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<h1>Function to set up a kinetic model with one or more state variables</h1>
<small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/mkinmod.R'><code>R/mkinmod.R</code></a></small>
<div class="hidden name"><code>mkinmod.Rd</code></div>
</div>
<div class="ref-description">
<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>
</div>
<pre class="usage"><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 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>...</th>
<td><p>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 "SFO", indeterminate order rate equation kinetics "IORE", or
single first order with reversible binding "SFORB" are implemented for all
variables, while "FOMC", "DFOP" and "HS" 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 "min"
(default) and the model for the compartment is "SFO" or "SFORB", an
additional component of the list can be "sink=FALSE" effectively fixing
the flux to sink to zero.</p></td>
</tr>
<tr>
<th>use_of_ff</th>
<td><p>Specification of the use of formation fractions in the
model equations and, if applicable, the coefficient matrix. If "min", a
minimum use of formation fractions is made in order to avoid fitting the
product of formation fractions and rate constants. If "max", formation
fractions are always used.</p></td>
</tr>
<tr>
<th>speclist</th>
<td><p>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.</p></td>
</tr>
<tr>
<th>quiet</th>
<td><p>Should messages be suppressed?</p></td>
</tr>
<tr>
<th>verbose</th>
<td><p>If <code>TRUE</code>, passed to <code>cfunction</code> if
applicable to give detailed information about the C function being built.</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>A list of class <code>mkinmod</code> for use with <code><a href='mkinfit.html'>mkinfit</a></code>,
containing, among others,</p>
<dt>diffs</dt><dd><p>A vector of string representations of differential equations, one for
each modelling variable.</p></dd>
<dt>map</dt><dd><p>A list containing named character vectors for each observed variable,
specifying the modelling variables by which it is represented.</p></dd>
<dt>use_of_ff</dt><dd><p>The content of <code>use_of_ff</code> is passed on in this list component.</p></dd>
<dt>coefmat</dt><dd><p>The coefficient matrix, if the system of differential equations can be
represented by one.</p></dd>
<dt>cf</dt><dd><p>If generated, the compiled function as returned by cfunction.</p></dd>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>For the definition of model types and their parameters, the equations given
in the FOCUS and NAFTA guidance documents are used.</p>
<h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
<p>The IORE submodel is not well tested for metabolites. When using this
model for metabolites, you may want to read the second note in the help
page to <code><a href='mkinfit.html'>mkinfit</a></code>.</p>
<h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
<p>FOCUS (2006) “Guidance Document on Estimating Persistence
and Degradation Kinetics from Environmental Fate Studies on Pesticides in
EU Registration” Report of the FOCUS Work Group on Degradation Kinetics,
EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
<a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
<p>NAFTA Technical Working Group on Pesticides (not dated) Guidance for
Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>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'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></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'><-</span> <span class='fu'>mkinmod</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>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
<span class='co'># \dontrun{</span>
<span class='co'># The above model used to be specified like this, before the advent of mkinsub()</span>
<span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(
<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>),
<span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
<span class='co'># Show details of creating the C function</span>
<span class='no'>SFO_SFO</span> <span class='kw'><-</span> <span class='fu'>mkinmod</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='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#> Compilation argument:
#> /usr/lib/R/bin/R CMD SHLIB file66a9718e919b.c 2> file66a9718e919b.c.err.txt
#> Program source:
#> 1: #include <R.h>
#> 2:
#> 3:
#> 4: static double parms [3];
#> 5: #define k_parent_sink parms[0]
#> 6: #define k_parent_m1 parms[1]
#> 7: #define k_m1_sink parms[2]
#> 8:
#> 9: void initpar(void (* odeparms)(int *, double *)) {
#> 10: int N = 3;
#> 11: odeparms(&N, parms);
#> 12: }
#> 13:
#> 14:
#> 15: void func ( int * n, double * t, double * y, double * f, double * rpar, int * ipar ) {
#> 16:
#> 17: f[0] = - k_parent_sink * y[0] - k_parent_m1 * y[0];
#> 18: f[1] = + k_parent_m1 * y[0] - k_m1_sink * y[1];
#> 19: }</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
<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='no'>m_synth_DFOP_par</span> <span class='kw'><-</span> <span class='fu'>mkinmod</span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"DFOP"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</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='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>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='no'>fit_DFOP_par_c</span> <span class='kw'><-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>m_synth_DFOP_par</span>,
<span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>12</span>]]$<span class='no'>data</span>,
<span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='co'># }</span></div></pre>
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