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-rw-r--r--docs/reference/mkinmod.html57
1 files changed, 28 insertions, 29 deletions
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index b25f2da3..d1204e2e 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -10,23 +10,27 @@
<!-- jquery -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
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+
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+<script src="../bootstrap-toc.js"></script>
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@@ -40,7 +44,6 @@
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" />
@@ -58,7 +61,7 @@ list of lists can be given in the speclist argument." />
</head>
- <body>
+ <body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -72,7 +75,7 @@ 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-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span>
</span>
</div>
@@ -116,7 +119,12 @@ list of lists can be given in the speclist argument." />
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
-
+ <li>
+ <a href="http://github.com/jranke/mkin/">
+ <span class="fab fa fab fa-github fa-lg"></span>
+
+ </a>
+</li>
</ul>
</div><!--/.nav-collapse -->
@@ -131,7 +139,7 @@ list of lists can be given in the speclist argument." />
<div class="col-md-9 contents">
<div class="page-header">
<h1>Function to set up a kinetic model with one or more state variables</h1>
-
+ <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/mkinmod.R'><code>R/mkinmod.R</code></a></small>
<div class="hidden name"><code>mkinmod.Rd</code></div>
</div>
@@ -205,7 +213,7 @@ applicable to give detailed information about the C function being built.</p></t
<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>
+ <dt>cf</dt><dd><p>If generated, the compiled function as returned by cfunction.</p></dd>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
@@ -244,7 +252,7 @@ in the FOCUS and NAFTA guidance documents are used.</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 file414965c335f6.c 2&gt; file414965c335f6.c.err.txt
+#&gt; /usr/lib/R/bin/R CMD SHLIB file66a9718e919b.c 2&gt; file66a9718e919b.c.err.txt
#&gt; Program source:
#&gt; 1: #include &lt;R.h&gt;
#&gt; 2:
@@ -277,19 +285,10 @@ in the FOCUS and NAFTA guidance documents are used.</p>
<span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='co'># }</span></div></pre>
</div>
- <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
- <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>
-
- <h2>Author</h2>
- <p>Johannes Ranke</p>
+ <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+ <nav id="toc" data-toggle="toc" class="sticky-top">
+ <h2 data-toc-skip>Contents</h2>
+ </nav>
</div>
</div>
@@ -300,7 +299,7 @@ in the FOCUS and NAFTA guidance documents are used.</p>
</div>
<div class="pkgdown">
- <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+ <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
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