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diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html
index 63635f9a..7a96be3b 100644
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@@ -6,14 +6,14 @@
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@@ -56,6 +56,7 @@
<a href="../reference/index.html">Reference</a>
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+
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/jranke/mkin">
@@ -67,16 +68,17 @@
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- <h1>
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+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>
</h1>
-</div>
+ </div>
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- <div class="col-md-9">
<p>Time course of 2,4,5-trichlorophenoxyacetic acid, and the corresponding
2,4,5-trichlorophenol and 2,4,5-trichloroanisole as recovered in diethylether
@@ -85,31 +87,31 @@
<pre><span class='no'>mccall81_245T</span></pre>
- <div class="Format">
- <h2>Format</h2>
+ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
- <p>A dataframe containing the following variables.
+ <p>A dataframe containing the following variables.
<dl class='dl-horizontal'>
<dt><code>name</code></dt><dd>the name of the compound observed. Note that T245 is used as
an acronym for 2,4,5-T. T245 is a legitimate object name
in R, which is necessary for specifying models using
- <code>mkinmod</code>.</dd>
+ <code><a href='mkinmod.html'>mkinmod</a></code>.</dd>
<dt><code>time</code></dt><dd>a numeric vector containing sampling times in days after
treatment</dd>
<dt><code>value</code></dt><dd>a numeric vector containing concentrations in percent of applied radioactivity</dd>
<dt><code>soil</code></dt><dd>a factor containing the name of the soil</dd>
</dl></p>
- </div>
-
- <div class="Source">
- <h2>Source</h2>
+
+ <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
- <p>McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labeled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107
+ <p>McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labeled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107
<a href = 'http://dx.doi.org/10.1021/jf00103a026'>http://dx.doi.org/10.1021/jf00103a026</a></p>
- </div>
- <h2 id="examples">Examples</h2>
- <pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(<span class='kw'>T245</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'>"phenol"</span>),
+
+ <h2 class="hasAnchor" id="examples">
+ <a class="anchor" href="#examples"></a>
+ Examples
+ </h2>
+ <pre class="examples"><div class='input'> <span class='no'>SFO_SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>T245</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'>"phenol"</span>),
<span class='kw'>phenol</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'>"anisole"</span>),
<span class='kw'>anisole</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'><strong class='text-info'>Successfully compiled differential equation model from auto-generated C code.</strong></div><div class='input'> <span class='co'>## Not run: ------------------------------------</span>
<span class='co'># fit.1 &lt;- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"))</span>
@@ -117,13 +119,13 @@
<span class='co'># </span>
<span class='co'>## ---------------------------------------------</span>
<span class='co'># No covariance matrix and k_phenol_sink is really small, therefore fix it to zero</span>
- <span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinfit</span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>),
+ <span class='no'>fit.2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO_SFO</span>, <span class='fu'>subset</span>(<span class='no'>mccall81_245T</span>, <span class='no'>soil</span> <span class='kw'>==</span> <span class='st'>"Commerce"</span>),
<span class='kw'>parms.ini</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='kw'>k_phenol_sink</span> <span class='kw'>=</span> <span class='fl'>0</span>),
<span class='kw'>fixed_parms</span> <span class='kw'>=</span> <span class='st'>"k_phenol_sink"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
<span class='fu'>summary</span>(<span class='no'>fit.2</span>, <span class='kw'>data</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt; mkin version: 0.9.44.9000
#&gt; R version: 3.3.1
-#&gt; Date of fit: Thu Oct 6 10:47:34 2016
-#&gt; Date of summary: Thu Oct 6 10:47:34 2016
+#&gt; Date of fit: Wed Oct 26 23:16:47 2016
+#&gt; Date of summary: Wed Oct 26 23:16:47 2016
#&gt;
#&gt; Equations:
#&gt; d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245
@@ -133,7 +135,7 @@
#&gt;
#&gt; Model predictions using solution type deSolve
#&gt;
-#&gt; Fitted with method Port using 246 model solutions performed in 1.492 s
+#&gt; Fitted with method Port using 246 model solutions performed in 1.487 s
#&gt;
#&gt; Weighting: none
#&gt;
@@ -216,12 +218,29 @@
#&gt; anisole 103.784 344.763
#&gt; </div></pre>
</div>
- <div class="col-md-3">
+ <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+ <h2>Contents</h2>
+ <ul class="nav nav-pills nav-stacked">
+
+ <li><a href="#format">Format</a></li>
+
+ <li><a href="#source">Source</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
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