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<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>
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<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>
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<a class="dropdown-item" href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
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<a class="dropdown-item" href="../articles/web_only/saem_benchmarks.html">Benchmark timings for saem.mmkin</a>
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<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>
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<img src="" class="logo" alt=""><h1>Fit one or more kinetic models with one or more state variables to one or
more datasets</h1>
<small class="dont-index">Source: <a href="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 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 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>
<span> cores <span class="op">=</span> <span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Sys.info.html" class="external-link">Sys.info</a></span><span class="op">(</span><span class="op">)</span><span class="op">[</span><span class="st">"sysname"</span><span class="op">]</span> <span class="op">==</span> <span class="st">"Windows"</span><span class="op">)</span> <span class="fl">1</span> <span class="kw">else</span> <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">detectCores</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> cluster <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span> <span class="va">...</span></span>
<span><span class="op">)</span></span>
<span></span>
<span><span class="co"># S3 method for mmkin</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>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
</div>
<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
list of <code><a href="mkinmod.html">mkinmod</a></code> objects.</p></dd>
<dt>datasets</dt>
<dd><p>An optionally named list of datasets suitable as observed
data for <code><a href="mkinfit.html">mkinfit</a></code>.</p></dd>
<dt>cores</dt>
<dd><p>The number of cores to be used for multicore processing. This
is only used when the <code>cluster</code> argument is <code>NULL</code>. On Windows
machines, cores > 1 is not supported, you need to use the <code>cluster</code>
argument to use multiple logical processors. Per default, all cores
detected by <code><a href="https://rdrr.io/r/parallel/detectCores.html" class="external-link">parallel::detectCores()</a></code> are used, except on Windows where
the default is 1.</p></dd>
<dt>cluster</dt>
<dd><p>A cluster as returned by <code>makeCluster</code> to be used
for parallel execution.</p></dd>
<dt>...</dt>
<dd><p>Not used.</p></dd>
<dt>x</dt>
<dd><p>An mmkin object.</p></dd>
</dl></div>
<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>
<p>objects and/or try-errors that can be indexed using the model names for the
first index (row index) and the dataset names for the second index (column
index).</p>
</div>
<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 class="section level2">
<h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
<p>Johannes Ranke</p>
</div>
<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>
<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="st">"M2"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> M2 <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>, use_of_ff <span class="op">=</span> <span class="st">"max"</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-in"><span></span></span>
<span class="r-in"><span><span class="va">m_synth_FOMC_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">"FOMC"</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="st">"M2"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> M2 <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>, use_of_ff <span class="op">=</span> <span class="st">"max"</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-in"><span></span></span>
<span class="r-in"><span><span class="va">models</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>SFO_lin <span class="op">=</span> <span class="va">m_synth_SFO_lin</span>, FOMC_lin <span class="op">=</span> <span class="va">m_synth_FOMC_lin</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">datasets</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">synthetic_data_for_UBA_2014</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">3</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="va">x</span><span class="op">$</span><span class="va">data</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">datasets</span><span class="op">)</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Dataset"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">time_default</span> <span class="op"><-</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">fits.0</span> <span class="op"><-</span> <span class="fu">mmkin</span><span class="op">(</span><span class="va">models</span>, <span class="va">datasets</span>, quiet <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">time_1</span> <span class="op"><-</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">fits.4</span> <span class="op"><-</span> <span class="fu">mmkin</span><span class="op">(</span><span class="va">models</span>, <span class="va">datasets</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-in"><span></span></span>
<span class="r-in"><span><span class="va">time_default</span></span></span>
<span class="r-out co"><span class="r-pr">#></span> user system elapsed </span>
<span class="r-out co"><span class="r-pr">#></span> 1.653 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> 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>
<span class="r-out co"><span class="r-pr">#></span> parent_M1 parent_sink M1_M2 M1_sink </span>
<span class="r-out co"><span class="r-pr">#></span> 0.7340481 0.2659519 0.7505690 0.2494310 </span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> $distimes</span>
<span class="r-out co"><span class="r-pr">#></span> DT50 DT90</span>
<span class="r-out co"><span class="r-pr">#></span> parent 0.8777689 2.915885</span>
<span class="r-out co"><span class="r-pr">#></span> M1 2.3257403 7.725942</span>
<span class="r-out co"><span class="r-pr">#></span> M2 33.7201060 112.015767</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># plot.mkinfit handles rows or columns of mmkin result objects</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="va">fits.0</span><span class="op">[</span><span class="fl">1</span>, <span class="op">]</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="mmkin-1.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[</span><span class="fl">1</span>, <span class="op">]</span>, obs_var <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">"M1"</span>, <span class="st">"M2"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="mmkin-2.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[</span>, <span class="fl">1</span><span class="op">]</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="mmkin-3.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="co"># Use double brackets to extract a single mkinfit object, which will be plotted</span></span></span>
<span class="r-in"><span><span class="co"># by plot.mkinfit and can be plotted using plot_sep</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="va">fits.0</span><span class="op">[[</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span>, sep_obs <span class="op">=</span> <span class="cn">TRUE</span>, show_residuals <span class="op">=</span> <span class="cn">TRUE</span>, show_errmin <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="mmkin-4.png" alt="" width="700" height="433"></span>
<span class="r-in"><span><span class="fu"><a href="plot.mkinfit.html">plot_sep</a></span><span class="op">(</span><span class="va">fits.0</span><span class="op">[[</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="co"># Plotting with mmkin (single brackets, extracting an mmkin object) does not</span></span></span>
<span class="r-in"><span><span class="co"># allow to plot the observed variables separately</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="va">fits.0</span><span class="op">[</span><span class="fl">1</span>, <span class="fl">1</span><span class="op">]</span><span class="op">)</span></span></span>
<span class="r-plt img"><img src="mmkin-5.png" alt="" width="700" height="433"></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># On Windows, we can use multiple cores by making a cluster first</span></span></span>
<span class="r-in"><span><span class="va">cl</span> <span class="op"><-</span> <span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">makePSOCKcluster</a></span><span class="op">(</span><span class="fl">12</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="va">f</span> <span class="op"><-</span> <span class="fu">mmkin</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>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>A <span class="op">=</span> <span class="va">FOCUS_2006_A</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>, D <span class="op">=</span> <span class="va">FOCUS_2006_D</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> cluster <span class="op">=</span> <span class="va">cl</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/print.html" class="external-link">print</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> <mmkin> object</span>
<span class="r-out co"><span class="r-pr">#></span> Status of individual fits:</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> dataset</span>
<span class="r-out co"><span class="r-pr">#></span> model A B C D </span>
<span class="r-out co"><span class="r-pr">#></span> SFO OK OK OK OK</span>
<span class="r-out co"><span class="r-pr">#></span> FOMC C OK OK OK</span>
<span class="r-out co"><span class="r-pr">#></span> DFOP OK OK OK OK</span>
<span class="r-out co"><span class="r-pr">#></span> </span>
<span class="r-out co"><span class="r-pr">#></span> C: Optimisation did not converge:</span>
<span class="r-out co"><span class="r-pr">#></span> false convergence (8)</span>
<span class="r-out co"><span class="r-pr">#></span> OK: No warnings</span>
<span class="r-in"><span><span class="co"># We get false convergence for the FOMC fit to FOCUS_2006_A because this</span></span></span>
<span class="r-in"><span><span class="co"># dataset is really SFO, and the FOMC fit is overparameterised</span></span></span>
<span class="r-in"><span><span class="fu">parallel</span><span class="fu">::</span><span class="fu"><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">stopCluster</a></span><span class="op">(</span><span class="va">cl</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="co"># }</span></span></span>
<span class="r-in"><span></span></span>
</code></pre></div>
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