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<!-- 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 one or more kinetic models with one or more state variables to one or
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    <div class="page-header">
    <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="hidden name"><code>mmkin.Rd</code></div>
    </div>

    <div class="ref-description">
    <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="sourceCode"><pre class="sourceCode r"><code><span class="fu">mmkin</span><span class="op">(</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 class="va">datasets</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>,
  cluster <span class="op">=</span> <span class="cn">NULL</span>,
  <span class="va">...</span>
<span class="op">)</span>

<span class="co"># S3 method for 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>, <span class="va">...</span><span class="op">)</span></code></pre></div>
    </div>

    <div id="arguments">
    <h2>Arguments</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 &gt; 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><a href="https://rdrr.io/r/parallel/makeCluster.html" class="external-link">makeCluster</a></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 id="value">
    <h2>Value</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>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 id="see-also">
    <h2>See also</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>
    <p>Johannes Ranke</p>
    </div>

    <div id="ref-examples">
    <h2>Examples</h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"></span>
<span class="r-in"><span class="co"># \dontrun{</span></span>
<span class="r-in"><span class="va">m_synth_SFO_lin</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">"SFO"</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="st">"M2"</span><span class="op">)</span>,</span>
<span class="r-in">                           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 class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
<span class="r-in"></span>
<span class="r-in"><span class="va">m_synth_FOMC_lin</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">"FOMC"</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="st">"M2"</span><span class="op">)</span>,</span>
<span class="r-in">                            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 class="r-msg co"><span class="r-pr">#&gt;</span> Temporary DLL for differentials generated and loaded</span>
<span class="r-in"></span>
<span class="r-in"><span class="va">models</span> <span class="op">&lt;-</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 class="r-in"><span class="va">datasets</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">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 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">datasets</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">"Dataset"</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">3</span><span class="op">)</span></span>
<span class="r-in"></span>
<span class="r-in"><span class="va">time_default</span> <span class="op">&lt;-</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">&lt;-</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 class="r-in"><span class="va">time_1</span> <span class="op">&lt;-</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">&lt;-</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 class="r-in"></span>
<span class="r-in"><span class="va">time_default</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>    user  system elapsed </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  35.152   1.185   8.439 </span>
<span class="r-in"><span class="va">time_1</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span>    user  system elapsed </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>  14.744   0.008  14.768 </span>
<span class="r-in"></span>
<span class="r-in"><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 class="r-out co"><span class="r-pr">#&gt;</span> $ff</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   parent_M1 parent_sink       M1_M2     M1_sink </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   0.7340481   0.2659519   0.7505683   0.2494317 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> $distimes</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>             DT50       DT90</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> parent  0.877769   2.915885</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> M1      2.325744   7.725955</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> M2     33.720111 112.015785</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-in"></span>
<span class="r-in"><span class="co"># plot.mkinfit handles rows or columns of mmkin result objects</span></span>
<span class="r-in"><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 class="r-plt img"><img src="mmkin-1.png" alt="" width="700" height="433"></span>
<span class="r-in"><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 class="r-plt img"><img src="mmkin-2.png" alt="" width="700" height="433"></span>
<span class="r-in"><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 class="r-plt img"><img src="mmkin-3.png" alt="" width="700" height="433"></span>
<span class="r-in"><span class="co"># Use double brackets to extract a single mkinfit object, which will be plotted</span></span>
<span class="r-in"><span class="co"># by plot.mkinfit and can be plotted using plot_sep</span></span>
<span class="r-in"><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 class="r-plt img"><img src="mmkin-4.png" alt="" width="700" height="433"></span>
<span class="r-in"><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 class="r-in"><span class="co"># Plotting with mmkin (single brackets, extracting an mmkin object) does not</span></span>
<span class="r-in"><span class="co"># allow to plot the observed variables separately</span></span>
<span class="r-in"><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 class="r-plt img"><img src="mmkin-5.png" alt="" width="700" height="433"></span>
<span class="r-in"></span>
<span class="r-in"><span class="co"># On Windows, we can use multiple cores by making a cluster using the parallel</span></span>
<span class="r-in"><span class="co"># package, which gets loaded with mkin, and passing it to mmkin, e.g.</span></span>
<span class="r-in"><span class="va">cl</span> <span class="op">&lt;-</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 class="r-in"><span class="va">f</span> <span class="op">&lt;-</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 class="r-in">  <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 class="r-in">  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 class="r-in"><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 class="r-out co"><span class="r-pr">#&gt;</span> &lt;mmkin&gt; object</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Status of individual fits:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>       dataset</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> model  A  B  C  D </span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   SFO  OK OK OK OK</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   FOMC C  OK OK OK</span>
<span class="r-out co"><span class="r-pr">#&gt;</span>   DFOP OK OK OK OK</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> OK: No warnings</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> C: Optimisation did not converge:</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> false convergence (8)</span>
<span class="r-in"><span class="co"># We get false convergence for the FOMC fit to FOCUS_2006_A because this</span></span>
<span class="r-in"><span class="co"># dataset is really SFO, and the FOMC fit is overparameterised</span></span>
<span class="r-in"><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 class="r-in"><span class="co"># }</span></span>
<span class="r-in"></span>
</code></pre></div>
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