From 063ae84c199e1223a620fe512ab8713371119f5f Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Tue, 28 Mar 2017 10:44:50 +0200
Subject: Change vignette format for twa vignette, update docs

---
 docs/index.html | 27 +++++++++++++++------------
 1 file changed, 15 insertions(+), 12 deletions(-)

(limited to 'docs/index.html')

diff --git a/docs/index.html b/docs/index.html
index 654bb363..0a353ee5 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -50,6 +50,9 @@
     <li>
       <a href="articles/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
     </li>
+    <li>
+      <a href="articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+    </li>
   </ul>
 </li>
 <li>
@@ -76,33 +79,33 @@
   <div class="contents col-md-9">
     <div id="mkin" class="section level1">
 <div class="page-header"><h1 class="hasAnchor">
-<a href="#mkin" class="anchor"> </a>mkin</h1></div>
+<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>
 <div id="installation" class="section level2">
 <h2 class="hasAnchor">
-<a href="#installation" class="anchor"> </a>Installation</h2>
+<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"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">install.packages</span>(<span class="st">"mkin"</span>)</code></pre></div>
 </div>
 <div id="background" class="section level2">
 <h2 class="hasAnchor">
-<a href="#background" class="anchor"> </a>Background</h2>
+<a href="#background" class="anchor"></a>Background</h2>
 <p>In the regulatory evaluation of chemical substances like plant protection products (pesticides), biocides and other chemicals, degradation data play an important role. For the evaluation of pesticide degradation experiments, detailed guidance and helpful tools have been developed as detailed in ‘Credits and historical remarks’ below.</p>
 </div>
 <div id="usage" class="section level2">
 <h2 class="hasAnchor">
-<a href="#usage" class="anchor"> </a>Usage</h2>
+<a href="#usage" class="anchor"></a>Usage</h2>
 <p>For a start, have a look a the code examples provided for <a href="http://kinfit.r-forge.r-project.org/mkin_static/reference/plot.mkinfit.html"><code>plot.mkinfit</code></a> and <a href="http://kinfit.r-forge.r-project.org/mkin_static/reference/plot.mmkin.html"><code>plot.mmkin</code></a>, and at the package vignettes <a href="http://kinfit.r-forge.r-project.org/mkin_static/articles/FOCUS_L.html"><code>FOCUS L</code></a> and <a href="http://kinfit.r-forge.r-project.org/mkin_static/articles/FOCUS_D.html"><code>FOCUS D</code></a>.</p>
 </div>
 <div id="documentation" class="section level2">
 <h2 class="hasAnchor">
-<a href="#documentation" class="anchor"> </a>Documentation</h2>
+<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>
 </div>
 <div id="features" class="section level2">
 <h2 class="hasAnchor">
-<a href="#features" class="anchor"> </a>Features</h2>
+<a href="#features" class="anchor"></a>Features</h2>
 <ul>
 <li>Highly flexible model specification using <a href="http://kinfit.r-forge.r-project.org/mkin_static/reference/mkinmod.html"><code>mkinmod</code></a>, including equilibrium reactions and using the single first-order reversible binding (SFORB) model, which will automatically create two latent state variables for the observed variable.</li>
 <li>As of version 0.9-39, fitting of several models to several datasets, optionally in parallel, is supported, see for example <a href="http://kinfit.r-forge.r-project.org/mkin_static/reference/plot.mmkin.html"><code>plot.mmkin</code></a>.</li>
@@ -119,17 +122,17 @@
 </div>
 <div id="gui" class="section level2">
 <h2 class="hasAnchor">
-<a href="#gui" class="anchor"> </a>GUI</h2>
+<a href="#gui" class="anchor"></a>GUI</h2>
 <p>There is a graphical user interface that I consider useful for real work. 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>
 </div>
 <div id="news" class="section level2">
 <h2 class="hasAnchor">
-<a href="#news" class="anchor"> </a>News</h2>
+<a href="#news" class="anchor"></a>News</h2>
 <p>Yes, there is a ChangeLog, for the latest <a href="https://cran.r-project.org/package=mkin/news.html">CRAN release</a> and one for the <a href="https://github.com/jranke/mkin/blob/master/NEWS.md">github master branch</a>.</p>
 </div>
 <div id="credits-and-historical-remarks" class="section level2">
 <h2 class="hasAnchor">
-<a href="#credits-and-historical-remarks" class="anchor"> </a>Credits and historical remarks</h2>
+<a href="#credits-and-historical-remarks" class="anchor"></a>Credits and historical remarks</h2>
 <p><code>mkin</code> would not be possible without the underlying software stack consisting of R and the packages <a href="https://cran.r-project.org/package=deSolve">deSolve</a> and <a href="https://cran.r-project.org/package=FME">FME</a>, to say the least.</p>
 <p>It 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://focus.jrc.ec.europa.eu/dk">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>
@@ -141,7 +144,7 @@
 </div>
 <div id="development" class="section level2">
 <h2 class="hasAnchor">
-<a href="#development" class="anchor"> </a>Development</h2>
+<a href="#development" class="anchor"></a>Development</h2>
 <p>Contributions are welcome! Your <a href="https://help.github.com/articles/fork-a-repo">mkin fork</a> is just a mouse click away… The master branch on github should always be in good shape, I implement new features in separate branches now. If you prefer subversion, project members for the <a href="http://r-forge.r-project.org/R/?group_id=615">r-forge project</a> are welcome as well. Generally, the source code of the latest CRAN version should be available there. You can also browse the source code at <a href="http://cgit.jrwb.de/mkin">cgit.jrwb.de/mkin</a>.</p>
 </div>
 </div>
@@ -164,12 +167,12 @@
 <li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> </li>
 <li><a href="authors.html">All authors...</a></li>
 </ul>
-<html><body>
+<div>
 <h2>Dev status</h2>
 <ul class="list-unstyled">
 <li><a href="https://cran.r-project.org/package=mkin"><img src="https://www.r-pkg.org/badges/version/mkin"></a></li>
 </ul>
-</body></html>
+</div>
 </div>
 </div>
 
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