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-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.6</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span>
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@@ -74,7 +74,14 @@
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-      <h1>Example evaluation of FOCUS Example Dataset D</h1>
+      <h1 data-toc-skip>Example evaluation of FOCUS Example Dataset D</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2019-11-01</h4>
-      
+            <h4 class="date">2020-05-07</h4>
       
+      <small class="dont-index">Source: <a href="http://github.com/jranke/mkin/blob/master/vignettes/FOCUS_D.Rmd"><code>vignettes/FOCUS_D.Rmd</code></a></small>
       <div class="hidden name"><code>FOCUS_D.Rmd</code></div>
 
     </div>
@@ -100,8 +107,8 @@
     
     
 <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 at 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" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/library.html">library</a></span>(mkin, <span class="dt">quietly =</span> <span class="ot">TRUE</span>)</a>
-<a class="sourceLine" id="cb1-2" title="2"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(FOCUS_<span class="dv">2006</span>_D)</a></code></pre></div>
+<div class="sourceCode" id="cb1"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/library.html">library</a></span>(<span class="no">mkin</span>, <span class="kw">quietly</span> <span class="kw">=</span> <span class="fl">TRUE</span>)
+<span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">FOCUS_2006_D</span>)</pre></body></html></div>
 <pre><code>##      name time  value
 ## 1  parent    0  99.46
 ## 2  parent    0 102.04
@@ -149,29 +156,29 @@
 ## 44     m1  120  33.31</code></pre>
 <p>Next we specify the degradation model: The parent compound degrades with simple first-order kinetics (SFO) to one metabolite named m1, which also degrades with SFO kinetics.</p>
 <p>The call to mkinmod returns a degradation model. The differential equations represented in R code can be found in the character vector <code>$diffs</code> of the <code>mkinmod</code> object. If a C compiler (gcc) is installed and functional, the differential equation model will be compiled from auto-generated C code.</p>
-<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1">SFO_SFO &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="dt">parent =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>), <span class="dt">m1 =</span> <span class="kw"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</a></code></pre></div>
+<div class="sourceCode" id="cb3"><html><body><pre class="r"><span class="no">SFO_SFO</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/mkinmod.html">mkinmod</a></span>(<span class="kw">parent</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>, <span class="st">"m1"</span>), <span class="kw">m1</span> <span class="kw">=</span> <span class="fu"><a href="../reference/mkinsub.html">mkinsub</a></span>(<span class="st">"SFO"</span>))</pre></body></html></div>
 <pre><code>## Successfully compiled differential equation model from auto-generated C code.</code></pre>
-<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/print.html">print</a></span>(SFO_SFO<span class="op">$</span>diffs)</a></code></pre></div>
+<div class="sourceCode" id="cb5"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/print.html">print</a></span>(<span class="no">SFO_SFO</span>$<span class="no">diffs</span>)</pre></body></html></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" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" title="1">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>)</a></code></pre></div>
-<pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with
-## value of zero were removed from the data</code></pre>
+<div class="sourceCode" id="cb7"><html><body><pre class="r"><span class="no">fit</span> <span class="kw">&lt;-</span> <span class="fu"><a href="../reference/mkinfit.html">mkinfit</a></span>(<span class="no">SFO_SFO</span>, <span class="no">FOCUS_2006_D</span>, <span class="kw">quiet</span> <span class="kw">=</span> <span class="fl">TRUE</span>)</pre></body></html></div>
+<pre><code>## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE): Observations with value
+## of zero were removed from the data</code></pre>
 <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" id="cb9"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb9-1" title="1"><span class="kw"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(fit, <span class="dt">lpos =</span> <span class="kw"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>))</a></code></pre></div>
+<div class="sourceCode" id="cb9"><html><body><pre class="r"><span class="fu"><a href="../reference/plot.mkinfit.html">plot_sep</a></span>(<span class="no">fit</span>, <span class="kw">lpos</span> <span class="kw">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html">c</a></span>(<span class="st">"topright"</span>, <span class="st">"bottomright"</span>))</pre></body></html></div>
 <p><img src="FOCUS_D_files/figure-html/plot-1.png" width="768"></p>
 <p>Confidence intervals for the parameter estimates are obtained using the <code>mkinparplot</code> function.</p>
-<div class="sourceCode" id="cb10"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb10-1" title="1"><span class="kw"><a href="../reference/mkinparplot.html">mkinparplot</a></span>(fit)</a></code></pre></div>
+<div class="sourceCode" id="cb10"><html><body><pre class="r"><span class="fu"><a href="../reference/mkinparplot.html">mkinparplot</a></span>(<span class="no">fit</span>)</pre></body></html></div>
 <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" id="cb11"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb11-1" title="1"><span class="kw"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(fit)</a></code></pre></div>
-<pre><code>## mkin version used for fitting:    0.9.49.6 
-## R version used for fitting:       3.6.1 
-## Date of fit:     Fri Nov  1 10:10:44 2019 
-## Date of summary: Fri Nov  1 10:10:44 2019 
+<div class="sourceCode" id="cb11"><html><body><pre class="r"><span class="fu"><a href="https://rdrr.io/r/base/summary.html">summary</a></span>(<span class="no">fit</span>)</pre></body></html></div>
+<pre><code>## mkin version used for fitting:    0.9.49.11 
+## R version used for fitting:       4.0.0 
+## Date of fit:     Thu May  7 08:59:27 2020 
+## Date of summary: Thu May  7 08:59:27 2020 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -179,7 +186,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted using 389 model solutions performed in 1.015 s
+## Fitted using 389 model solutions performed in 1.031 s
 ## 
 ## Error model: Constant variance 
 ## 
@@ -212,18 +219,18 @@
 ## sigma                3.126    0.35850  2.396   3.855
 ## 
 ## Parameter correlation:
-##                     parent_0 log_k_parent_sink log_k_parent_m1
-## parent_0           1.000e+00         6.067e-01      -6.372e-02
-## log_k_parent_sink  6.067e-01         1.000e+00      -8.550e-02
-## log_k_parent_m1   -6.372e-02        -8.550e-02       1.000e+00
-## log_k_m1_sink     -1.688e-01        -6.252e-01       4.731e-01
-## sigma              1.164e-09        -8.908e-10       1.652e-08
-##                   log_k_m1_sink      sigma
-## parent_0             -1.688e-01  1.164e-09
-## log_k_parent_sink    -6.252e-01 -8.908e-10
-## log_k_parent_m1       4.731e-01  1.652e-08
-## log_k_m1_sink         1.000e+00 -1.340e-10
-## sigma                -1.340e-10  1.000e+00
+##                     parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
+## parent_0           1.000e+00         6.067e-01      -6.372e-02    -1.688e-01
+## log_k_parent_sink  6.067e-01         1.000e+00      -8.550e-02    -6.252e-01
+## log_k_parent_m1   -6.372e-02        -8.550e-02       1.000e+00     4.731e-01
+## log_k_m1_sink     -1.688e-01        -6.252e-01       4.731e-01     1.000e+00
+## sigma              5.287e-10         3.306e-09       4.421e-08    -3.319e-10
+##                        sigma
+## parent_0           5.287e-10
+## log_k_parent_sink  3.306e-09
+## log_k_parent_m1    4.421e-08
+## log_k_m1_sink     -3.319e-10
+## sigma              1.000e+00
 ## 
 ## Backtransformed parameters:
 ## Confidence intervals for internally transformed parameters are asymmetric.
@@ -295,7 +302,7 @@
 ##   120       m1    33.31  28.78984  4.520e+00</code></pre>
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-        
+        <li>
+  <a href="http://github.com/jranke/mkin/">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
       </ul>
       
     </div><!--/.nav-collapse -->
@@ -132,16 +141,24 @@
       <h3>All vignettes</h3>
       <p class="section-desc"></p>
 
-      <ul>
-        <li><a href="FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a></li>
-        <li><a href="FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a></li>
-        <li><a href="mkin.html">Introduction to mkin</a></li>
-        <li><a href="twa.html">Calculation of time weighted average concentrations with mkin</a></li>
-        <li><a href="web_only/FOCUS_Z.html">Example evaluation of FOCUS dataset Z</a></li>
-        <li><a href="web_only/NAFTA_examples.html">Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</a></li>
-        <li><a href="web_only/benchmarks.html">Benchmark timings for mkin on various systems</a></li>
-        <li><a href="web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a></li>
-      </ul>
+      <dl>
+        <dt><a href="FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a></dt>
+        <dd></dt>
+        <dt><a href="FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a></dt>
+        <dd></dt>
+        <dt><a href="mkin.html">Introduction to mkin</a></dt>
+        <dd></dt>
+        <dt><a href="twa.html">Calculation of time weighted average concentrations with mkin</a></dt>
+        <dd></dt>
+        <dt><a href="web_only/FOCUS_Z.html">Example evaluation of FOCUS dataset Z</a></dt>
+        <dd></dt>
+        <dt><a href="web_only/NAFTA_examples.html">Evaluation of example datasets from Attachment 1 to the US EPA SOP for the NAFTA guidance</a></dt>
+        <dd></dt>
+        <dt><a href="web_only/benchmarks.html">Benchmark timings for mkin on various systems</a></dt>
+        <dd></dt>
+        <dt><a href="web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a></dt>
+        <dd></dt>
+      </dl>
     </div>
   </div>
 </div>
@@ -153,7 +170,7 @@
 </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>
 </div>
 
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