Static documentation rebuilt by pkgdown

1 files changed, 66 insertions, 69 deletions

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--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -8,11 +8,13 @@
 
 <title>Function to set up a kinetic model with one or more state variables — mkinmod • mkin</title>
 
+
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@@ -32,18 +34,17 @@
 
 
 
-<meta property="og:title" content="Function to set up a kinetic model with one or more state variables — mkinmod" />
 
-<meta property="og:description" content="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.
-For the definition of model types and their parameters, the equations given
-  in the FOCUS and NAFTA guidance documents are used." />
+<meta property="og:title" content="Function to set up a kinetic model with one or more state variables — mkinmod" />
+<meta property="og:description" content="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." />
 <meta name="twitter:card" content="summary" />
 
 
 
+
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@@ -114,7 +115,6 @@ For the definition of model types and their parameters, the equations given
   <a href="../news/index.html">News</a>
 </li>
       </ul>
-      
       <ul class="nav navbar-nav navbar-right">
         
       </ul>
@@ -136,49 +136,47 @@ For the definition of model types and their parameters, the equations given
     </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>
-<p>For the definition of model types and their parameters, the equations given
-  in the FOCUS and NAFTA guidance documents are used.</p>
-    
+    <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>
-    
+    <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>
+      <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>
+      <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>
+      <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>
@@ -186,44 +184,46 @@ For the definition of model types and their parameters, the equations given
     </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>
+      <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</p>
-<dt>diffs</dt><dd><p>A vector of string representations of differential equations,
-      one for each modelling variable.</p></dd>
-    <dt>parms</dt><dd><p>A vector of parameter names occurring in the differential equations.</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>
+    <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>ll</dt><dd><p>The likelihood function, taking the parameter vector as the first argument.</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 (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>
-    
+    <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,
+    <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>
-    
+  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>
+    <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='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>
@@ -239,7 +239,7 @@ For the definition of model types and their parameters, the equations given
 <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 file663b71dc323f.c 2&gt; file663b71dc323f.c.err.txt 
+#&gt;  /usr/lib/R/bin/R CMD SHLIB file59d942b9ac06.c 2&gt; file59d942b9ac06.c.err.txt 
 #&gt; Program source:
 #&gt;   1: #include &lt;R.h&gt;
 #&gt;   2: 
@@ -260,7 +260,7 @@ For the definition of model types and their parameters, the equations given
 #&gt;  17: f[0] = - k_parent_sink * y[0] - k_parent_m1 * y[0];
 #&gt;  18: f[1] = + k_parent_m1 * y[0] - k_m1_sink * 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'># 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>),
@@ -276,13 +276,10 @@ For the definition of model types and their parameters, the equations given
     <h2>Contents</h2>
     <ul class="nav nav-pills nav-stacked">
       <li><a href="#arguments">Arguments</a></li>
-      
       <li><a href="#value">Value</a></li>
-
+      <li><a href="#details">Details</a></li>
       <li><a href="#note">Note</a></li>
-
       <li><a href="#references">References</a></li>
-      
       <li><a href="#examples">Examples</a></li>
     </ul>