Merge branch 'master' of kolab:mkin

1 files changed, 25 insertions, 33 deletions

diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index 5703b188..c1287905 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -18,12 +18,24 @@
 <!-- Font Awesome icons -->
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+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<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 name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -70,6 +82,9 @@
       <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
     </li>
     <li>
+      <a href="../articles/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+    </li>
+    <li>
       <a href="../articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
     </li>
     <li>
@@ -83,12 +98,7 @@
       </ul>
       
       <ul class="nav navbar-nav navbar-right">
-        <li>
-  <a href="http://github.com/jranke/mkin">
-    <span class="fa fa-github fa-lg"></span>
-     
-  </a>
-</li>
+        
       </ul>
     </div><!--/.nav-collapse -->
   </div><!--/.container -->
@@ -182,7 +192,7 @@
   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>
+  <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>
@@ -196,36 +206,17 @@
 <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'>
-
+</div><span class='co'># NOT RUN {</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'>list</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'>list</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='kw'>m1</span> <span class='kw'>=</span> <span class='fu'>list</span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))
+
 <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 file519167a14b3a.c 2&gt; file519167a14b3a.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_sink parms[0]
-#&gt;   6: #define k_parent_m1 parms[1]
-#&gt;   7: #define k_m1_sink 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_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='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>)
+
 <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'>c</span>(<span class='st'>"M1"</span>, <span class='st'>"M2"</span>)),
@@ -235,7 +226,8 @@
 
 <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>)</div></pre>
+                          <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
+<span class='co'># }</span></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
@@ -264,7 +256,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
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