Update online docs for release version

1 files changed, 15 insertions, 11 deletions

diff --git a/docs/index.html b/docs/index.html
index ce5d6a9a..42084fc0 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -37,7 +37,7 @@
       </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">0.9.50.2</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.3</span>
       </span>
     </div>
 
@@ -74,6 +74,9 @@
     <li>
       <a href="articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
     </li>
+    <li>
+      <a href="articles/web_only/benchmarks.html">Some benchmark timings</a>
+    </li>
   </ul>
 </li>
 <li>
@@ -82,7 +85,7 @@
       </ul>
 <ul class="nav navbar-nav navbar-right">
 <li>
-  <a href="http://github.com/jranke/mkin/">
+  <a href="https://github.com/jranke/mkin/">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -103,12 +106,13 @@
 <div class="page-header"><h1 class="hasAnchor">
 <a href="#mkin" class="anchor"></a>mkin</h1></div>
 
-<p>The R package <strong>mkin</strong> provides calculation routines for the analysis of chemical degradation data, including <b>m</b>ulticompartment <b>kin</b>etics as needed for modelling the formation and decline of transformation products, or if several compartments are involved.</p>
+<p>The R package <strong>mkin</strong> provides calculation routines for the analysis of chemical degradation data, including <b>m</b>ulticompartment <b>kin</b>etics as needed for modelling the formation and decline of transformation products, or if several degradation compartments are involved.</p>
 <div id="installation" class="section level2">
 <h2 class="hasAnchor">
 <a href="#installation" class="anchor"></a>Installation</h2>
 <p>You can install the latest released version from <a href="https://cran.r-project.org/package=mkin">CRAN</a> from within R:</p>
-<div class="sourceCode" id="cb1"><pre class="r"><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span>(<span class="st">"mkin"</span>)</pre></div>
+<div class="sourceCode" id="cb1"><pre class="downlit">
+<span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html">install.packages</a></span><span class="op">(</span><span class="st">"mkin"</span><span class="op">)</span></pre></div>
 </div>
 <div id="background" class="section level2">
 <h2 class="hasAnchor">
@@ -123,7 +127,7 @@
 <div id="documentation" class="section level2">
 <h2 class="hasAnchor">
 <a href="#documentation" class="anchor"></a>Documentation</h2>
-<p>The HTML documentation is available at <a href="https://pkgdown.jrwb.de/mkin">jrwb.de</a>, at <a href="http://jranke.github.io/mkin">github</a> and at <a href="http://kinfit.r-forge.r-project.org/mkin_static/index.html">R-Forge</a>.</p>
+<p>The HTML documentation of the latest version released to CRAN is available at <a href="https://pkgdown.jrwb.de/mkin/">jrwb.de</a> and <a href="https://jranke.github.io/mkin/">github</a>. Documentation of the development version is found in the <a href="https://pkgdown.jrwb.de/mkin/dev/">‘dev’ subdirectory</a>.</p>
 </div>
 <div id="features" class="section level2">
 <h2 class="hasAnchor">
@@ -148,7 +152,7 @@
 <div id="gui" class="section level2">
 <h2 class="hasAnchor">
 <a href="#gui" class="anchor"></a>GUI</h2>
-<p>There is a graphical user interface that may be useful. Please refer to its <a href="http://kinfit.r-forge.r-project.org/gmkin_static">documentation page</a> for installation instructions and a manual.</p>
+<p>There is a graphical user interface that may be useful. Please refer to its <a href="https://pkgdown.jrwb.de/gmkin/">documentation page</a> for installation instructions and a manual.</p>
 </div>
 <div id="news" class="section level2">
 <h2 class="hasAnchor">
@@ -162,10 +166,10 @@
 <p><code>mkin</code> could not have been written without me being introduced to regulatory fate modelling of pesticides by Adrian Gurney during my time at Harlan Laboratories Ltd (formerly RCC Ltd). <code>mkin</code> greatly profits from and largely follows the work done by the <a href="http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics">FOCUS Degradation Kinetics Workgroup</a>, as detailed in their guidance document from 2006, slightly updated in 2011 and in 2014.</p>
 <p>Also, it was inspired by the first version of KinGUI developed by BayerCropScience, which is based on the MatLab runtime environment.</p>
 <p>The companion package <a href="http://kinfit.r-forge.r-project.org/kinfit_static/index.html">kinfit</a> (now deprecated) was <a href="https://r-forge.r-project.org/scm/viewvc.php?view=rev&amp;root=kinfit&amp;revision=2">started in 2008</a> and <a href="https://cran.r-project.org/src/contrib/Archive/kinfit/">first published</a> on CRAN on 01 May 2010.</p>
-<p>The first <code>mkin</code> code was <a href="https://r-forge.r-project.org/scm/viewvc.php?view=rev&amp;root=kinfit&amp;revision=8">published on 11 May 2010</a> and the <a href="https://cran.r-project.org/src/contrib/Archive/mkin">first CRAN version</a> on 18 May 2010.</p>
+<p>The first <code>mkin</code> code was <a href="https://r-forge.r-project.org/scm/viewvc.php?view=rev&amp;root=kinfit&amp;revision=8">published on 11 May 2010</a> and the <a href="https://cran.r-project.org/src/contrib/Archive/mkin/">first CRAN version</a> on 18 May 2010.</p>
 <p>In 2011, Bayer Crop Science started to distribute an R based successor to KinGUI named KinGUII whose R code is based on <code>mkin</code>, but which added, among other refinements, a closed source graphical user interface (GUI), iteratively reweighted least squares (IRLS) optimisation of the variance for each of the observed variables, and Markov Chain Monte Carlo (MCMC) simulation functionality, similar to what is available e.g. in the <code>FME</code> package.</p>
 <p>Somewhat in parallel, Syngenta has sponsored the development of an <code>mkin</code> and KinGUII based GUI application called CAKE, which also adds IRLS and MCMC, is more limited in the model formulation, but puts more weight on usability. CAKE is available for download from the <a href="https://www.tessella.com/showcase/computer-assisted-kinetic-evaluation">CAKE website</a>, where you can also find a zip archive of the R scripts derived from <code>mkin</code>, published under the GPL license.</p>
-<p>Finally, there is <a href="http://github.com/zhenglei-gao/KineticEval">KineticEval</a>, which contains a further development of the scripts used for KinGUII, so the different tools will hopefully be able to learn from each other in the future as well.</p>
+<p>Finally, there is <a href="https://github.com/zhenglei-gao/KineticEval">KineticEval</a>, which contains a further development of the scripts used for KinGUII, so the different tools will hopefully be able to learn from each other in the future as well.</p>
 </div>
 <div id="references" class="section level2">
 <h2 class="hasAnchor">
@@ -197,9 +201,9 @@ Ranke J, Wöltjen J, Meinecke S (2018) Comparison of software tools for kinetic
 <ul class="list-unstyled">
 <li>Download from CRAN at <br><a href="https://cloud.r-project.org/package=mkin">https://​cloud.r-project.org/​package=mkin</a>
 </li>
-<li>Browse source code at <br><a href="http://github.com/jranke/mkin/">http://​github.com/​jranke/​mkin/​</a>
+<li>Browse source code at <br><a href="https://github.com/jranke/mkin/">https://​github.com/​jranke/​mkin/​</a>
 </li>
-<li>Report a bug at <br><a href="http://github.com/jranke/mkin/issues">http://​github.com/​jranke/​mkin/​issues</a>
+<li>Report a bug at <br><a href="https://github.com/jranke/mkin/issues/">https://​github.com/​jranke/​mkin/​issues/​</a>
 </li>
 </ul>
 </div>
@@ -234,7 +238,7 @@ Ranke J, Wöltjen J, Meinecke S (2018) Comparison of software tools for kinetic
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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