Make tests more platform independent, update docs

author: Johannes Ranke <jranke@uni-bremen.de> 2022-03-02 18:03:54 +0100
committer: Johannes Ranke <jranke@uni-bremen.de> 2022-03-02 18:03:54 +0100
commit: 2bb59c88d49b193f278916ad9cc4de83c0de9604 (patch)
tree: f286bba254d7c5f2d32eeb2b11f6148938b0e1e1 /docs/reference/summary.saem.mmkin.html
parent: 351248d07f810ccb6c497633a02cd48ee35526e6 (diff)
1 files changed, 230 insertions, 0 deletions
diff --git a/docs/reference/summary.saem.mmkin.html b/docs/reference/summary.saem.mmkin.html
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+<!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
+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="../reference/index.html">Functions and data</a>
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+      <a href="../articles/web_only/dimethenamid_2018.html">Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models</a>
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+      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
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+      <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
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+      <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
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+      <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
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+      <a href="../articles/web_only/benchmarks.html">Some benchmark timings</a>
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+</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>
+    </div>
+
+    <div class="ref-description">
+    <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
+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="sourceCode"><pre class="sourceCode r"><code><span class="co"># S3 method for saem.mmkin</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">FALSE</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, distimes <span class="op">=</span> <span class="cn">TRUE</span>, <span class="va">...</span><span class="op">)</span>
+
+<span class="co"># S3 method for summary.saem.mmkin</span>
+<span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, digits <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="fl">3</span>, <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"digits"</span><span class="op">)</span> <span class="op">-</span> <span class="fl">3</span><span class="op">)</span>, 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></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>object</dt>
+<dd><p>an object of class <a href="saem.html">saem.mmkin</a></p></dd>
+<dt>data</dt>
+<dd><p>logical, indicating whether the full data should be included in
+the summary.</p></dd>
+<dt>verbose</dt>
+<dd><p>Should the summary be verbose?</p></dd>
+<dt>distimes</dt>
+<dd><p>logical, indicating whether DT50 and DT90 values should be
+included.</p></dd>
+<dt>...</dt>
+<dd><p>optional arguments passed to methods like <code>print</code>.</p></dd>
+<dt>x</dt>
+<dd><p>an object of class summary.saem.mmkin</p></dd>
+<dt>digits</dt>
+<dd><p>Number of digits to use for printing</p></dd>
+</dl></div>
+    <div id="value">
+    <h2>Value</h2>
+    <p>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>obtained in the fit, with at least the following additional components</p>
+<dl><dt>saemixversion, mkinversion, Rversion</dt>
+<dd><p>The saemix, mkin and R versions used</p></dd>
+<dt>date.fit, date.summary</dt>
+<dd><p>The dates where the fit and the summary were
+produced</p></dd>
+<dt>diffs</dt>
+<dd><p>The differential equations used in the degradation model</p></dd>
+<dt>use_of_ff</dt>
+<dd><p>Was maximum or minimum use made of formation fractions</p></dd>
+<dt>data</dt>
+<dd><p>The data</p></dd>
+<dt>confint_trans</dt>
+<dd><p>Transformed parameters as used in the optimisation, with confidence intervals</p></dd>
+<dt>confint_back</dt>
+<dd><p>Backtransformed parameters, with confidence intervals if available</p></dd>
+<dt>confint_errmod</dt>
+<dd><p>Error model parameters with confidence intervals</p></dd>
+<dt>ff</dt>
+<dd><p>The estimated formation fractions derived from the fitted
+model.</p></dd>
+<dt>distimes</dt>
+<dd><p>The DT50 and DT90 values for each observed variable.</p></dd>
+<dt>SFORB</dt>
+<dd><p>If applicable, eigenvalues of SFORB components of the model.</p></dd>
+</dl><p>The print method is called for its side effect, i.e. printing the summary.</p>
+    </div>
+    <div id="author">
+    <h2>Author</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="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span class="co"># Generate five datasets following DFOP-SFO kinetics</span></span>
+<span class="r-in"><span class="va">sampling_times</span> <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">3</span>, <span class="fl">7</span>, <span class="fl">14</span>, <span class="fl">28</span>, <span class="fl">60</span>, <span class="fl">90</span>, <span class="fl">120</span><span class="op">)</span></span>
+<span class="r-in"><span class="va">dfop_sfo</span> <span class="op">&lt;-</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 class="r-in"> m1 <span class="op">=</span> <span class="fu"><a href="mkinmod.html">mkinsub</a></span><span class="op">(</span><span class="st">"SFO"</span><span class="op">)</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span class="r-in"><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">1234</span><span class="op">)</span></span>
+<span class="r-in"><span class="va">k1_in</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="fl">5</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">0.1</span><span class="op">)</span>, <span class="fl">0.3</span><span class="op">)</span></span>
+<span class="r-in"><span class="va">k2_in</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="fl">5</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">0.02</span><span class="op">)</span>, <span class="fl">0.3</span><span class="op">)</span></span>
+<span class="r-in"><span class="va">g_in</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">plogis</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">5</span>, <span class="fu"><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">qlogis</a></span><span class="op">(</span><span class="fl">0.5</span><span class="op">)</span>, <span class="fl">0.3</span><span class="op">)</span><span class="op">)</span></span>
+<span class="r-in"><span class="va">f_parent_to_m1_in</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">plogis</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">5</span>, <span class="fu"><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">qlogis</a></span><span class="op">(</span><span class="fl">0.3</span><span class="op">)</span>, <span class="fl">0.3</span><span class="op">)</span><span class="op">)</span></span>
+<span class="r-in"><span class="va">k_m1_in</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/Lognormal.html" class="external-link">rlnorm</a></span><span class="op">(</span><span class="fl">5</span>, <span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log</a></span><span class="op">(</span><span class="fl">0.02</span><span class="op">)</span>, <span class="fl">0.3</span><span class="op">)</span></span>
+<span class="r-in"></span>
+<span class="r-in"><span class="va">pred_dfop_sfo</span> <span class="op">&lt;-</span> <span class="kw">function</span><span class="op">(</span><span class="va">k1</span>, <span class="va">k2</span>, <span class="va">g</span>, <span class="va">f_parent_to_m1</span>, <span class="va">k_m1</span><span class="op">)</span> <span class="op">{</span></span>
+<span class="r-in">  <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">dfop_sfo</span>,</span>
+<span class="r-in">    <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k1 <span class="op">=</span> <span class="va">k1</span>, k2 <span class="op">=</span> <span class="va">k2</span>, g <span class="op">=</span> <span class="va">g</span>, f_parent_to_m1 <span class="op">=</span> <span class="va">f_parent_to_m1</span>, k_m1 <span class="op">=</span> <span class="va">k_m1</span><span class="op">)</span>,</span>
+<span class="r-in">    <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span>
+<span class="r-in">    <span class="va">sampling_times</span><span class="op">)</span></span>
+<span class="r-in"><span class="op">}</span></span>
+<span class="r-in"></span>
+<span class="r-in"><span class="va">ds_mean_dfop_sfo</span> <span class="op">&lt;-</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">5</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 class="r-in">  <span class="fu"><a href="mkinpredict.html">mkinpredict</a></span><span class="op">(</span><span class="va">dfop_sfo</span>,</span>
+<span class="r-in">    <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>k1 <span class="op">=</span> <span class="va">k1_in</span><span class="op">[</span><span class="va">i</span><span class="op">]</span>, k2 <span class="op">=</span> <span class="va">k2_in</span><span class="op">[</span><span class="va">i</span><span class="op">]</span>, g <span class="op">=</span> <span class="va">g_in</span><span class="op">[</span><span class="va">i</span><span class="op">]</span>,</span>
+<span class="r-in">      f_parent_to_m1 <span class="op">=</span> <span class="va">f_parent_to_m1_in</span><span class="op">[</span><span class="va">i</span><span class="op">]</span>, k_m1 <span class="op">=</span> <span class="va">k_m1_in</span><span class="op">[</span><span class="va">i</span><span class="op">]</span><span class="op">)</span>,</span>
+<span class="r-in">    <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>parent <span class="op">=</span> <span class="fl">100</span>, m1 <span class="op">=</span> <span class="fl">0</span><span class="op">)</span>,</span>
+<span class="r-in">    <span class="va">sampling_times</span><span class="op">)</span></span>
+<span class="r-in"><span class="op">}</span><span class="op">)</span></span>
+<span class="r-in"><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_mean_dfop_sfo</span><span class="op">)</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"ds"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">5</span><span class="op">)</span></span>
+<span class="r-in"></span>
+<span class="r-in"><span class="va">ds_syn_dfop_sfo</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">lapply</a></span><span class="op">(</span><span class="va">ds_mean_dfop_sfo</span>, <span class="kw">function</span><span class="op">(</span><span class="va">ds</span><span class="op">)</span> <span class="op">{</span></span>
+<span class="r-in">  <span class="fu"><a href="add_err.html">add_err</a></span><span class="op">(</span><span class="va">ds</span>,</span>
+<span class="r-in">    sdfunc <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">value</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">sqrt</a></span><span class="op">(</span><span class="fl">1</span><span class="op">^</span><span class="fl">2</span> <span class="op">+</span> <span class="va">value</span><span class="op">^</span><span class="fl">2</span> <span class="op">*</span> <span class="fl">0.07</span><span class="op">^</span><span class="fl">2</span><span class="op">)</span>,</span>
+<span class="r-in">    n <span class="op">=</span> <span class="fl">1</span><span class="op">)</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span></span>
+<span class="r-in"><span class="op">}</span><span class="op">)</span></span>
+<span class="r-in"></span>
+<span class="r-in"><span class="co"># \dontrun{</span></span>
+<span class="r-in"><span class="co"># Evaluate using mmkin and saem</span></span>
+<span class="r-in"><span class="va">f_mmkin_dfop_sfo</span> <span class="op">&lt;-</span> <span class="fu"><a href="mmkin.html">mmkin</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span><span class="va">dfop_sfo</span><span class="op">)</span>, <span class="va">ds_syn_dfop_sfo</span>,</span>
+<span class="r-in">  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">5</span><span class="op">)</span></span>
+<span class="r-in"><span class="va">f_saem_dfop_sfo</span> <span class="op">&lt;-</span> <span class="fu"><a href="saem.html">saem</a></span><span class="op">(</span><span class="va">f_mmkin_dfop_sfo</span><span class="op">)</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  </span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in rxModelVars_(obj):</span> Not compatible with STRSXP: [type=NULL].</span>
+<span class="r-in"><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 class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in h(simpleError(msg, call)):</span> error in evaluating the argument 'object' in selecting a method for function 'summary': object 'f_saem_dfop_sfo' not found</span>
+<span class="r-in"><span class="co"># }</span></span>
+<span class="r-in"></span>
+</code></pre></div>
+    </div>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
+</div>
+
+
+      <footer><div class="copyright">
+  <p></p><p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
+</div>
+
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+
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+  
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+  </body></html>
+
author	Johannes Ranke <jranke@uni-bremen.de>	2022-03-02 18:03:54 +0100
committer	Johannes Ranke <jranke@uni-bremen.de>	2022-03-02 18:03:54 +0100
commit	2bb59c88d49b193f278916ad9cc4de83c0de9604 (patch)
tree	f286bba254d7c5f2d32eeb2b11f6148938b0e1e1 /docs/reference/summary.saem.mmkin.html
parent	351248d07f810ccb6c497633a02cd48ee35526e6 (diff)