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  <h1>
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  <div class="col-md-9">
    
    <p>The function usually takes several expressions, each assigning a compound name to 
  a list, specifying the kinetic model type and reaction or transfer to other
  observed compartments. Instead of specifying several expressions, a list
  of lists can be given in the speclist argument.</p>

    <p>For the definition of model types and their parameters, the equations given
  in the FOCUS and NAFTA guidance documents are used.</p>
    

    <pre><span class='fu'>mkinmod</span>(<span class='no'>...</span>, <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"min"</span>, <span class='kw'>speclist</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
    
    <h2>Arguments</h2>
    <dl class="dl-horizontal">
      <dt>...</dt>
      <dd>
    For each observed variable, a list has to be specified as an argument, containing
    at least a component <code>type</code>, specifying the type of kinetics to use
    for the variable. Currently, single first order kinetics &quot;SFO&quot;, 
    indeterminate order rate equation kinetics &quot;IORE&quot;, or
    single first order with reversible binding &quot;SFORB&quot; are implemented for all
    variables, while 
    &quot;FOMC&quot;, &quot;DFOP&quot; and &quot;HS&quot; can additionally be chosen for the first
    variable which is assumed to be the source compartment.
    Additionally, each component of the list can include a character vector <code>to</code>,
    specifying names of variables to which a transfer is to be assumed in the
    model.
    If the argument <code>use_of_ff</code> is set to &quot;min&quot; (default) and the model for 
    the compartment is &quot;SFO&quot; or &quot;SFORB&quot;, an additional component of the list
    can be &quot;sink=FALSE&quot; effectively fixing the flux to sink to zero.
  </dd>
      <dt>use_of_ff</dt>
      <dd>
    Specification of the use of formation fractions in the model equations and, if 
    applicable, the coefficient matrix. If &quot;min&quot;, a minimum use of formation 
    fractions is made in order to avoid fitting the product of formation fractions 
    and rate constants. If &quot;max&quot;, formation fractions are always used.
  </dd>
      <dt>speclist</dt>
      <dd>
    The specification of the observed variables and their submodel types and 
    pathways can be given as a single list using this argument. Default is NULL.
  </dd>
      <dt>quiet</dt>
      <dd>
    Should messages be suppressed?
  </dd>
      <dt>verbose</dt>
      <dd>
    If <code>TRUE</code>, passed to <code>cfunction</code> if applicable to give
    detailed information about the C function being built.
  </dd>
    </dl>
    
    <div class="Value">
      <h2>Value</h2>

      <p>A list of class <code>mkinmod</code> for use with <code>mkinfit</code>, containing</p>
    </div>

    <div class="Note">
      <h2>Note</h2>

      <p>The IORE submodel is not well tested (yet). When using this model for metabolites, 
  you may want to read the second note in the help page to 
  <code>mkinfit</code>.</p>
    </div>

    <div class="References">
      <h2>References</h2>

      <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence and
  Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
  Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
  <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p>
      <p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for
  Evaluating and Calculating Degradation Kinetics in Environmental 
  Media</p>
    </div>
    
    <h2 id="examples">Examples</h2>
    <pre class="examples"><div class='input'><span class='co'># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</span>
<span class='no'>SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))

<span class='co'># One parent compound, one metabolite, both single first order</span>
<span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(
  <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
  <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>mkinsub</span>(<span class='st'>"SFO"</span>))</div><div class='output'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'>
<span class='co'>## Not run: ------------------------------------</span>
<span class='co'># # The above model used to be specified like this, before the advent of mkinsub()</span>
<span class='co'># SFO_SFO &lt;- mkinmod(</span>
<span class='co'>#   parent = list(type = "SFO", to = "m1"),</span>
<span class='co'>#   m1 = list(type = "SFO"))</span>
<span class='co'># </span>
<span class='co'># # Show details of creating the C function</span>
<span class='co'># SFO_SFO &lt;- mkinmod(</span>
<span class='co'>#   parent = mkinsub("SFO", "m1"),</span>
<span class='co'>#   m1 = mkinsub("SFO"), verbose = TRUE)</span>
<span class='co'># </span>
<span class='co'># # If we have several parallel metabolites </span>
<span class='co'># # (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span>
<span class='co'># m_synth_DFOP_par &lt;- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),</span>
<span class='co'>#                            M1 = mkinsub("SFO"),</span>
<span class='co'>#                            M2 = mkinsub("SFO"),</span>
<span class='co'>#                            use_of_ff = "max", quiet = TRUE)</span>
<span class='co'># </span>
<span class='co'># fit_DFOP_par_c &lt;- mkinfit(m_synth_DFOP_par, </span>
<span class='co'>#                           synthetic_data_for_UBA_2014[[12]]$data,</span>
<span class='co'>#                           quiet = TRUE)</span>
<span class='co'>## ---------------------------------------------</span></div></pre>
  </div>
  <div class="col-md-3">
    <h2>Author</h2>
    
  Johannes Ranke

  </div>
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