Static documentation rebuilt by pkgdown

author: Johannes Ranke <jranke@uni-bremen.de> 2018-06-06 02:12:52 +0200
committer: Johannes Ranke <jranke@uni-bremen.de> 2018-06-06 02:12:52 +0200
commit: 99a6582cd97c148686b06cf795a05a167b37645a (patch)
tree: cfc0ee0388b83bebaaa8d2b918789343e7f7c813
parent: b372baf353b693198a4d8417cf008d04f44dd14a (diff)
17 files changed, 690 insertions, 233 deletions
diff --git a/DESCRIPTION b/DESCRIPTION
index bc740bd..8f3f66c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -21,3 +21,4 @@ VignetteBuilder: knitr
 BugReports: http://github.com/jranke/gmkin/issues
 URL: http://kinfit.r-forge.r-project.org/gmkin_static,
      http://pkgdown.jrwb.de/gmkin
+RoxygenNote: 6.0.1
diff --git a/docs/articles/gmkin_manual.html b/docs/articles/gmkin_manual.html
index f283cf6..dc2ef4d 100644
--- a/docs/articles/gmkin_manual.html
+++ b/docs/articles/gmkin_manual.html
@@ -8,8 +8,8 @@
 <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">
-<!-- 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">
+<!-- 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><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet">
+<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]>
@@ -18,7 +18,7 @@
 <![endif]-->
 </head>
 <body>
-    <div class="container template-vignette">
+    <div class="container template-article">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
     <div class="navbar-header">
@@ -27,8 +27,12 @@
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
-      <a class="navbar-brand" href="../index.html">gmkin</a>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">gmkin</a>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.6.8</span>
+      </span>
     </div>
+
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
 <li>
@@ -53,7 +57,7 @@
   </ul>
 </li>
 <li>
-  <a href="../news/index.html">News</a>
+  <a href="../news/index.html">Changelog</a>
 </li>
       </ul>
 <ul class="nav navbar-nav navbar-right"></ul>
@@ -66,17 +70,20 @@
 
       
       </header><div class="row">
-  <div class="col-md-9">
+  <div class="col-md-9 contents">
     <div class="page-header toc-ignore">
       <h1>Manual for gmkin</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2018-03-01</h4>
-          </div>
+            <h4 class="date">2018-06-06</h4>
+      
+      
+      <div class="hidden name"><code>gmkin_manual.Rmd</code></div>
+
+    </div>
 
     
     
-<div class="contents">
 <div id="introduction" class="section level2">
 <h2 class="hasAnchor">
 <a href="#introduction" class="anchor"></a>Introduction</h2>
@@ -234,22 +241,22 @@
 <h3 class="hasAnchor">
 <a href="#fitting-the-model" class="anchor"></a>Fitting the model</h3>
 <p>In many cases the starting parameters and the fit options do not need to be modified and the model fitting process can simply be started by pressing the “Run fit” button. In the R console, the progressive reduction in the model cost can be monitored and will be displayed in the following way:</p>
-<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">Model cost at call  <span class="dv">1</span> :<span class="st">  </span><span class="fl">15156.12</span> 
-Model cost at call  <span class="dv">3</span> :<span class="st">  </span><span class="fl">15156.12</span> 
-Model cost at call  <span class="dv">7</span> :<span class="st">  </span><span class="fl">14220.79</span> 
-Model cost at call  <span class="dv">8</span> :<span class="st">  </span><span class="fl">14220.79</span> 
-Model cost at call  <span class="dv">11</span> :<span class="st">  </span><span class="fl">14220.79</span> 
-Model cost at call  <span class="dv">12</span> :<span class="st">  </span><span class="fl">3349.268</span> 
-Model cost at call  <span class="dv">15</span> :<span class="st">  </span><span class="fl">3349.268</span> 
-Model cost at call  <span class="dv">17</span> :<span class="st">  </span><span class="fl">788.6367</span> 
-Model cost at call  <span class="dv">18</span> :<span class="st">  </span><span class="fl">788.6366</span> 
-Model cost at call  <span class="dv">22</span> :<span class="st">  </span><span class="fl">374.0575</span> 
-Model cost at call  <span class="dv">23</span> :<span class="st">  </span><span class="fl">374.0575</span> 
-Model cost at call  <span class="dv">27</span> :<span class="st">  </span><span class="fl">371.2135</span> 
-Model cost at call  <span class="dv">28</span> :<span class="st">  </span><span class="fl">371.2135</span> 
-Model cost at call  <span class="dv">32</span> :<span class="st">  </span><span class="fl">371.2134</span> 
-Model cost at call  <span class="dv">36</span> :<span class="st">  </span><span class="fl">371.2134</span> 
-Model cost at call  <span class="dv">37</span> :<span class="st">  </span><span class="fl">371.2134</span> 
+<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r">Model cost at call  <span class="dv">1</span> <span class="op">:</span><span class="st">  </span><span class="fl">15156.12</span> 
+Model cost at call  <span class="dv">3</span> <span class="op">:</span><span class="st">  </span><span class="fl">15156.12</span> 
+Model cost at call  <span class="dv">7</span> <span class="op">:</span><span class="st">  </span><span class="fl">14220.79</span> 
+Model cost at call  <span class="dv">8</span> <span class="op">:</span><span class="st">  </span><span class="fl">14220.79</span> 
+Model cost at call  <span class="dv">11</span> <span class="op">:</span><span class="st">  </span><span class="fl">14220.79</span> 
+Model cost at call  <span class="dv">12</span> <span class="op">:</span><span class="st">  </span><span class="fl">3349.268</span> 
+Model cost at call  <span class="dv">15</span> <span class="op">:</span><span class="st">  </span><span class="fl">3349.268</span> 
+Model cost at call  <span class="dv">17</span> <span class="op">:</span><span class="st">  </span><span class="fl">788.6367</span> 
+Model cost at call  <span class="dv">18</span> <span class="op">:</span><span class="st">  </span><span class="fl">788.6366</span> 
+Model cost at call  <span class="dv">22</span> <span class="op">:</span><span class="st">  </span><span class="fl">374.0575</span> 
+Model cost at call  <span class="dv">23</span> <span class="op">:</span><span class="st">  </span><span class="fl">374.0575</span> 
+Model cost at call  <span class="dv">27</span> <span class="op">:</span><span class="st">  </span><span class="fl">371.2135</span> 
+Model cost at call  <span class="dv">28</span> <span class="op">:</span><span class="st">  </span><span class="fl">371.2135</span> 
+Model cost at call  <span class="dv">32</span> <span class="op">:</span><span class="st">  </span><span class="fl">371.2134</span> 
+Model cost at call  <span class="dv">36</span> <span class="op">:</span><span class="st">  </span><span class="fl">371.2134</span> 
+Model cost at call  <span class="dv">37</span> <span class="op">:</span><span class="st">  </span><span class="fl">371.2134</span> 
 Optimisation by method Port successfully terminated.</code></pre></div>
 <p>If plotting of the fitting progress was selected, a new separate graphics window should either pop up, or a graphics window previously started for this purpose will be reused.</p>
 <p>If your screen size allows for it, you can arrange the R plotting window and the R console in a way that you can see everything at the same time:</p>
@@ -364,7 +371,6 @@ Optimisation by method Port successfully terminated.</code></pre></div>
 <!-- vim: set foldmethod=syntax ts=2 sw=2 expandtab: -->
 </div>
 </div>
-</div>
   </div>
 
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
@@ -399,5 +405,7 @@ Optimisation by method Port successfully terminated.</code></pre></div>
       </footer>
 </div>
 
+  
+
   </body>
 </html>
diff --git a/docs/articles/index.html b/docs/articles/index.html
index bfd24e2..c7c7845 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -21,13 +21,19 @@
 <!-- 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>
 
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" 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>
 
@@ -40,7 +46,7 @@
   </head>
 
   <body>
-    <div class="container template-vignette-index">
+    <div class="container template-article-index">
       <header>
       <div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
@@ -50,8 +56,12 @@
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
-      <a class="navbar-brand" href="../index.html">gmkin</a>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">gmkin</a>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.6.8</span>
+      </span>
     </div>
+
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
@@ -76,13 +86,14 @@
   </ul>
 </li>
 <li>
-  <a href="../news/index.html">News</a>
+  <a href="../news/index.html">Changelog</a>
 </li>
       </ul>
       
       <ul class="nav navbar-nav navbar-right">
         
       </ul>
+      
     </div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
@@ -90,12 +101,12 @@
       
       </header>
 
-      <div class="page-header">
-  <h1>Articles <small>version&nbsp;0.6.8</small></h1>
-</div>
-
 <div class="row">
-  <div class="col-md-9">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+      <h1>Articles</h1>
+    </div>
+
     <div class="section ">
       <h3>All vignettes</h3>
       <p class="section-desc"></p>
@@ -119,5 +130,8 @@
       </footer>
    </div>
 
+  
+
   </body>
 </html>
+
diff --git a/docs/authors.html b/docs/authors.html
index fa7d1eb..3e0114c 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -21,13 +21,19 @@
 <!-- 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>
 
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" 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>
 
@@ -50,8 +56,12 @@
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
-      <a class="navbar-brand" href="index.html">gmkin</a>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="index.html">gmkin</a>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.6.8</span>
+      </span>
     </div>
+
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
@@ -76,13 +86,14 @@
   </ul>
 </li>
 <li>
-  <a href="news/index.html">News</a>
+  <a href="news/index.html">Changelog</a>
 </li>
       </ul>
       
       <ul class="nav navbar-nav navbar-right">
         
       </ul>
+      
     </div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
@@ -90,8 +101,8 @@
       
       </header>
 
-      <div class="row">
-  <div class="contents col-md-12">
+<div class="row">
+  <div class="contents col-md-9">
     <div class="page-header">
       <h1>Authors</h1>
     </div>
@@ -128,5 +139,8 @@
       </footer>
    </div>
 
+  
+
   </body>
 </html>
+
diff --git a/docs/docsearch.css b/docs/docsearch.css
new file mode 100644
index 0000000..e5f1fe1
--- /dev/null
+++ b/docs/docsearch.css
@@ -0,0 +1,148 @@
+/* Docsearch -------------------------------------------------------------- */
+/*
+  Source: https://github.com/algolia/docsearch/
+  License: MIT
+*/
+
+.algolia-autocomplete {
+  display: block;
+  -webkit-box-flex: 1;
+  -ms-flex: 1;
+  flex: 1
+}
+
+.algolia-autocomplete .ds-dropdown-menu {
+  width: 100%;
+  min-width: none;
+  max-width: none;
+  padding: .75rem 0;
+  background-color: #fff;
+  background-clip: padding-box;
+  border: 1px solid rgba(0, 0, 0, .1);
+  box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175);
+}
+
+@media (min-width:768px) {
+  .algolia-autocomplete .ds-dropdown-menu {
+      width: 175%
+  }
+}
+
+.algolia-autocomplete .ds-dropdown-menu::before {
+  display: none
+}
+
+.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] {
+  padding: 0;
+  background-color: rgb(255,255,255);
+  border: 0;
+  max-height: 80vh;
+}
+
+.algolia-autocomplete .ds-dropdown-menu .ds-suggestions {
+  margin-top: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion {
+  padding: 0;
+  overflow: visible
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--category-header {
+  padding: .125rem 1rem;
+  margin-top: 0;
+  font-size: 1.3em;
+  font-weight: 500;
+  color: #00008B;
+  border-bottom: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--wrapper {
+    float: none;
+    padding-top: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column {
+  float: none;
+  width: auto;
+  padding: 0;
+  text-align: left
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--content {
+  float: none;
+  width: auto;
+  padding: 0
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--content::before {
+  display: none
+}
+
+.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header {
+  padding-top: .75rem;
+  margin-top: .75rem;
+  border-top: 1px solid rgba(0, 0, 0, .1)
+}
+
+.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column {
+  display: block;
+  padding: .1rem 1rem;
+  margin-bottom: 0.1;
+  font-size: 1.0em;
+  font-weight: 400
+  /* display: none */
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--title {
+  display: block;
+  padding: .25rem 1rem;
+  margin-bottom: 0;
+  font-size: 0.9em;
+  font-weight: 400
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--text {
+  padding: 0 1rem .5rem;
+  margin-top: -.25rem;
+  font-size: 0.8em;
+  font-weight: 400;
+  line-height: 1.25
+}
+
+.algolia-autocomplete .algolia-docsearch-footer {
+  width: 110px;
+  height: 20px;
+  z-index: 3;
+  margin-top: 10.66667px;
+  float: right;
+  font-size: 0;
+  line-height: 0;
+}
+
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+  background-repeat: no-repeat;
+  background-position: 50%;
+  background-size: 100%;
+  overflow: hidden;
+  text-indent: -9000px;
+  width: 100%;
+  height: 100%;
+  display: block;
+  transform: translate(-8px);
+}
+
+.algolia-autocomplete .algolia-docsearch-suggestion--highlight {
+  color: #FF8C00;
+  background: rgba(232, 189, 54, 0.1)
+}
+
+
+.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight {
+  box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5)
+}
+
+.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content {
+  background-color: rgba(192, 192, 192, .15)
+}
diff --git a/docs/docsearch.js b/docs/docsearch.js
new file mode 100644
index 0000000..b35504c
--- /dev/null
+++ b/docs/docsearch.js
@@ -0,0 +1,85 @@
+$(function() {
+
+  // register a handler to move the focus to the search bar
+  // upon pressing shift + "/" (i.e. "?")
+  $(document).on('keydown', function(e) {
+    if (e.shiftKey && e.keyCode == 191) {
+      e.preventDefault();
+      $("#search-input").focus();
+    }
+  });
+
+  $(document).ready(function() {
+    // do keyword highlighting
+    /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */
+    var mark = function() {
+
+      var referrer = document.URL ;
+      var paramKey = "q" ;
+
+      if (referrer.indexOf("?") !== -1) {
+        var qs = referrer.substr(referrer.indexOf('?') + 1);
+        var qs_noanchor = qs.split('#')[0];
+        var qsa = qs_noanchor.split('&');
+        var keyword = "";
+
+        for (var i = 0; i < qsa.length; i++) {
+          var currentParam = qsa[i].split('=');
+
+          if (currentParam.length !== 2) {
+            continue;
+          }
+
+          if (currentParam[0] == paramKey) {
+            keyword = decodeURIComponent(currentParam[1].replace(/\+/g, "%20"));
+          }
+        }
+
+        if (keyword !== "") {
+          $(".contents").unmark({
+            done: function() {
+              $(".contents").mark(keyword);
+            }
+          });
+        }
+      }
+    };
+
+    mark();
+  });
+});
+
+/* Search term highlighting ------------------------------*/
+
+function matchedWords(hit) {
+  var words = [];
+
+  var hierarchy = hit._highlightResult.hierarchy;
+  // loop to fetch from lvl0, lvl1, etc.
+  for (var idx in hierarchy) {
+    words = words.concat(hierarchy[idx].matchedWords);
+  }
+
+  var content = hit._highlightResult.content;
+  if (content) {
+    words = words.concat(content.matchedWords);
+  }
+
+  // return unique words
+  var words_uniq = [...new Set(words)];
+  return words_uniq;
+}
+
+function updateHitURL(hit) {
+
+  var words = matchedWords(hit);
+  var url = "";
+
+  if (hit.anchor) {
+    url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor;
+  } else {
+    url = hit.url + '?q=' + escape(words.join(" "));
+  }
+
+  return url;
+}
diff --git a/docs/index.html b/docs/index.html
index 1f2056b..a654b22 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -8,8 +8,8 @@
 <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">
-<!-- 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">
+<!-- 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><!-- sticky kit --><script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
+<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.">
@@ -29,8 +29,12 @@
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
-      <a class="navbar-brand" href="index.html">gmkin</a>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="index.html">gmkin</a>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.6.8</span>
+      </span>
     </div>
+
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
 <li>
@@ -55,7 +59,7 @@
   </ul>
 </li>
 <li>
-  <a href="news/index.html">News</a>
+  <a href="news/index.html">Changelog</a>
 </li>
       </ul>
 <ul class="nav navbar-nav navbar-right"></ul>
@@ -97,7 +101,7 @@
 <div class="sourceCode"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><span class="kw">drat::</span>addRepo(<span class="st">"jranke"</span>)</code></pre></div>
 <p>and install as usual</p>
 <div class="sourceCode"><pre class="sourceCode s"><code class="sourceCode gnuassembler">install.packages(<span class="st">"gmkin"</span>)</code></pre></div>
-<p>The latest changes to gmkin are recorded in the <a href="https://github.com/jranke/gmkin/blob/master/NEWS.md">NEWS</a> file, more details can be found in the <a href="https://github.com/jranke/gmkin/commits/master">commit history</a>.</p>
+<p>The latest changes to gmkin are recorded in the <a href="https://github.com/jranke/gmkin/blob/master/NEWS.html">NEWS</a> file, more details can be found in the <a href="https://github.com/jranke/gmkin/commits/master">commit history</a>.</p>
 <p><img src="gmkin_screenshot.png" alt="gmkin screenshot"></p>
 </div>
 </div>
@@ -159,19 +163,28 @@ while (TRUE) {
   </div>
 
   <div class="col-md-3" id="sidebar">
-    <h2>Links</h2>
+    <div class="links">
+<h2>Links</h2>
 <ul class="list-unstyled">
 <li>Report a bug at <br><a href="http://github.com/jranke/gmkin/issues">http://github.com/jranke/gmkin/issues</a>
 </li>
 </ul>
+</div>
+<div class="license">
 <h2>License</h2>
-<p>GPL</p>
+<ul class="list-unstyled">
+<li>GPL</li>
+</ul>
+</div>
+<div class="developers">
 <h2>Developers</h2>
 <ul class="list-unstyled">
 <li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small>  </li>
 <li><a href="authors.html">All authors...</a></li>
 </ul>
 </div>
+
+  </div>
 </div>
 
 
@@ -186,5 +199,7 @@ while (TRUE) {
       </footer>
 </div>
 
+  
+
   </body>
 </html>
diff --git a/docs/news/index.html b/docs/news/index.html
index 78f1749..24be3d7 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -6,7 +6,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-<title>All news • gmkin</title>
+<title>Changelog • gmkin</title>
 
 <!-- jquery -->
 <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -21,13 +21,19 @@
 <!-- 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>
 
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" 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" />
+
+
+
+<meta property="og:title" content="Changelog" />
+
+
+
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -50,8 +56,12 @@
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
-      <a class="navbar-brand" href="../index.html">gmkin</a>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">gmkin</a>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.6.8</span>
+      </span>
     </div>
+
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
@@ -76,13 +86,14 @@
   </ul>
 </li>
 <li>
-  <a href="../news/index.html">News</a>
+  <a href="../news/index.html">Changelog</a>
 </li>
       </ul>
       
       <ul class="nav navbar-nav navbar-right">
         
       </ul>
+      
     </div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
@@ -90,15 +101,13 @@
       
       </header>
 
-      <div class="row">
-
-  <div class="col-md-9">
+<div class="row">
+  <div class="col-md-9 contents">
     <div class="page-header">
-      <h1>Change log <small>All releases</small></h1>
+      <h1>Changelog <small></small></h1>
+      
     </div>
 
-    <div class="contents">
-    </div>
   </div>
 
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
@@ -123,5 +132,8 @@
       </footer>
    </div>
 
+  
+
   </body>
 </html>
+
diff --git a/docs/pkgdown.css b/docs/pkgdown.css
index 181fe63..6ca2f37 100644
--- a/docs/pkgdown.css
+++ b/docs/pkgdown.css
@@ -1,13 +1,32 @@
-/* Sticker footer */
+/* Sticky footer */
+
+/**
+ * Basic idea: https://philipwalton.github.io/solved-by-flexbox/demos/sticky-footer/
+ * Details: https://github.com/philipwalton/solved-by-flexbox/blob/master/assets/css/components/site.css
+ *
+ * .Site -> body > .container
+ * .Site-content -> body > .container .row
+ * .footer -> footer
+ *
+ * Key idea seems to be to ensure that .container and __all its parents__
+ * have height set to 100%
+ *
+ */
+
+html, body {
+  height: 100%;
+}
+
 body > .container {
   display: flex;
-  padding-top: 60px;
-  min-height: calc(100vh);
+  height: 100%;
   flex-direction: column;
+
+  padding-top: 60px;
 }
 
 body > .container .row {
-  flex: 1;
+  flex: 1 0 auto;
 }
 
 footer {
@@ -16,6 +35,7 @@ footer {
   border-top: 1px solid #e5e5e5;
   color: #666;
   display: flex;
+  flex-shrink: 0;
 }
 footer p {
   margin-bottom: 0;
@@ -38,6 +58,12 @@ img {
   max-width: 100%;
 }
 
+/* Typographic tweaking ---------------------------------*/
+
+.contents h1.page-header {
+  margin-top: calc(-60px + 1em);
+}
+
 /* Section anchors ---------------------------------*/
 
 a.anchor {
@@ -68,7 +94,7 @@ a.anchor {
 
 .contents h1, .contents h2, .contents h3, .contents h4 {
   padding-top: 60px;
-  margin-top: -60px;
+  margin-top: -40px;
 }
 
 /* Static header placement on mobile devices */
@@ -108,7 +134,6 @@ a.anchor {
 /* Reference index & topics ----------------------------------------------- */
 
 .ref-index th {font-weight: normal;}
-.ref-index h2 {font-size: 20px;}
 
 .ref-index td {vertical-align: top;}
 .ref-index .alias {width: 40%;}
@@ -192,3 +217,16 @@ a.sourceLine:hover {
 .hasCopyButton:hover button.btn-copy-ex {
   visibility: visible;
 }
+
+/* mark.js ----------------------------*/
+
+mark {
+  background-color: rgba(255, 255, 51, 0.5);
+  border-bottom: 2px solid rgba(255, 153, 51, 0.3);
+  padding: 1px;
+}
+
+/* vertical spacing after htmlwidgets */
+.html-widget {
+  margin-bottom: 10px;
+}
diff --git a/docs/pkgdown.js b/docs/pkgdown.js
index 64b20df..de9bd72 100644
--- a/docs/pkgdown.js
+++ b/docs/pkgdown.js
@@ -1,94 +1,110 @@
-$(function() {
-
-  $("#sidebar")
-    .stick_in_parent({offset_top: 40})
-    .on('sticky_kit:bottom', function(e) {
-      $(this).parent().css('position', 'static');
-    })
-    .on('sticky_kit:unbottom', function(e) {
-      $(this).parent().css('position', 'relative');
+/* http://gregfranko.com/blog/jquery-best-practices/ */
+(function($) {
+  $(function() {
+
+    $("#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
     });
 
-  $('body').scrollspy({
-    target: '#sidebar',
-    offset: 60
-  });
+    $('[data-toggle="tooltip"]').tooltip();
+
+    var cur_path = paths(location.pathname);
+    var links = $("#navbar ul li a");
+    var max_length = -1;
+    var pos = -1;
+    for (var i = 0; i < links.length; i++) {
+      if (links[i].getAttribute("href") === "#")
+        continue;
+      var path = paths(links[i].pathname);
+
+      var length = prefix_length(cur_path, path);
+      if (length > max_length) {
+        max_length = length;
+        pos = i;
+      }
+    }
 
-  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);
+    // Add class to parent <li>, and enclosing <li> if in dropdown
+    if (pos >= 0) {
+      var menu_anchor = $(links[pos]);
       menu_anchor.parent().addClass("active");
       menu_anchor.closest("li.dropdown").addClass("active");
     }
   });
-});
 
-function paths(pathname) {
-  var pieces = pathname.split("/");
-  pieces.shift(); // always starts with /
+  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);
+  }
 
-  var end = pieces[pieces.length - 1];
-  if (end === "index.html" || end === "")
-    pieces.pop();
-  return(pieces);
-}
+  function prefix_length(needle, haystack) {
+    if (needle.length > haystack.length)
+      return(0);
 
-function is_prefix(needle, haystack) {
-  if (needle.length > haystack.lengh)
-    return(false);
+    // Special case for length-0 haystack, since for loop won't run
+    if (haystack.length === 0) {
+      return(needle.length === 0 ? 1 : 0);
+    }
 
-  for (var i = 0; i < haystack.length; i++) {
-    if (needle[i] != haystack[i])
-      return(false);
-  }
+    for (var i = 0; i < haystack.length; i++) {
+      if (needle[i] != haystack[i])
+        return(i);
+    }
 
-  return(true);
-}
+    return(haystack.length);
+  }
 
-/* Clipboard --------------------------*/
+  /* 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);
-}
+  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>";
+  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");
+      $(".examples, div.sourceCode").addClass("hasCopyButton");
 
-    // Insert copy buttons:
-    $(copyButton).prependTo(".hasCopyButton");
+      // Insert copy buttons:
+      $(copyButton).prependTo(".hasCopyButton");
 
-    // Initialize tooltips:
-    $('.btn-copy-ex').tooltip({container: 'body'});
+      // Initialize tooltips:
+      $('.btn-copy-ex').tooltip({container: 'body'});
 
-    // Initialize clipboard:
-    var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
-      text: function(trigger) {
-        return trigger.parentNode.textContent;
-      }
-    });
+      // 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('success', function(e) {
+        changeTooltipMessage(e.trigger, 'Copied!');
+        e.clearSelection();
+      });
 
-    clipboardBtnCopies.on('error', function() {
-      changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      clipboardBtnCopies.on('error', function() {
+        changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+      });
     });
-  });
-}
-
+  }
+})(window.jQuery || window.$)
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
new file mode 100644
index 0000000..75e5968
--- /dev/null
+++ b/docs/pkgdown.yml
@@ -0,0 +1,6 @@
+pandoc: 1.19.2.4
+pkgdown: 1.1.0
+pkgdown_sha: ~
+articles:
+  gmkin_manual: gmkin_manual.html
+
diff --git a/docs/reference/FOCUS_2006.html b/docs/reference/FOCUS_2006.html
index ca9b5ce..93153ad 100644
--- a/docs/reference/FOCUS_2006.html
+++ b/docs/reference/FOCUS_2006.html
@@ -21,18 +21,24 @@
 <!-- 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>
 
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" 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>
 
@@ -55,8 +61,12 @@
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
-      <a class="navbar-brand" href="../index.html">gmkin</a>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">gmkin</a>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.6.8</span>
+      </span>
     </div>
+
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
@@ -81,13 +91,14 @@
   </ul>
 </li>
 <li>
-  <a href="../news/index.html">News</a>
+  <a href="../news/index.html">Changelog</a>
 </li>
       </ul>
       
       <ul class="nav navbar-nav navbar-right">
         
       </ul>
+      
     </div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
@@ -95,17 +106,21 @@
       
       </header>
 
-      <div class="row">
+<div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Example gmkin workspace for Datasets C and D from the FOCUS Kinetics report</h1>
+    
+    <div class="hidden name"><code>FOCUS_2006.Rd</code></div>
     </div>
 
+    <div class="ref-description">
     
     <p>An <code><a href='gmkinws.html'>gmkinws</a></code> object with data taken from FOCUS (2006), Appendix
   3. This is the the workspace that is loaded into <code><a href='gmkin.html'>gmkin</a></code> by
   default.</p>
     
+    </div>
 
     <pre class="usage"><span class='no'>FOCUS_2006</span></pre>
         
@@ -157,5 +172,8 @@
       </footer>
    </div>
 
+  
+
   </body>
 </html>
+
diff --git a/docs/reference/FOCUS_2006_Z.html b/docs/reference/FOCUS_2006_Z.html
index 4eff2a7..ee01417 100644
--- a/docs/reference/FOCUS_2006_Z.html
+++ b/docs/reference/FOCUS_2006_Z.html
@@ -21,16 +21,22 @@
 <!-- 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>
 
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" 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>
 
@@ -53,8 +59,12 @@
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
-      <a class="navbar-brand" href="../index.html">gmkin</a>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">gmkin</a>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.6.8</span>
+      </span>
     </div>
+
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
@@ -79,13 +89,14 @@
   </ul>
 </li>
 <li>
-  <a href="../news/index.html">News</a>
+  <a href="../news/index.html">Changelog</a>
 </li>
       </ul>
       
       <ul class="nav navbar-nav navbar-right">
         
       </ul>
+      
     </div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
@@ -93,15 +104,19 @@
       
       </header>
 
-      <div class="row">
+<div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Example gmkin workspace for Dataset Z from the FOCUS Kinetics report</h1>
+    
+    <div class="hidden name"><code>FOCUS_2006_Z.Rd</code></div>
     </div>
 
+    <div class="ref-description">
     
     <p>Data taken from FOCUS (2006), Appendix 7, p. 350.</p>
     
+    </div>
 
     <pre class="usage"><span class='no'>FOCUS_2006_Z</span></pre>
         
@@ -152,5 +167,8 @@
       </footer>
    </div>
 
+  
+
   </body>
 </html>
+
diff --git a/docs/reference/UBA_model_gallery.html b/docs/reference/UBA_model_gallery.html
index 4157743..00f84ae 100644
--- a/docs/reference/UBA_model_gallery.html
+++ b/docs/reference/UBA_model_gallery.html
@@ -21,12 +21,15 @@
 <!-- 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>
 
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" 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
@@ -36,6 +39,9 @@
   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>
 
@@ -58,8 +64,12 @@
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
-      <a class="navbar-brand" href="../index.html">gmkin</a>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">gmkin</a>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.6.8</span>
+      </span>
     </div>
+
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
@@ -84,13 +94,14 @@
   </ul>
 </li>
 <li>
-  <a href="../news/index.html">News</a>
+  <a href="../news/index.html">Changelog</a>
 </li>
       </ul>
       
       <ul class="nav navbar-nav navbar-right">
         
       </ul>
+      
     </div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
@@ -98,12 +109,15 @@
       
       </header>
 
-      <div class="row">
+<div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>A collection of some standard kinetic models</h1>
+    
+    <div class="hidden name"><code>UBA_model_gallery.Rd</code></div>
     </div>
 
+    <div class="ref-description">
     
     <p>The UBA model gallery contains predefined kinetic models for some common use
   cases, with metabolites named as in the commonly used PELMO degradation
@@ -112,6 +126,7 @@
   defined by Michael Klein (2010) for DegKinManager, with the exception of the
   kinetic sorption model.</p>
     
+    </div>
 
     <pre class="usage"><span class='fu'>data</span>(<span class='st'>"UBA_model_gallery"</span>)</pre>
         
@@ -158,5 +173,8 @@
       </footer>
    </div>
 
+  
+
   </body>
 </html>
+
diff --git a/docs/reference/gmkin.html b/docs/reference/gmkin.html
index 75548cb..70c2d07 100644
--- a/docs/reference/gmkin.html
+++ b/docs/reference/gmkin.html
@@ -21,18 +21,24 @@
 <!-- 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>
 
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" 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>
 
@@ -55,8 +61,12 @@
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
-      <a class="navbar-brand" href="../index.html">gmkin</a>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">gmkin</a>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.6.8</span>
+      </span>
     </div>
+
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
@@ -81,13 +91,14 @@
   </ul>
 </li>
 <li>
-  <a href="../news/index.html">News</a>
+  <a href="../news/index.html">Changelog</a>
 </li>
       </ul>
       
       <ul class="nav navbar-nav navbar-right">
         
       </ul>
+      
     </div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
@@ -95,21 +106,25 @@
       
       </header>
 
-      <div class="row">
+<div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Start a graphical user interface (GUI) based on the <code>gWidgetsWWW2</code> toolkit.</h1>
+    
+    <div class="hidden name"><code>gmkin.Rd</code></div>
     </div>
 
+    <div class="ref-description">
     
     <p>This function starts a browser based GUI. Please visit the 
   <a href='http://github.com/jverzani/gWidgetsWWW2'>github page of gWidgetsWWW2</a> 
   for an explanation how this toolkit works.</p>
     
+    </div>
 
     <pre class="usage"><span class='fu'>gmkin</span>(<span class='no'>script_name</span>, <span class='kw'>show.log</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
     
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
@@ -176,5 +191,8 @@
       </footer>
    </div>
 
+  
+
   </body>
 </html>
+
diff --git a/docs/reference/gmkinws.html b/docs/reference/gmkinws.html
index 2c1f509..e0fee8b 100644
--- a/docs/reference/gmkinws.html
+++ b/docs/reference/gmkinws.html
@@ -21,16 +21,22 @@
 <!-- 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>
 
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" 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>
 
@@ -53,8 +59,12 @@
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
-      <a class="navbar-brand" href="../index.html">gmkin</a>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">gmkin</a>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.6.8</span>
+      </span>
     </div>
+
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
@@ -79,13 +89,14 @@
   </ul>
 </li>
 <li>
-  <a href="../news/index.html">News</a>
+  <a href="../news/index.html">Changelog</a>
 </li>
       </ul>
       
       <ul class="nav navbar-nav navbar-right">
         
       </ul>
+      
     </div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
@@ -93,15 +104,19 @@
       
       </header>
 
-      <div class="row">
+<div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>A workspace class for gmkin</h1>
+    
+    <div class="hidden name"><code>gmkinws.Rd</code></div>
     </div>
 
+    <div class="ref-description">
     
     <p>Datasets, models and fits are stored in lists.</p>
     
+    </div>
 
     <pre class="usage"><span class='no'>gmkinws</span></pre>
         
@@ -146,5 +161,8 @@ by the names used in the models contained in field m</p></dd>
       </footer>
    </div>
 
+  
+
   </body>
 </html>
+
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 3fd068b..1b9bd74 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -21,13 +21,19 @@
 <!-- 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>
 
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" 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>
 
@@ -50,8 +56,12 @@
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
-      <a class="navbar-brand" href="../index.html">gmkin</a>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">gmkin</a>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.6.8</span>
+      </span>
     </div>
+
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
@@ -76,13 +86,14 @@
   </ul>
 </li>
 <li>
-  <a href="../news/index.html">News</a>
+  <a href="../news/index.html">Changelog</a>
 </li>
       </ul>
       
       <ul class="nav navbar-nav navbar-right">
         
       </ul>
+      
     </div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
@@ -90,64 +101,60 @@
       
       </header>
 
-      <div class="row">
-  <div class="col-md-9">
+<div class="row">
+  <div class="contents col-md-9">
     <div class="page-header">
-      <h1>
-        Reference
-        <small>version&nbsp;0.6.8</small>
-      </h1>
+      <h1>Reference</h1>
     </div>
 
-    <div class="contents">
-      <table class="ref-index">
-
-      <colgroup>
-        <col class="alias" />
-        <col class="title" />
-      </colgroup>
-
-      <tbody>
-        <tr>
-          <th colspan="2">
-            <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-            <p class="section-desc"></p>
-          </th>
-        </tr>
-        <tr>
-          <!--  -->
-          <td>
-            <p><code><a href="FOCUS_2006_Z.html">FOCUS_2006_Z</a></code> </p>
-          </td>
-          <td><p>Example gmkin workspace for Dataset Z from the FOCUS Kinetics report</p></td>
-        </tr><tr>
-          <!--  -->
-          <td>
-            <p><code><a href="FOCUS_2006.html">FOCUS_2006</a></code> </p>
-          </td>
-          <td><p>Example gmkin workspace for Datasets C and D from the FOCUS Kinetics report</p></td>
-        </tr><tr>
-          <!--  -->
-          <td>
-            <p><code><a href="gmkin.html">gmkin</a></code> </p>
-          </td>
-          <td><p>Start a graphical user interface (GUI) based on the <code>gWidgetsWWW2</code> toolkit.</p></td>
-        </tr><tr>
-          <!--  -->
-          <td>
-            <p><code><a href="gmkinws.html">gmkinws</a></code> </p>
-          </td>
-          <td><p>A workspace class for gmkin</p></td>
-        </tr><tr>
-          <!--  -->
-          <td>
-            <p><code><a href="UBA_model_gallery.html">data</a></code> </p>
-          </td>
-          <td><p>A collection of some standard kinetic models</p></td>
-        </tr>
-      </tbody>
-      </table>
-    </div>
+    <table class="ref-index">
+
+    <colgroup>
+      
+      <col class="alias" />
+      <col class="title" />
+    </colgroup>
+
+    <tbody>
+      <tr>
+        <th colspan="2">
+          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
+          <p class="section-desc"></p>
+        </th>
+      </tr>
+      <tr>
+        
+        <td>
+          <p><code><a href="FOCUS_2006.html">FOCUS_2006</a></code> </p>
+        </td>
+        <td><p>Example gmkin workspace for Datasets C and D from the FOCUS Kinetics report</p></td>
+      </tr><tr>
+        
+        <td>
+          <p><code><a href="FOCUS_2006_Z.html">FOCUS_2006_Z</a></code> </p>
+        </td>
+        <td><p>Example gmkin workspace for Dataset Z from the FOCUS Kinetics report</p></td>
+      </tr><tr>
+        
+        <td>
+          <p><code><a href="UBA_model_gallery.html">UBA_model_gallery</a></code> </p>
+        </td>
+        <td><p>A collection of some standard kinetic models</p></td>
+      </tr><tr>
+        
+        <td>
+          <p><code><a href="gmkin.html">gmkin()</a></code> </p>
+        </td>
+        <td><p>Start a graphical user interface (GUI) based on the <code>gWidgetsWWW2</code> toolkit.</p></td>
+      </tr><tr>
+        
+        <td>
+          <p><code><a href="gmkinws.html">gmkinws</a></code> </p>
+        </td>
+        <td><p>A workspace class for gmkin</p></td>
+      </tr>
+    </tbody>
+    </table>
   </div>
 
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
@@ -170,5 +177,8 @@
       </footer>
    </div>
 
+  
+
   </body>
 </html>
+
author	Johannes Ranke <jranke@uni-bremen.de>	2018-06-06 02:12:52 +0200
committer	Johannes Ranke <jranke@uni-bremen.de>	2018-06-06 02:12:52 +0200
commit	99a6582cd97c148686b06cf795a05a167b37645a (patch)
tree	cfc0ee0388b83bebaaa8d2b918789343e7f7c813
parent	b372baf353b693198a4d8417cf008d04f44dd14a (diff)