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@@ -6,13 +6,16 @@
 <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 more datasets — mmkin • mkin</title>
+<title>Fit one or more kinetic models with one or more state variables to one or
+more datasets — mmkin • mkin</title>
+
 
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@@ -32,14 +35,16 @@
 
 
 
-<meta property="og:title" content="Fit one or more kinetic models with one or more state variables to one or more datasets — mmkin" />
 
-<meta property="og:description" content="This function calls mkinfit on all combinations of models and datasets
-  specified in its first two arguments." />
+<meta property="og:title" content="Fit one or more kinetic models with one or more state variables to one or
+more datasets — mmkin" />
+<meta property="og:description" content="This function calls mkinfit on all combinations of models and
+datasets specified in its first two arguments." />
 <meta name="twitter:card" content="summary" />
 
 
 
+
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@@ -110,7 +115,6 @@
   <a href="../news/index.html">News</a>
 </li>
       </ul>
-      
       <ul class="nav navbar-nav navbar-right">
         
       </ul>
@@ -126,65 +130,64 @@
 <div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
-    <h1>Fit one or more kinetic models with one or more state variables to one or more datasets</h1>
+    <h1>Fit one or more kinetic models with one or more state variables to one or
+more datasets</h1>
     
     <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>
-    
+    <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>
 
-    <pre class="usage"><span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>,
-      <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span>(<span class='fu'>detectCores</span>()/<span class='fl'>2</span>), <span class='kw'>cluster</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
-    
+    <pre class="usage"><span class='fu'>mmkin</span>(<span class='kw'>models</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span>), <span class='no'>datasets</span>,
+  <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>round</a></span>(<span class='fu'>detectCores</span>()/<span class='fl'>2</span>), <span class='kw'>cluster</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)</pre>
+
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
       <th>models</th>
-      <td><p>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.</p></td>
+      <td><p>Either a character vector of shorthand names like 
+<code><a href='https://rdrr.io/r/base/c.html'>c("SFO", "FOMC", "DFOP", "HS", "SFORB")</a></code>, or an optionally named
+list of <code><a href='mkinmod.html'>mkinmod</a></code> objects.</p></td>
     </tr>
     <tr>
       <th>datasets</th>
-      <td><p>An optionally named list of datasets suitable as observed data for
-    <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td>
+      <td><p>An optionally named list of datasets suitable as observed
+data for <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td>
     </tr>
     <tr>
       <th>cores</th>
-      <td><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.</p></td>
+      <td><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.</p></td>
     </tr>
     <tr>
       <th>cluster</th>
-      <td><p>A cluster as returned by <code>makeCluster</code> to be used for parallel
-    execution.</p></td>
+      <td><p>A cluster as returned by <code>makeCluster</code> to be used
+for parallel execution.</p></td>
     </tr>
     <tr>
       <th>...</th>
       <td><p>Further arguments that will be passed to <code><a href='mkinfit.html'>mkinfit</a></code>.</p></td>
     </tr>
     </table>
-    
+
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
-    <p>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.</p>
-    
+    <p>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.</p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>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 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>
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='co'># \dontrun{</span>
+    <pre class="examples"><div class='input'>
+<span class='co'># \dontrun{</span>
 <span class='no'>m_synth_SFO_lin</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M1"</span>),
                            <span class='kw'>M1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"M2"</span>),
                            <span class='kw'>M2</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
@@ -199,8 +202,8 @@
 <span class='no'>time_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fits.4</span> <span class='kw'>&lt;-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>))
 
 <span class='no'>time_default</span></div><div class='output co'>#&gt;        User      System verstrichen 
-#&gt;       0.016       0.029       4.960 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt;        User      System verstrichen 
-#&gt;      19.084       0.004      19.099 </div><div class='input'>
+#&gt;       0.011       0.032       4.774 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#&gt;        User      System verstrichen 
+#&gt;      18.676       0.000      18.687 </div><div class='input'>
 <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#&gt; $ff
 #&gt;   parent_M1 parent_sink       M1_M2     M1_sink 
 #&gt;   0.7340481   0.2659519   0.7505684   0.2494316 
@@ -221,17 +224,15 @@
 <span class='co'># Plotting with mmkin (single brackets, extracting an mmkin object) does not</span>
 <span class='co'># allow to plot the observed variables separately</span>
 <span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='no'>fits.0</span>[<span class='fl'>1</span>, <span class='fl'>1</span>])</div><div class='img'><img src='mmkin-5.png' alt='' width='700' height='433' /></div><div class='input'># }
+
 </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
     <ul class="nav nav-pills nav-stacked">
       <li><a href="#arguments">Arguments</a></li>
-      
       <li><a href="#value">Value</a></li>
-
       <li><a href="#see-also">See also</a></li>
-      
       <li><a href="#examples">Examples</a></li>
     </ul>