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authorJohannes Ranke <jranke@uni-bremen.de>2016-09-10 05:21:52 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2016-09-10 05:55:25 +0200
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+<!DOCTYPE html>
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+ <meta charset="utf-8">
+<title>mmkin. mkin 0.9.44.9000</title>
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+<meta name="author" content="
+ Johannes Ranke
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+ <div class="container">
+ <a class="brand" href="index.html">mkin 0.9.44.9000</a>
+ <div class="nav">
+ <ul class="nav">
+ <li><a href="index.html">Home</a></li>
+ <li><a href="reference.html">Reference</a></li>
+ </ul>
+ </div>
+ </div>
+ </div>
+</div>
+
+
+ <div class="container">
+ <header>
+
+ </header>
+
+ <h1>
+ Fit one or more kinetic models with one or more state variables to one or more datasets
+</h1>
+
+<div class="row">
+ <div class="span8">
+ <h2>Usage</h2>
+ <pre><span class="functioncall"><a href='mmkin.html'>mmkin</a></span><span class="keyword">(</span><span class="symbol">models</span><span class="keyword">,</span> <span class="symbol">datasets</span><span class="keyword">,</span>
+ <span class="argument">cores</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/Round'>round</a></span><span class="keyword">(</span><span class="functioncall"><a href='http://www.rdocumentation.org/packages/parallel/topics/detectCores'>detectCores</a></span><span class="keyword">(</span><span class="keyword">)</span><span class="keyword">/</span><span class="number">2</span><span class="keyword">)</span><span class="keyword">,</span> <span class="argument">cluster</span>&nbsp;<span class="argument">=</span>&nbsp;NULL<span class="keyword">,</span> <span class="symbol">...</span><span class="keyword">)</span></pre>
+
+ <h2>Arguments</h2>
+ <dl>
+ <dt>models</dt>
+ <dd>
+ Either a character vector of shorthand names (&quot;SFO&quot;, &quot;FOMC&quot;, &quot;DFOP&quot;,
+ &quot;HS&quot;, &quot;SFORB&quot;), or an optionally named list of <code><a href='mkinmod.html'>mkinmod</a></code>
+ objects.
+ </dd>
+ <dt>datasets</dt>
+ <dd>
+ An optionally named list of datasets suitable as observed data for
+ <code><a href='mkinfit.html'>mkinfit</a></code>.
+ </dd>
+ <dt>cores</dt>
+ <dd>
+ The number of cores to be used for multicore processing. This is only
+ used when the <code>cluster</code> argument is <code>NULL</code>.
+ </dd>
+ <dt>cluster</dt>
+ <dd>
+ A cluster as returned by <code><a href='http://www.rdocumentation.org/packages/parallel/topics/makeCluster'>makeCluster</a></code> to be used for parallel
+ execution.
+ </dd>
+ <dt>...</dt>
+ <dd>
+ Further arguments that will be passed to <code><a href='mkinfit.html'>mkinfit</a></code>.
+ </dd>
+ </dl>
+
+ <div class="Description">
+ <h2>Description</h2>
+
+ <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="Value">
+ <h2>Value</h2>
+
+ <p><dl>
+ A matrix of <code><a href='mkinfit.html'>mkinfit</a></code> objects that can be indexed using the model
+ and dataset names as row and column indices.
+</dl></p>
+
+ </div>
+
+ <h2 id="examples">Examples</h2>
+ <pre class="examples"><div class='input'><span class="comment">## Not run: ------------------------------------</span>
+<span class="comment"># m_synth_SFO_lin &lt;- mkinmod(parent = mkinsub("SFO", "M1"),</span>
+<span class="comment"># M1 = mkinsub("SFO", "M2"),</span>
+<span class="comment"># M2 = mkinsub("SFO"), use_of_ff = "max")</span>
+<span class="comment"># </span>
+<span class="comment"># m_synth_FOMC_lin &lt;- mkinmod(parent = mkinsub("FOMC", "M1"),</span>
+<span class="comment"># M1 = mkinsub("SFO", "M2"),</span>
+<span class="comment"># M2 = mkinsub("SFO"), use_of_ff = "max")</span>
+<span class="comment"># </span>
+<span class="comment"># models &lt;- list(SFO_lin = m_synth_SFO_lin, FOMC_lin = m_synth_FOMC_lin)</span>
+<span class="comment"># datasets &lt;- lapply(synthetic_data_for_UBA_2014[1:3], function(x) x$data)</span>
+<span class="comment"># names(datasets) &lt;- paste("Dataset", 1:3)</span>
+<span class="comment"># </span>
+<span class="comment"># time_default &lt;- system.time(fits.0 &lt;- mmkin(models, datasets))</span>
+<span class="comment"># time_1 &lt;- system.time(fits.1 &lt;- mmkin(models, datasets, cores = 1))</span>
+<span class="comment"># </span>
+<span class="comment"># time_default</span>
+<span class="comment"># time_1</span>
+<span class="comment"># </span>
+<span class="comment"># endpoints(fits[["SFO_lin", 2]])</span>
+<span class="comment"># </span>
+<span class="comment"># # Plot.mkinfit handles rows or columns of mmkin result objects</span>
+<span class="comment"># plot(fits.0[1, ])</span>
+<span class="comment"># plot(fits.0[1, ], obs_var = c("M1", "M2"))</span>
+<span class="comment"># plot(fits.0[, 1])</span>
+<span class="comment"># # Use double brackets to extract a single mkinfit object, which will be plotted</span>
+<span class="comment"># # by plot.mkinfit</span>
+<span class="comment"># plot(fits.0[[1, 1]], sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE)</span>
+<span class="comment"># # Plotting with mmkin (single brackets, extracting an mmkin object) does not</span>
+<span class="comment"># # allow to plot the observed variables separately</span>
+<span class="comment"># plot(fits.0[1, 1])</span>
+<span class="comment">## ---------------------------------------------</span></div></pre>
+ </div>
+ <div class="span4 sidebar">
+ <!-- <ul>
+ <li>mmkin</li>
+ </ul>
+ <ul>
+ <li> optimize </li>
+ </ul> -->
+
+ <h2>See also</h2>
+ <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>
+
+
+
+ <h2>Author</h2>
+
+ Johannes Ranke
+
+
+ </div>
+</div>
+
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