Static documentation rebuilt by current pkgdown

13 files changed, 437 insertions, 81 deletions

diff --git a/docs/articles/gmkin_manual.html b/docs/articles/gmkin_manual.html
index 389ffdb..f283cf6 100644
--- a/docs/articles/gmkin_manual.html
+++ b/docs/articles/gmkin_manual.html
@@ -8,8 +8,11 @@
 <title>Manual for gmkin • gmkin</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">
 <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
+<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script><script src="../pkgdown.js"></script><meta property="og:title" content="Manual for gmkin">
+<meta property="og:description" content="">
+<meta name="twitter:card" content="summary">
+<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]-->
@@ -29,10 +32,25 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
 <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu">
 <li>
-  <a href="../articles/index.html">Articles</a>
+      <a href="../articles/gmkin_manual.html">Manual for gmkin</a>
+    </li>
+  </ul>
 </li>
 <li>
   <a href="../news/index.html">News</a>
@@ -53,7 +71,7 @@
       <h1>Manual for gmkin</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2017-11-15</h4>
+            <h4 class="date">2018-03-01</h4>
           </div>
 
     
@@ -351,7 +369,8 @@ Optimisation by method Port successfully terminated.</code></pre></div>
 
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
         <div id="tocnav">
-      <h2>Contents</h2>
+      <h2 class="hasAnchor">
+<a href="#tocnav" class="anchor"></a>Contents</h2>
       <ul class="nav nav-pills nav-stacked">
 <li><a href="#introduction">Introduction</a></li>
       <li><a href="#starting-gmkin">Starting gmkin</a></li>
@@ -374,7 +393,7 @@ Optimisation by method Port successfully terminated.</code></pre></div>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 20f744f..bfd24e2 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -18,12 +18,16 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
-
+  
+  
+<meta property="og:title" content="Articles" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,10 +55,25 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Reference</a>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
 </li>
 <li>
-  <a href="../articles/index.html">Articles</a>
+  <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu">
+    <li>
+      <a href="../articles/gmkin_manual.html">Manual for gmkin</a>
+    </li>
+  </ul>
 </li>
 <li>
   <a href="../news/index.html">News</a>
@@ -94,7 +113,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/authors.html b/docs/authors.html
index bd091af..fa7d1eb 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -18,12 +18,16 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="pkgdown.css" rel="stylesheet">
 <script src="jquery.sticky-kit.min.js"></script>
 <script src="pkgdown.js"></script>
-
+  
+  
+<meta property="og:title" content="Authors" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,10 +55,25 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="reference/index.html">Reference</a>
+  <a href="index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
 </li>
 <li>
-  <a href="articles/index.html">Articles</a>
+  <a href="reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu">
+    <li>
+      <a href="articles/gmkin_manual.html">Manual for gmkin</a>
+    </li>
+  </ul>
 </li>
 <li>
   <a href="news/index.html">News</a>
@@ -79,15 +98,15 @@
 
     <ul class="list-unstyled">
       <li>
-        <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright&nbsp;holder.
+        <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright holder. 
         </p>
       </li>
       <li>
-        <p><strong>Stefan Meinecke</strong>. Contributor.
+        <p><strong>Stefan Meinecke</strong>. Contributor. 
         </p>
       </li>
       <li>
-        <p><strong>Eurofins Regulatory AG</strong>. Copyright&nbsp;holder.
+        <p><strong>Eurofins Regulatory AG</strong>. Copyright holder. 
         </p>
       </li>
     </ul>
@@ -103,7 +122,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/index.html b/docs/index.html
index a868144..1f2056b 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -8,8 +8,13 @@
 <title>Graphical User Interface for Fitting Kinetic Models to Chemical Degradation Data • gmkin</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">
 <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
+<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
+<script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><meta property="og:title" content="Graphical User Interface for Fitting Kinetic Models to Chemical Degradation Data">
+<meta property="og:description" content="Browser based graphical user interface for R package mkin, based
+  on the gWidgetsWWW2 package. Both gmkin and gWidgetsWWW2 are developed on
+  GitHub, but are also available from the R-Forge repository.">
+<meta name="twitter:card" content="summary">
+<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]-->
@@ -29,10 +34,25 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
 <li>
+  <a href="index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="reference/index.html">Reference</a>
 </li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu">
 <li>
-  <a href="articles/index.html">Articles</a>
+      <a href="articles/gmkin_manual.html">Manual for gmkin</a>
+    </li>
+  </ul>
 </li>
 <li>
   <a href="news/index.html">News</a>
@@ -52,7 +72,7 @@
     <div id="gmkin" class="section level1">
 <div class="page-header"><h1 class="hasAnchor">
 <a href="#gmkin" class="anchor"></a>gmkin</h1></div>
-
+<p>The R package <a href="https://pkgdown.jrwb.de/gmkin">gmkin</a> provides a browser based graphical user interface (GUI) for fitting kinetic models to chemical degradation data based on R package <a href="https://pkgdown.jrwb.de/mkin">mkin</a>. The GUI is based on the <a href="http://github.com/jverzani/gWidgetsWWW2">gWidgetsWWW2</a> package developed by John Verzani. The GUI elements are created by the JavaScript library ExtJS which is bundled with gWidgetsWWW2.</p>
 <div id="system-requirements" class="section level2">
 <h2 class="hasAnchor">
 <a href="#system-requirements" class="anchor"></a>System requirements</h2>
@@ -148,15 +168,9 @@ while (TRUE) {
 <p>GPL</p>
 <h2>Developers</h2>
 <ul class="list-unstyled">
-<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> </li>
+<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small>  </li>
 <li><a href="authors.html">All authors...</a></li>
 </ul>
-<h2>Dev status</h2>
-<ul class="list-unstyled">
-<li><a href="https://pkgdown.jrwb.de/gmkin">gmkin</a></li>
-<li><a href="https://pkgdown.jrwb.de/mkin">mkin</a></li>
-<li><a href="http://github.com/jverzani/gWidgetsWWW2">gWidgetsWWW2</a></li>
-</ul>
 </div>
 </div>
 
@@ -166,7 +180,7 @@ while (TRUE) {
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/news/index.html b/docs/news/index.html
index 77bd232..78f1749 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -18,12 +18,16 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
-
+  
+  
+<meta property="og:title" content="All news" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,10 +55,25 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Reference</a>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
 </li>
 <li>
-  <a href="../articles/index.html">Articles</a>
+  <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu">
+    <li>
+      <a href="../articles/gmkin_manual.html">Manual for gmkin</a>
+    </li>
+  </ul>
 </li>
 <li>
   <a href="../news/index.html">News</a>
@@ -98,7 +117,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/pkgdown.css b/docs/pkgdown.css
index 9c437c7..181fe63 100644
--- a/docs/pkgdown.css
+++ b/docs/pkgdown.css
@@ -34,6 +34,10 @@ img.icon {
   float: right;
 }
 
+img {
+  max-width: 100%;
+}
+
 /* Section anchors ---------------------------------*/
 
 a.anchor {
@@ -96,6 +100,11 @@ a.anchor {
   margin-bottom: 0.5em;
 }
 
+.orcid {
+  height: 16px;
+  vertical-align: middle;
+}
+
 /* Reference index & topics ----------------------------------------------- */
 
 .ref-index th {font-weight: normal;}
@@ -133,15 +142,30 @@ pre, code {
   color: #333;
 }
 
-pre img {
+pre code {
+  overflow: auto;
+  word-wrap: normal;
+  white-space: pre;
+}
+
+pre .img {
+  margin: 5px 0;
+}
+
+pre .img img {
   background-color: #fff;
   display: block;
+  height: auto;
 }
 
 code a, pre a {
   color: #375f84;
 }
 
+a.sourceLine:hover {
+  text-decoration: none;
+}
+
 .fl      {color: #1514b5;}
 .fu      {color: #000000;} /* function */
 .ch,.st  {color: #036a07;} /* string */
@@ -152,3 +176,19 @@ code a, pre a {
 .error   { color: orange;  font-weight: bolder;}
 .warning { color: #6A0366; font-weight: bolder;}
 
+/* Clipboard --------------------------*/
+
+.hasCopyButton {
+  position: relative;
+}
+
+.btn-copy-ex {
+  position: absolute;
+  right: 0;
+  top: 0;
+  visibility: hidden;
+}
+
+.hasCopyButton:hover button.btn-copy-ex {
+  visibility: visible;
+}
diff --git a/docs/pkgdown.js b/docs/pkgdown.js
index c8b38c4..64b20df 100644
--- a/docs/pkgdown.js
+++ b/docs/pkgdown.js
@@ -1,8 +1,94 @@
 $(function() {
-  $("#sidebar").stick_in_parent({offset_top: 40});
+
+  $("#sidebar")
+    .stick_in_parent({offset_top: 40})
+    .on('sticky_kit:bottom', function(e) {
+      $(this).parent().css('position', 'static');
+    })
+    .on('sticky_kit:unbottom', function(e) {
+      $(this).parent().css('position', 'relative');
+    });
+
   $('body').scrollspy({
     target: '#sidebar',
     offset: 60
   });
 
+  var cur_path = paths(location.pathname);
+  $("#navbar ul li a").each(function(index, value) {
+    if (value.text == "Home")
+      return;
+    if (value.getAttribute("href") === "#")
+      return;
+
+    var path = paths(value.pathname);
+    if (is_prefix(cur_path, path)) {
+      // Add class to parent <li>, and enclosing <li> if in dropdown
+      var menu_anchor = $(value);
+      menu_anchor.parent().addClass("active");
+      menu_anchor.closest("li.dropdown").addClass("active");
+    }
+  });
 });
+
+function paths(pathname) {
+  var pieces = pathname.split("/");
+  pieces.shift(); // always starts with /
+
+  var end = pieces[pieces.length - 1];
+  if (end === "index.html" || end === "")
+    pieces.pop();
+  return(pieces);
+}
+
+function is_prefix(needle, haystack) {
+  if (needle.length > haystack.lengh)
+    return(false);
+
+  for (var i = 0; i < haystack.length; i++) {
+    if (needle[i] != haystack[i])
+      return(false);
+  }
+
+  return(true);
+}
+
+/* Clipboard --------------------------*/
+
+function changeTooltipMessage(element, msg) {
+  var tooltipOriginalTitle=element.getAttribute('data-original-title');
+  element.setAttribute('data-original-title', msg);
+  $(element).tooltip('show');
+  element.setAttribute('data-original-title', tooltipOriginalTitle);
+}
+
+if(Clipboard.isSupported()) {
+  $(document).ready(function() {
+    var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+
+    $(".examples").addClass("hasCopyButton");
+
+    // Insert copy buttons:
+    $(copyButton).prependTo(".hasCopyButton");
+
+    // Initialize tooltips:
+    $('.btn-copy-ex').tooltip({container: 'body'});
+
+    // Initialize clipboard:
+    var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      text: function(trigger) {
+        return trigger.parentNode.textContent;
+      }
+    });
+
+    clipboardBtnCopies.on('success', function(e) {
+      changeTooltipMessage(e.trigger, 'Copied!');
+      e.clearSelection();
+    });
+
+    clipboardBtnCopies.on('error', function() {
+      changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
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+}
+
diff --git a/docs/reference/FOCUS_2006.html b/docs/reference/FOCUS_2006.html
index 2c9d327..ca9b5ce 100644
--- a/docs/reference/FOCUS_2006.html
+++ b/docs/reference/FOCUS_2006.html
@@ -18,12 +18,21 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
-
+  
+  
+<meta property="og:title" content="Example gmkin workspace for Datasets C and D from the FOCUS Kinetics report — FOCUS_2006" />
+
+<meta property="og:description" content="An gmkinws object with data taken from FOCUS (2006), Appendix
+  3. This is the the workspace that is loaded into gmkin by
+  default." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,10 +60,25 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Reference</a>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
 </li>
 <li>
-  <a href="../articles/index.html">Articles</a>
+  <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu">
+    <li>
+      <a href="../articles/gmkin_manual.html">Manual for gmkin</a>
+    </li>
+  </ul>
 </li>
 <li>
   <a href="../news/index.html">News</a>
@@ -96,16 +120,16 @@
   Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
   Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
   EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
-  <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p>
+  <a href='http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p>
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'>  <span class='fu'>not_run</span>({
-    <span class='fu'>save</span>(<span class='no'>FOCUS_2006</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"FOCUS_2006.RData"</span>)
-    <span class='co'># Now you can load the file "FOCUS_2006.RData" from gmkin,</span>
-    <span class='co'># restoring the workspace that is loaded at startup.</span>
+    <pre class="examples"><div class='input'>  </div><span class='co'># NOT RUN {</span>
+  <span class='fu'>save</span>(<span class='no'>FOCUS_2006</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"FOCUS_2006.RData"</span>)
+  <span class='co'># Now you can load the file "FOCUS_2006.RData" from gmkin,</span>
+  <span class='co'># restoring the workspace that is loaded at startup.</span>
 
-})</div></pre>
+<span class='co'># }</span></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
@@ -127,7 +151,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/FOCUS_2006_Z.html b/docs/reference/FOCUS_2006_Z.html
index dff1b0e..4eff2a7 100644
--- a/docs/reference/FOCUS_2006_Z.html
+++ b/docs/reference/FOCUS_2006_Z.html
@@ -18,12 +18,19 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Example gmkin workspace for Dataset Z from the FOCUS Kinetics report — FOCUS_2006_Z" />
 
+<meta property="og:description" content="Data taken from FOCUS (2006), Appendix 7, p. 350." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,10 +58,25 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Reference</a>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
 </li>
 <li>
-  <a href="../articles/index.html">Articles</a>
+  <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu">
+    <li>
+      <a href="../articles/gmkin_manual.html">Manual for gmkin</a>
+    </li>
+  </ul>
 </li>
 <li>
   <a href="../news/index.html">News</a>
@@ -94,15 +116,15 @@
   Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
   Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
   EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
-  <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p>
+  <a href='http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p>
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'>  <span class='fu'>not_run</span>({
-    <span class='fu'>save</span>(<span class='no'>FOCUS_2006_Z</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"FOCUS_2006_Z.RData"</span>)
-    <span class='co'># Now you can load the file "FOCUS_2006_Z.RData" from gmkin</span>
+    <pre class="examples"><div class='input'>  </div><span class='co'># NOT RUN {</span>
+  <span class='fu'>save</span>(<span class='no'>FOCUS_2006_Z</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"FOCUS_2006_Z.RData"</span>)
+  <span class='co'># Now you can load the file "FOCUS_2006_Z.RData" from gmkin</span>
 
-})</div></pre>
+<span class='co'># }</span></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
@@ -124,7 +146,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/UBA_model_gallery.html b/docs/reference/UBA_model_gallery.html
index 74fc20b..4157743 100644
--- a/docs/reference/UBA_model_gallery.html
+++ b/docs/reference/UBA_model_gallery.html
@@ -18,12 +18,24 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="A collection of some standard kinetic models — UBA_model_gallery" />
 
+<meta property="og:description" content="The UBA model gallery contains predefined kinetic models for some common use
+  cases, with metabolites named as in the commonly used PELMO degradation
+  scheme (Jene 1998).  Please use the model gallery of the gmkin
+  GUI to see their definitions.  The models use the topology of the models
+  defined by Michael Klein (2010) for DegKinManager, with the exception of the
+  kinetic sorption model." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,10 +63,25 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Reference</a>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
 </li>
 <li>
-  <a href="../articles/index.html">Articles</a>
+  <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu">
+    <li>
+      <a href="../articles/gmkin_manual.html">Manual for gmkin</a>
+    </li>
+  </ul>
 </li>
 <li>
   <a href="../news/index.html">News</a>
@@ -125,7 +152,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/gmkin.html b/docs/reference/gmkin.html
index 961372e..75548cb 100644
--- a/docs/reference/gmkin.html
+++ b/docs/reference/gmkin.html
@@ -18,12 +18,21 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
-
+  
+  
+<meta property="og:title" content="Start a graphical user interface (GUI) based on the <code>gWidgetsWWW2</code> toolkit. — gmkin" />
+
+<meta property="og:description" content="This function starts a browser based GUI. Please visit the 
+  github page of gWidgetsWWW2 
+  for an explanation how this toolkit works." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,10 +60,25 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Reference</a>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
 </li>
 <li>
-  <a href="../articles/index.html">Articles</a>
+  <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu">
+    <li>
+      <a href="../articles/gmkin_manual.html">Manual for gmkin</a>
+    </li>
+  </ul>
 </li>
 <li>
   <a href="../news/index.html">News</a>
@@ -79,7 +103,7 @@
 
     
     <p>This function starts a browser based GUI. Please visit the 
-  <a href = 'http://github.com/jverzani/gWidgetsWWW2'>github page of gWidgetsWWW2</a> 
+  <a href='http://github.com/jverzani/gWidgetsWWW2'>github page of gWidgetsWWW2</a> 
   for an explanation how this toolkit works.</p>
     
 
@@ -107,19 +131,21 @@
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'>  <span class='co'>## Not run: gmkin() # Start the gmkin GUI</span>
-  <span class='fu'>not_run</span>({
-      <span class='no'>g</span> <span class='kw'>&lt;-</span> <span class='fu'>gmkin</span>()
-
-      <span class='co'># Only for debugging or other advanced usage:</span>
-      <span class='no'>session</span> <span class='kw'>&lt;-</span> <span class='kw'>gmkin</span><span class='kw'>:::</span><span class='fu'>get_current_session</span>(<span class='no'>g</span>)
-      <span class='no'>session</span>$<span class='no'>p.df</span>
-      <span class='no'>session</span>$<span class='no'>ds.df</span>
-      <span class='no'>session</span>$<span class='no'>ds.cur</span>
-      <span class='no'>session</span>$<span class='no'>m.cur</span>
-      <span class='no'>session</span>$<span class='no'>ws</span>
-
-})</div></pre>
+    <pre class="examples"><div class='input'>  </div><span class='co'># NOT RUN {</span>
+<span class='fu'>gmkin</span>()
+<span class='co'># }</span><div class='input'> # Start the gmkin GUI
+  </div><span class='co'># NOT RUN {</span>
+    <span class='no'>g</span> <span class='kw'>&lt;-</span> <span class='fu'>gmkin</span>()
+
+    <span class='co'># Only for debugging or other advanced usage:</span>
+    <span class='no'>session</span> <span class='kw'>&lt;-</span> <span class='kw pkg'>gmkin</span><span class='kw ns'>:::</span><span class='fu'>get_current_session</span>(<span class='no'>g</span>)
+    <span class='no'>session</span>$<span class='no'>p.df</span>
+    <span class='no'>session</span>$<span class='no'>ds.df</span>
+    <span class='no'>session</span>$<span class='no'>ds.cur</span>
+    <span class='no'>session</span>$<span class='no'>m.cur</span>
+    <span class='no'>session</span>$<span class='no'>ws</span>
+
+<span class='co'># }</span></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
@@ -144,7 +170,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/gmkinws.html b/docs/reference/gmkinws.html
index 28f6014..2c1f509 100644
--- a/docs/reference/gmkinws.html
+++ b/docs/reference/gmkinws.html
@@ -18,12 +18,19 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="A workspace class for gmkin — gmkinws" />
 
+<meta property="og:description" content="Datasets, models and fits are stored in lists." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,10 +58,25 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Reference</a>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
 </li>
 <li>
-  <a href="../articles/index.html">Articles</a>
+  <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu">
+    <li>
+      <a href="../articles/gmkin_manual.html">Manual for gmkin</a>
+    </li>
+  </ul>
 </li>
 <li>
   <a href="../news/index.html">News</a>
@@ -118,7 +140,7 @@ by the names used in the models contained in field m</p></dd>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 6f21a01..3fd068b 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -18,12 +18,16 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
-
+  
+  
+<meta property="og:title" content="Function reference" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,10 +55,25 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Reference</a>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
 </li>
 <li>
-  <a href="../articles/index.html">Articles</a>
+  <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu">
+    <li>
+      <a href="../articles/gmkin_manual.html">Manual for gmkin</a>
+    </li>
+  </ul>
 </li>
 <li>
   <a href="../news/index.html">News</a>
@@ -145,7 +164,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>