aboutsummaryrefslogblamecommitdiff
path: root/inst/web/mmkin.html
blob: b3e7a6fd242e485de58e38b7bb49362c7e6855a6 (plain) (tree)
1
2
3
4
5


                          
                                 





























                                                                                      
                                               






































































                                                                                                                                               

                                                                                        
  

                                                                                         

                                                                             
                                                       
  
                                                                      




                                                                           









                                                                                 





























                                                                                                                                                       
<!DOCTYPE html>
<html lang="en">
  <head>
    <meta charset="utf-8">
<title>mmkin. mkin 0.9.43</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="author" content="
  Johannes Ranke
">

<link href="css/bootstrap.css" rel="stylesheet">
<link href="css/bootstrap-responsive.css" rel="stylesheet">
<link href="css/highlight.css" rel="stylesheet">
<link href="css/staticdocs.css" rel="stylesheet">

<!--[if lt IE 9]>
  <script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
<![endif]-->

<script type="text/x-mathjax-config">
  MathJax.Hub.Config({
    tex2jax: {
      inlineMath: [ ['$','$'], ["\\(","\\)"] ],
      processEscapes: true
    }
  });
</script>
<script type="text/javascript"
  src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
</script>
  </head>

  <body>
    <div class="navbar">
  <div class="navbar-inner">
    <div class="container">
      <a class="brand" href="#">mkin 0.9.43</a>
      <div class="nav">
        <ul class="nav">
          <li><a href="index.html"><i class="icon-home icon-white"></i> Index</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><div>mmkin(models, datasets, cores&nbsp;=&nbsp;round(detectCores()/2), cluster&nbsp;=&nbsp;NULL, ...)</div></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.inside-r.org/r-doc/parallel/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'>## Not run: 
# m_synth_SFO_lin &lt;- mkinmod(parent = mkinsub(&quot;SFO&quot;, &quot;M1&quot;),
#                            M1 = mkinsub(&quot;SFO&quot;, &quot;M2&quot;),
#                            M2 = mkinsub(&quot;SFO&quot;), use_of_ff = &quot;max&quot;)
# 
# m_synth_FOMC_lin &lt;- mkinmod(parent = mkinsub(&quot;FOMC&quot;, &quot;M1&quot;),
#                             M1 = mkinsub(&quot;SFO&quot;, &quot;M2&quot;),
#                             M2 = mkinsub(&quot;SFO&quot;), use_of_ff = &quot;max&quot;)
# 
# models &lt;- list(SFO_lin = m_synth_SFO_lin, FOMC_lin = m_synth_FOMC_lin)
# datasets &lt;- lapply(synthetic_data_for_UBA_2014[1:3], function(x) x$data)
# names(datasets) &lt;- paste(&quot;Dataset&quot;, 1:3)
# 
# time_default &lt;- system.time(fits.0 &lt;- mmkin(models, datasets))
# time_1 &lt;- system.time(fits.1 &lt;- mmkin(models, datasets, cores = 1))
# 
# time_default
# time_1
# 
# endpoints(fits[[&quot;SFO_lin&quot;, 2]])
# 
# # Plot.mkinfit handles rows or columns of mmkin result objects
# plot(fits.0[1, ])
# plot(fits.0[1, ], obs_var = c(&quot;M1&quot;, &quot;M2&quot;))
# plot(fits.0[, 1])
# # Use double brackets to extract a single mkinfit object, which will be plotted
# # by plot.mkinfit
# plot(fits.0[[1, 1]], sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE)
# # Plotting with mmkin (single brackets, extracting an mmkin object) does not
# # allow to plot the observed variables separately
# plot(fits.0[1, 1])
# ## End(Not run)
</div></pre>
  </div>
  <div class="span4">
    <!-- <ul>
      <li>mmkin</li>
    </ul>
    <ul>
      <li> optimize </li>
    </ul> -->
      
    <h2>See also</h2>
    
  <code><a href='Extract.mmkin.html'>[.mmkin</a></code> for subsetting, <code><a href='plot.mmkin.html'>plot.mmkin</a></code> for plotting.

    
    <h2>Author</h2>
    
  Johannes Ranke

    
  </div>
</div>
      
      <footer>
      <p class="pull-right"><a href="#">Back to top</a></p>
<p>Built by <a href="https://github.com/hadley/staticdocs">staticdocs</a>. Styled with <a href="http://twitter.github.com/bootstrap">bootstrap</a>.</p>
      </footer>
    </div>
  </body>
</html>

Contact - Imprint