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authorJohannes Ranke <jranke@uni-bremen.de>2016-09-10 05:21:52 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2016-09-10 05:55:25 +0200
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+
+ <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><span class="functioncall"><a href='mkinmod.html'>mkinmod</a></span><span class="keyword">(</span><span class="symbol">...</span><span class="keyword">,</span> <span class="argument">use_of_ff</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="string">"min"</span><span class="keyword">,</span> <span class="argument">speclist</span>&nbsp;<span class="argument">=</span>&nbsp;NULL<span class="keyword">,</span> <span class="argument">quiet</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">FALSE</span><span class="keyword">,</span> <span class="argument">verbose</span>&nbsp;<span class="argument">=</span>&nbsp;<span class="number">FALSE</span><span class="keyword">)</span></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 &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><a href='http://www.rdocumentation.org/packages/inline/topics/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'><span class="comment"># Specify the SFO model (this is not needed any more, as we can now mkinfit("SFO", ...)</span>
+<span class="symbol">SFO</span> <span class="assignement">&lt;-</span> <span class="functioncall"><a href='mkinmod.html'>mkinmod</a></span><span class="keyword">(</span><span class="argument">parent</span> <span class="argument">=</span> <span class="functioncall"><a href='http://www.rdocumentation.org/packages/base/topics/list'>list</a></span><span class="keyword">(</span><span class="argument">type</span> <span class="argument">=</span> <span class="string">"SFO"</span><span class="keyword">)</span><span class="keyword">)</span>
+
+<span class="comment"># One parent compound, one metabolite, both single first order</span>
+<span class="symbol">SFO_SFO</span> <span class="assignement">&lt;-</span> <span class="functioncall"><a href='mkinmod.html'>mkinmod</a></span><span class="keyword">(</span>
+ <span class="argument">parent</span> <span class="argument">=</span> <span class="functioncall"><a href='mkinsub.html'>mkinsub</a></span><span class="keyword">(</span><span class="string">"SFO"</span><span class="keyword">,</span> <span class="string">"m1"</span><span class="keyword">)</span><span class="keyword">,</span>
+ <span class="argument">m1</span> <span class="argument">=</span> <span class="functioncall"><a href='mkinsub.html'>mkinsub</a></span><span class="keyword">(</span><span class="string">"SFO"</span><span class="keyword">)</span><span class="keyword">)</span></div>
+<strong class='message'>Successfully compiled differential equation model from auto-generated C code.</strong>
+<div class='input'>
+<span class="comment">## Not run: ------------------------------------</span>
+<span class="comment"># # The above model used to be specified like this, before the advent of mkinsub()</span>
+<span class="comment"># SFO_SFO &lt;- mkinmod(</span>
+<span class="comment"># parent = list(type = "SFO", to = "m1"),</span>
+<span class="comment"># m1 = list(type = "SFO"))</span>
+<span class="comment"># </span>
+<span class="comment"># # Show details of creating the C function</span>
+<span class="comment"># SFO_SFO &lt;- mkinmod(</span>
+<span class="comment"># parent = mkinsub("SFO", "m1"),</span>
+<span class="comment"># m1 = mkinsub("SFO"), verbose = TRUE)</span>
+<span class="comment"># </span>
+<span class="comment"># # If we have several parallel metabolites </span>
+<span class="comment"># # (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span>
+<span class="comment"># m_synth_DFOP_par &lt;- mkinmod(parent = mkinsub("DFOP", c("M1", "M2")),</span>
+<span class="comment"># M1 = mkinsub("SFO"),</span>
+<span class="comment"># M2 = mkinsub("SFO"),</span>
+<span class="comment"># use_of_ff = "max", quiet = TRUE)</span>
+<span class="comment"># </span>
+<span class="comment"># fit_DFOP_par_c &lt;- mkinfit(m_synth_DFOP_par, </span>
+<span class="comment"># synthetic_data_for_UBA_2014[[12]]$data,</span>
+<span class="comment"># quiet = TRUE)</span>
+<span class="comment">## ---------------------------------------------</span></div></pre>
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+ Johannes Ranke
+
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