmkin: Set plot margins correctly, also case single fit plotted, main title placed reasonable way. plot.mkinfit: Correct default values col_obs, pch_obs lty_obs case obs_vars specified.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"major-changes-0-9-42","dir":"Changelog","previous_headings":"","what":"Major changes","title":"mkin 0.9.42 (2016-03-25)","text":"Add argument from_max_mean mkinfit, fitting decline maximum observed value models single observed variable","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"minor-changes-0-9-42","dir":"Changelog","previous_headings":"","what":"Minor changes","title":"mkin 0.9.42 (2016-03-25)","text":"Add plots compiled_models vignette Give explanatory error message mkinmod fails due missing definition target variable print.mkinmod(): Improve formatting printing mkinmod model definitions","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"minor-changes-0-9-41","dir":"Changelog","previous_headings":"","what":"Minor changes","title":"mkin 0.9-41 (2015-11-09)","text":"Add R6 class mkinds representing datasets printing method Add printing method mkinmod objects Make possible specify arbitrary strings names compounds mkinmod, show plot Use index.r file group help topics static documentation","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"bug-fixes-0-9-41","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"mkin 0.9-41 (2015-11-09)","text":"print.summary.mkinfit(): Avoid error occurred printing summaries generated mkin versions 0.9-36","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"bug-fixes-0-9-40","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"mkin 0.9-40 (2015-07-21)","text":"endpoints(): DFOP SFORB models, optimize() used, make use fact DT50 must DT50_k1 DT50_k2 (DFOP) DT50_b1 DT50_b2 (SFORB), optimize() sometimes find minimum. Likewise finding DT90 values. Also fit log scale make function efficient.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"internal-changes-0-9-40","dir":"Changelog","previous_headings":"","what":"Internal changes","title":"mkin 0.9-40 (2015-07-21)","text":"DESCRIPTION, NAMESPACE, R/*.R: Import () stats, graphics methods packages, qualify function calls non-base packages installed R avoid NOTES made R CMD check –-cran upcoming R versions.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"major-changes-0-9-39","dir":"Changelog","previous_headings":"","what":"Major changes","title":"mkin 0.9-39 (2015-06-26)","text":"New function mmkin(): function takes character vector model shorthand names, alternatively list mkinmod models, well list dataset main arguments. returns matrix mkinfit objects, row model column dataset. subsetting method single brackets available. Fitting models parallel using parallel package supported. New function plot.mmkin(): Plots single-row single-column mmkin objects including residual plots.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"bug-fixes-0-9-39","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"mkin 0.9-39 (2015-06-26)","text":"mkinparplot(): Fix x axis scaling rate constants formation fractions got confused introduction t-values transformed parameters.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"minor-changes-0-9-38","dir":"Changelog","previous_headings":"","what":"Minor changes","title":"mkin 0.9-38 (2015-06-24)","text":"vignettes/compiled_models.html: Show performance improvement factor actually obtained building vignette, well mkin version, system info CPU model used building vignette. GNUMakefile,vignettes/*: Clean vignette generation include table contents HTML vignettes.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"bug-fixes-0-9-38","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"mkin 0.9-38 (2015-06-24)","text":"mkinmod(): generating C code derivatives, declare time variable needed remove ‘-W--unused-variable’ compiler flag C compiler used CRAN checks Solaris know .","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"major-changes-0-9-36","dir":"Changelog","previous_headings":"","what":"Major changes","title":"mkin 0.9-36 (2015-06-21)","text":"summary.mkinfit(): one-sided t-test significant difference untransformed parameters zero now always shown, based assumption normal distribution estimators untransformed parameters. Use caution, assumption unrealistic e.g. rate constants nonlinear kinetic models. compiler (gcc) installed, use version differential equation model compiled C code, huge performance boost models deSolve method works. mkinmod(): Create list component $cf (class CFuncList) list returned mkinmod, version can compiled autogenerated C code (see ). mkinfit(): Set default solution_type deSolve compiled version model present, except analytical solution possible.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"minor-changes-0-9-36","dir":"Changelog","previous_headings":"","what":"Minor changes","title":"mkin 0.9-36 (2015-06-21)","text":"Added simple showcase vignette evaluation FOCUS example dataset D","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"major-changes-0-9-35","dir":"Changelog","previous_headings":"","what":"Major changes","title":"mkin 0.9-35 (2015-05-15)","text":"Switch RUnit testthat testing","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"bug-fixes-0-9-35","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"mkin 0.9-35 (2015-05-15)","text":"mkinparplot(): Avoid warnings occurred confidence intervals available summary fit print.summary.mkinfit(): Fix printing summary case number iterations available NAMESPACE: export S3 methods plot.mkinfit, summary.mkinfit print.summary.mkinfit satisfy R CMD check R-devel mkinparplot(): Avoid warning R CMD check undeclared global variable Lower","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"new-features-0-9-35","dir":"Changelog","previous_headings":"","what":"New features","title":"mkin 0.9-35 (2015-05-15)","text":"mkinfit(): Report successful termination quiet = FALSE. helpful difficult problems fitted reweight.method = obs, progress often indicated reweighting. first test using results established expertise written German Federal Environmental Agency (UBA) added. Add synthetic datasets generated expertise written German Federal Environmental Agency UBA Add tests based datasets","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"new-features-0-9-34","dir":"Changelog","previous_headings":"","what":"New features","title":"mkin 0.9-34 (2014-11-22)","text":"Add convenience function mkinsub() creating lists used mkinmod() Add possibility fit indeterminate order rate equation (IORE) models using analytical solution (parent ) numeric solution. Paths IORE compounds metabolites supported using formation fractions (use_of_ff = ‘max’). Note numerical solution (method.ode = ‘deSolve’) IORE differential equations sometimes fails due numerical problems. Switch using Port algorithm (using model/trust region approach) per default. needing iterations Levenberg-Marquardt algorithm previously used per default, less sensitive starting parameters.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"minor-changes-0-9-34","dir":"Changelog","previous_headings":"","what":"Minor changes","title":"mkin 0.9-34 (2014-11-22)","text":"formatting differential equations summary improved Always include 0 y axis plotting fit","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"new-features-0-9-33","dir":"Changelog","previous_headings":"","what":"New features","title":"mkin 0.9-33 (2014-10-22)","text":"initial value (state.ini) observed variable highest observed residue set 100 case time zero observation state.ini = \"auto\" basic unit test mkinerrmin() written","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"bug-fixes-0-9-33","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"mkin 0.9-33 (2014-10-22)","text":"mkinfit(): internally fitted parameter g named g_ilr even transform_fractions=FALSE mkinfit(): initial value (state.ini) parent compound set parent () variable highest value observed data. mkinerrmin(): checking degrees freedom metabolites, check time zero value fixed instead checking observed value zero. ensures correct calculation degrees freedom also cases metabolite residue time zero greater zero. plot.mkinfit(): Avoid warning message using first component ylim occurred ylim specified explicitly","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"minor-changes-0-9-33","dir":"Changelog","previous_headings":"","what":"Minor changes","title":"mkin 0.9-33 (2014-10-22)","text":"formatting differential equations summary improved wrapping overly long lines FOCUS_Z vignette rebuilt improvement using width 70 avoid output outside grey area print.summary.mkinfit(): Avoid warning occurred gmkin showed summaries initial fits without iterations mkinfit(): Avoid warning occurred summarising fit performed maxitmodFit = 0 done gmkin configuring new fits.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"new-features-0-9-32","dir":"Changelog","previous_headings":"","what":"New features","title":"mkin 0.9-32 (2014-07-24)","text":"number degrees freedom difficult define case ilr transformation formation fractions. Now source compartment number ilr parameters (=number optimised parameters) divided number pathways metabolites (=number affected data series) leads fractional degrees freedom cases. default initial value first state value now taken mean observations time zero, available. kinetic model can alternatively specified shorthand name parent degradation models, e.g. SFO, DFOP. Optimisation method, number model evaluations time elapsed optimisation given summary mkinfit objects. maximum number iterations optimisation algorithm can specified using argument maxit.modFit mkinfit function. mkinfit gives warning fit converge (apply SANN method). warning included summary.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"bug-fixes-0-9-32","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"mkin 0.9-32 (2014-07-24)","text":"Avoid plotting artificial 0 residual time zero mkinresplot determination degrees freedom mkinerrmin, formation fractions accounted multiple times case parallel formation metabolites. See new feature described solution. transform_rates=FALSE mkinfit now also works FOMC HS models. Initial values formation fractions set cases. warning given fit converge method default Levenberg-Marquardt method Marq used.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"minor-changes-0-9-32","dir":"Changelog","previous_headings":"","what":"Minor changes","title":"mkin 0.9-32 (2014-07-24)","text":"Vignettes rebuilt reflect changes summary method. Algorithm Pseudo excluded needs user-defined parameter limits supported. Algorithm Newton excluded different way specify maximum number iterations appear provide additional benefits.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"bug-fixes-0-9-31","dir":"Changelog","previous_headings":"","what":"Bug fixes","title":"mkin 0.9-31 (2014-07-14)","text":"internal renaming optimised parameters Version 0.9-30 led errors determination degrees freedom chi2 error level calulations mkinerrmin() used summary function.","code":""},{"path":[]},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"new-features-0-9-30","dir":"Changelog","previous_headings":"","what":"New features","title":"mkin 0.9-30 (2014-07-11)","text":"now possible use formation fractions combination turning sink mkinmod().","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"major-changes-0-9-30","dir":"Changelog","previous_headings":"","what":"Major changes","title":"mkin 0.9-30 (2014-07-11)","text":"original transformed parameters now different names (e.g. k_parent log_k_parent. also differ many formation fractions pathway sink. order information blocks print.summary.mkinfit.R() ordered logical way.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"minor-changes-0-9-30","dir":"Changelog","previous_headings":"","what":"Minor changes","title":"mkin 0.9-30 (2014-07-11)","text":"vignette FOCUS_Z simplified use formation fractions turning sink, slightly amended use new versions DT50 values calculated since mkin 0.9-29. vignettes rebuilt reflect changes. ChangeLog renamed NEWS.md entries converted markdown syntax compatible tools::news() function built R. test suite overhauled. Tests DFOP SFORB models dataset FOCUS_2006_A removed, much dependent optimisation algorithm /starting parameters, dataset SFO (compare kinfit vignette). Also, Schaefer complex case can now fitted using formation fractions, ‘Port’ optimisation method also fit A2 way published Piacenza paper. checks introduced mkinfit(), leading warnings stopping execution unsupported combinations methods parameters requested.","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-09-29-2014-06-27","dir":"Changelog","previous_headings":"","what":"mkin 0.9-29 (2014-06-27)","title":"mkin 0.9-29 (2014-06-27)","text":"R/mkinresplot.R: Make possible specify xlim R/geometric_mean.R, man/geometric_mean.Rd: Add geometric mean function R/endpoints.R, man/endpoints.Rd: Calculate additional (pseudo)-DT50 values FOMC, DFOP, HS SFORB. Avoid calculation formation fractions rate constants directly fitted","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-09-28-2014-05-20","dir":"Changelog","previous_headings":"","what":"mkin 0.9-28 (2014-05-20)","title":"mkin 0.9-28 (2014-05-20)","text":"backtransform confidence intervals formation fractions one compound formed, parameters define pathways set Add historical remarks background main package vignette Correct ‘isotropic’ ‘isometric’ ilr transformation","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-09-27-2014-05-10","dir":"Changelog","previous_headings":"","what":"mkin 0.9-27 (2014-05-10)","title":"mkin 0.9-27 (2014-05-10)","text":"Fork GUI separate package gmkin DESCRIPTION, NAMESPACE, TODO: Adapt add copyright information Remove files belonging GUI Possibility fit without parameter transformations, using bounds implemented FME Add McCall 2,4,5-T dataset Enable selection observed variables plotting Add possibility show residual plot plot.mkinfit R/mkinparplot.R, man/mkinparplot.Rd: plot parameters confidence intervals Change vignette format Sweave knitr Split examples vignette FOCUS_L FOCUS_Z Remove warning constant formation fractions mkinmod based misconception Restrict unit test Schaefer data parent primary metabolites formation fraction DT50 A2 highly correlated passing test platform dependent. example, test fails 1 14 platforms CRAN today. Add Eurofins Regulatory AG copyright notices Import FME deSolve instead depending clean startup Add starter function GUI: gmkin() Change format workspace files gmkin can distributed documented package Add gmkin workspace datasets FOCUS_2006_gmkin FOCUS_2006_Z_gmkin","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-09-24-2013-11-06","dir":"Changelog","previous_headings":"","what":"mkin 0.9-24 (2013-11-06)","title":"mkin 0.9-24 (2013-11-06)","text":"Bugfix re-enabling fixing combination initial values state variables Default values kinetic rate constants 0.1 “salted” small increment avoid numeric artefacts eigenvalue based solutions Backtransform fixed ODE parameters summary","code":""},{"path":"https://pkgdown.jrwb.de/mkin/news/index.html","id":"mkin-09-22-2013-10-26","dir":"Changelog","previous_headings":"","what":"mkin 0.9-22 (2013-10-26)","title":"mkin 0.9-22 (2013-10-26)","text":"Get rid optimisation step mkinerrmin - unnecessary. Thanks KinGUII inspiration - actually equation 6-2 FOCUS kinetics p. 91 overlooked originally Fix plot.mkinfit passed graphical arguments like main solver use plot=TRUE mkinfit() example first successful fits simple GUI Fix iteratively reweighted least squares case many metabolites Unify naming initial values state variables Unify naming dataframes optimised fixed parameters summary Show weighting method residuals summary Correct output data case manual weighting Implement IRLS assuming different variances observed variables use 0 values time zero chi2 error level calculations. way done KinGUII makes sense. impact chi2 error levels output. Generally seem lower metabolites now, presumably mean observed values higher detailed list changes mkin source please consult commit history http://github.com/jranke/mkin","code":""}] diff --git a/vignettes/web_only/mkin_benchmarks.rda b/vignettes/web_only/mkin_benchmarks.rda Binary files differindex 662a5ddb..0922f13b 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 a319c941..4cdf205e 100644 --- a/vignettes/web_only/saem_benchmarks.rda +++ b/vignettes/web_only/saem_benchmarks.rda |
