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authorJohannes Ranke <jranke@uni-bremen.de>2020-05-27 06:06:08 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-05-27 06:06:08 +0200
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treee91f627fba0580ef237ecbc8f24d6294a59597d3 /docs/dev/reference/mkinmod.html
parent675a733fa2acc08daabb9b8b571c7d658f281f73 (diff)
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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'>"max"</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>deg_func</dt><dd><p>If generated, a function containing the solution of the degradation
+model.</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, a compiled function calculating the derivatives 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) &#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://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'>&lt;-</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='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'><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'>#&gt; <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'>&lt;-</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'>#&gt; <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'>&lt;-</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'>#&gt; Compilation argument:
+#&gt; /usr/lib/R/bin/R CMD SHLIB file1bc3f55ac46.c 2&gt; file1bc3f55ac46.c.err.txt
+#&gt; Program source:
+#&gt; 1: #include &lt;R.h&gt;
+#&gt; 2:
+#&gt; 3:
+#&gt; 4: static double parms [3];
+#&gt; 5: #define k_parent parms[0]
+#&gt; 6: #define f_parent_to_m1 parms[1]
+#&gt; 7: #define k_m1 parms[2]
+#&gt; 8:
+#&gt; 9: void initpar(void (* odeparms)(int *, double *)) {
+#&gt; 10: int N = 3;
+#&gt; 11: odeparms(&amp;N, parms);
+#&gt; 12: }
+#&gt; 13:
+#&gt; 14:
+#&gt; 15: void func ( int * n, double * t, double * y, double * f, double * rpar, int * ipar ) {
+#&gt; 16:
+#&gt; 17: f[0] = - k_parent * y[0];
+#&gt; 18: f[1] = + f_parent_to_m1 * k_parent * y[0] - k_m1 * y[1];
+#&gt; 19: }</div><div class='output co'>#&gt; <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'>&lt;-</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'>&lt;-</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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