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authorJohannes Ranke <jranke@uni-bremen.de>2015-11-09 09:05:15 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2015-11-09 09:05:15 +0100
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+ <header>
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+ </header>
+
+ <h1>
+ Function to set up a kinetic model with one or more state variables
+</h1>
+
+<div class="row">
+ <div class="span8">
+ <h2>Usage</h2>
+ <pre><div>mkinmod(..., use_of_ff&nbsp;=&nbsp;"min", speclist&nbsp;=&nbsp;NULL, quiet&nbsp;=&nbsp;FALSE, verbose&nbsp;=&nbsp;FALSE)</div></pre>
+
+ <h2>Arguments</h2>
+ <dl>
+ <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 "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.
+ </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 "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.
+ </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><a href='http://www.inside-r.org/packages/cran/inline/docs/cfunction'>cfunction</a></code> if applicable to give
+ detailed information about the C function being built.
+ </dd>
+ </dl>
+
+ <div class="Description">
+ <h2>Description</h2>
+
+ <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>
+
+ </div>
+
+ <div class="Value">
+ <h2>Value</h2>
+
+ <p><dl>
+ A list of class <code>mkinmod</code> for use with <code><a href='mkinfit.html'>mkinfit</a></code>, containing
+ <dt>diffs</dt><dd> A vector of string representations of differential equations,
+ one for each modelling variable. </dd></p>
+
+ <p><dt>parms</dt><dd> A vector of parameter names occurring in the differential equations. </dd></p>
+
+ <p><dt>map</dt><dd> A list containing named character vectors for each observed variable, specifying
+ the modelling variables by which it is represented. </dd></p>
+
+ <p><dt>use_of_ff</dt><dd> The content of <code>use_of_ff</code> is passed on in this list component. </dd></p>
+
+ <p><dt>coefmat</dt><dd> The coefficient matrix, if the system of differential equations can be
+ represented by one. </dd></p>
+
+ <p></dl></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><a href='mkinfit.html'>mkinfit</a></code>.</p>
+
+ </div>
+
+ <div class="References">
+ <h2>References</h2>
+
+ <p>FOCUS (2006) &#147;Guidance Document on Estimating Persistence and
+ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
+ Registration&#148; 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'># Specify the SFO model (this is not needed any more, as we can now mkinfit(&quot;SFO&quot;, ...)
+SFO &lt;- mkinmod(parent = list(type = &quot;SFO&quot;))
+
+# One parent compound, one metabolite, both single first order
+SFO_SFO &lt;- mkinmod(
+ parent = mkinsub(&quot;SFO&quot;, &quot;m1&quot;),
+ m1 = mkinsub(&quot;SFO&quot;))
+</div>
+<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong>
+<div class='input'>
+# The above model used to be specified like this, before the advent of mkinsub()
+SFO_SFO &lt;- mkinmod(
+ parent = list(type = &quot;SFO&quot;, to = &quot;m1&quot;),
+ m1 = list(type = &quot;SFO&quot;))
+</div>
+<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong>
+<div class='input'>
+# Show details of creating the C function
+SFO_SFO &lt;- mkinmod(
+ parent = mkinsub(&quot;SFO&quot;, &quot;m1&quot;),
+ m1 = mkinsub(&quot;SFO&quot;), verbose = TRUE)
+</div>
+<div class='output'>Compilation argument:
+ /usr/lib/R/bin/R CMD SHLIB file5a355b71ca9.c 2&gt; file5a355b71ca9.c.err.txt
+Program source:
+ 1: #include &lt;R.h&gt;
+ 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(&amp;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>
+<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong>
+<div class='input'>
+# If we have several parallel metabolites
+# (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)
+m_synth_DFOP_par &lt;- mkinmod(parent = mkinsub(&quot;DFOP&quot;, c(&quot;M1&quot;, &quot;M2&quot;)),
+ M1 = mkinsub(&quot;SFO&quot;),
+ M2 = mkinsub(&quot;SFO&quot;),
+ use_of_ff = &quot;max&quot;, quiet = TRUE)
+
+## Not run:
+# fit_DFOP_par_c &lt;- mkinfit(m_synth_DFOP_par,
+# synthetic_data_for_UBA_2014[[12]]$data,
+# quiet = TRUE)
+# ## End(Not run)
+</div></pre>
+ </div>
+ <div class="span4">
+ <!-- <ul>
+ <li>mkinmod</li>
+ </ul>
+ <ul>
+ <li> models </li>
+ </ul> -->
+
+
+ <h2>Author</h2>
+
+ Johannes Ranke
+
+
+ </div>
+</div>
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