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<title>mmkin. mkin 0.9.44.9000</title>
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Johannes Ranke
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<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> <span class="argument">=</span> <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> <span class="argument">=</span> 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 ("SFO", "FOMC", "DFOP",
"HS", "SFORB"), 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 <- 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 <- 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 <- list(SFO_lin = m_synth_SFO_lin, FOMC_lin = m_synth_FOMC_lin)</span>
<span class="comment"># datasets <- lapply(synthetic_data_for_UBA_2014[1:3], function(x) x$data)</span>
<span class="comment"># names(datasets) <- paste("Dataset", 1:3)</span>
<span class="comment"># </span>
<span class="comment"># time_default <- system.time(fits.0 <- mmkin(models, datasets))</span>
<span class="comment"># time_1 <- system.time(fits.1 <- 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>
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<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
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