Improve mkinmod docs

2 files changed, 57 insertions, 33 deletions

diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml
index 31ffe2ad..a7e9e750 100644
--- a/docs/dev/pkgdown.yml
+++ b/docs/dev/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
   NAFTA_examples: web_only/NAFTA_examples.html
   benchmarks: web_only/benchmarks.html
   compiled_models: web_only/compiled_models.html
-last_built: 2020-05-27T05:43Z
+last_built: 2020-05-27T06:53Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/dev/reference/mkinmod.html b/docs/dev/reference/mkinmod.html
index 80a72b2b..14b9eb1a 100644
--- a/docs/dev/reference/mkinmod.html
+++ b/docs/dev/reference/mkinmod.html
@@ -40,10 +40,9 @@
 
 
 <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 property="og:description" content="This function is usually called using a call to mkinsub() for each observed
+variable, specifying the corresponding submodel as well as outgoing pathways
+(see examples)." />
 
 
 <meta name="robots" content="noindex">
@@ -75,7 +74,7 @@ list of lists can be given in the speclist argument." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-danger" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
+        <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span>
       </span>
     </div>
 
@@ -147,10 +146,9 @@ list of lists can be given in the speclist argument." />
     </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>This function is usually called using a call to <code><a href='mkinsub.html'>mkinsub()</a></code> for each observed
+variable, specifying the corresponding submodel as well as outgoing pathways
+(see examples).</p>
     </div>
 
     <pre class="usage"><span class='fu'>mkinmod</span>(
@@ -166,19 +164,19 @@ list of lists can be given in the speclist argument.</p>
     <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"
+      <td><p>For each observed variable, a list as obtained by <code><a href='mkinsub.html'>mkinsub()</a></code>
+has to be specified as an argument (see examples).  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", "HS" and "logistic"
+can additionally be chosen for the first variable which is assumed to be
+the source compartment.
+Additionally, <code><a href='mkinsub.html'>mkinsub()</a></code> has an argument <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>
+additional <code><a href='mkinsub.html'>mkinsub()</a></code> argument can be <code>sink = FALSE</code>, effectively
+fixing the flux to sink to zero.</p></td>
     </tr>
     <tr>
       <th>use_of_ff</th>
@@ -200,14 +198,14 @@ argument. Default is NULL.</p></td>
     </tr>
     <tr>
       <th>verbose</th>
-      <td><p>If <code>TRUE</code>, passed to <code>cfunction</code> if
+      <td><p>If <code>TRUE</code>, passed to <code><a href='https://rdrr.io/pkg/inline/man/cfunction.html'>inline::cfunction()</a></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>,
+    <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>
@@ -225,11 +223,18 @@ returned by cfunction.</p></dd>
 
     <p>For the definition of model types and their parameters, the equations given
 in the FOCUS and NAFTA guidance documents are used.</p>
+<p>For kinetic models with more than one observed variable, a symbolic solution
+of the system of differential equations is included in the resulting
+mkinmod object in some cases, speeding up the solution.</p>
+<p>If a C compiler is found by <code><a href='https://rdrr.io/pkg/pkgbuild/man/has_compiler.html'>pkgbuild::has_compiler()</a></code> and there
+is more than one observed variable in the specification, C code is generated
+for evaluating the differential equations, compiled using
+<code><a href='https://rdrr.io/pkg/inline/man/cfunction.html'>inline::cfunction()</a></code> and added to the resulting mkinmod object.</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>
+model for metabolites, you may want to read the note in the help
+page to <a href='mkinfit.html'>mkinfit</a>.</p>
     <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
 
     <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence
@@ -258,7 +263,7 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
 <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;  /usr/lib/R/bin/R CMD SHLIB file15d25f6867c9.c 2&gt; file15d25f6867c9.c.err.txt 
 #&gt; Program source:
 #&gt;   1: #include &lt;R.h&gt;
 #&gt;   2: 
@@ -279,16 +284,35 @@ Evaluating and Calculating Degradation Kinetics in Environmental Media</p>
 #&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'># The symbolic solution which is available in this case is not</span>
+<span class='co'># made for human reading but for speed of computation</span>
+<span class='no'>SFO_SFO</span>$<span class='no'>deg_func</span></div><div class='output co'>#&gt; function (observed, odeini, odeparms) 
+#&gt; {
+#&gt;     predicted &lt;- numeric(0)
+#&gt;     with(as.list(odeparms), {
+#&gt;         t &lt;- observed[observed$name == "parent", "time"]
+#&gt;         predicted &lt;&lt;- c(predicted, SFO.solution(t, odeini["parent"], 
+#&gt;             k_parent))
+#&gt;         t &lt;- observed[observed$name == "m1", "time"]
+#&gt;         predicted &lt;&lt;- c(predicted, (((k_m1 - k_parent) * odeini["m1"] - 
+#&gt;             f_parent_to_m1 * k_parent * odeini["parent"]) * exp(-k_m1 * 
+#&gt;             t) + f_parent_to_m1 * k_parent * odeini["parent"] * 
+#&gt;             exp(-k_parent * t))/(k_m1 - k_parent))
+#&gt;     })
+#&gt;     return(predicted)
+#&gt; }
+#&gt; &lt;environment: 0x5555576161e0&gt;</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'>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>]]$<span class='no'>data</span>,
-                          <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+  <span class='no'>synthetic_data_for_UBA_2014</span><span class='kw'>[[</span><span class='fl'>12</span>]]$<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>
   </div>
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