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+++ 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" 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 " nlme.mmkin summary.nlme.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. Optionally
+(default is FALSE), the data are listed in full."><title>Summary method for class "nlme.mmkin" — summary.nlme.mmkin • 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="Summary method for class " nlme.mmkin summary.nlme.mmkin><meta property="og: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. Optionally
(default is FALSE), the data are listed in full."><!-- 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]>
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- <a href="../articles/prebuilt/2022_dmta_parent.html">Testing hierarchical parent degradation kinetics with residue data on dimethenamid and dimethenamid-P</a>
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- <a href="../articles/prebuilt/2023_mesotrione_parent.html">Testing covariate modelling in hierarchical parent degradation kinetics with residue data on mesotrione</a>
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- <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
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+ <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>
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+ <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>
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+<li class="nav-item">
+ <a class="nav-link" href="../news/index.html">News</a>
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- <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>
+
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+</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">#&gt;</span> nlme version used for fitting: 3.1.163 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mkin version used for pre-fitting: 1.2.6 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting: 4.3.1 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit: Mon Oct 30 09:39:53 2023 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Mon Oct 30 09:39:53 2023 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> R version used for fitting: 4.3.2 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of fit: Thu Nov 16 04:19:41 2023 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Date of summary: Thu Nov 16 04:19:41 2023 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Equations:</span>
<span class="r-out co"><span class="r-pr">#&gt;</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">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Model predictions using solution type analytical </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 0.451 s using 4 iterations</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Fitted in 0.182 s using 4 iterations</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Variance model: Two-component variance function </span>
<span class="r-out co"><span class="r-pr">#&gt;</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>
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