Merge branch 'master' of kolab:mkin

1 files changed, 15 insertions, 12 deletions

diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html
index d9dd8ad5..af04f755 100644
--- a/docs/articles/FOCUS_D.html
+++ b/docs/articles/FOCUS_D.html
@@ -8,8 +8,11 @@
 <title>Example evaluation of FOCUS Example Dataset D • mkin</title>
 <!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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@@ -77,7 +80,7 @@
       <h1>Example evaluation of FOCUS Example Dataset D</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2018-01-16</h4>
+            <h4 class="date">2018-03-01</h4>
           </div>
 
     
@@ -85,7 +88,7 @@
 <div class="contents">
 <p>This is just a very simple vignette showing how to fit a degradation model for a parent compound with one transformation product using <code>mkin</code>. After loading the library we look a the data. We have observed concentrations in the column named <code>value</code> at the times specified in column <code>time</code> for the two observed variables named <code>parent</code> and <code>m1</code>.</p>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(<span class="st">"mkin"</span>, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)
-<span class="kw">print</span>(FOCUS_2006_D)</code></pre></div>
+<span class="kw">print</span>(FOCUS_<span class="dv">2006</span>_D)</code></pre></div>
 <pre><code>##      name time  value
 ## 1  parent    0  99.46
 ## 2  parent    0 102.04
@@ -135,13 +138,13 @@
 <p>The call to mkinmod returns a degradation model. The differential equations represented in R code can be found in the character vector <code>$diffs</code> of the <code>mkinmod</code> object. If a C compiler (gcc) is installed and functional, the differential equation model will be compiled from auto-generated C code.</p>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>), <span class="dt">m1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</code></pre></div>
 <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">print</span>(SFO_SFO$diffs)</code></pre></div>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">print</span>(SFO_SFO<span class="op">$</span>diffs)</code></pre></div>
 <pre><code>##                                                       parent 
 ## "d_parent = - k_parent_sink * parent - k_parent_m1 * parent" 
 ##                                                           m1 
 ##             "d_m1 = + k_parent_m1 * parent - k_m1_sink * m1"</code></pre>
 <p>We do the fitting without progress report (<code>quiet = TRUE</code>).</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">fit &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_2006_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</code></pre></div>
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">fit &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mkinfit.html">mkinfit</a></span>(SFO_SFO, FOCUS_<span class="dv">2006</span>_D, <span class="dt">quiet =</span> <span class="ot">TRUE</span>)</code></pre></div>
 <p>A plot of the fit including a residual plot for both observed variables is obtained using the <code>plot_sep</code> method for <code>mkinfit</code> objects, which shows separate graphs for all compounds and their residuals.</p>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(fit, <span class="dt">lpos =</span> <span class="kw">c</span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>))</code></pre></div>
 <p><img src="FOCUS_D_files/figure-html/plot-1.png" width="768"></p>
@@ -150,10 +153,10 @@
 <p><img src="FOCUS_D_files/figure-html/plot_2-1.png" width="768"></p>
 <p>A comprehensive report of the results is obtained using the <code>summary</code> method for <code>mkinfit</code> objects.</p>
 <div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">summary</span>(fit)</code></pre></div>
-<pre><code>## mkin version:    0.9.46.1 
-## R version:       3.4.1 
-## Date of fit:     Thu Sep 14 12:15:01 2017 
-## Date of summary: Thu Sep 14 12:15:02 2017 
+<pre><code>## mkin version:    0.9.46.3 
+## R version:       3.4.3 
+## Date of fit:     Thu Mar  1 14:17:55 2018 
+## Date of summary: Thu Mar  1 14:17:55 2018 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -161,7 +164,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 1.14 s
+## Fitted with method Port using 153 model solutions performed in 0.993 s
 ## 
 ## Weighting: none
 ## 
@@ -286,7 +289,7 @@
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