Static documentation rebuilt by pkgdown

author: Johannes Ranke <jranke@uni-bremen.de> 2019-03-14 15:25:49 +0100
committer: Johannes Ranke <jranke@uni-bremen.de> 2019-03-14 15:25:49 +0100
commit: 0e9109db089217fea76cb5481db2ed5f3f861f03 (patch)
tree: a4c692e73aef34a9506f2d22b516d06a601ad8b4 /docs
parent: 63c27ce7f02c1fc03a1777d924c6fd2b25318963 (diff)
14 files changed, 195 insertions, 180 deletions
diff --git a/docs/articles/gmkin_manual.html b/docs/articles/gmkin_manual.html
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+++ b/docs/articles/gmkin_manual.html
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@@ -22,14 +22,15 @@
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+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
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         <a class="navbar-link" href="../index.html">gmkin</a>
-        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.6.9</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.9</span>
       </span>
     </div>
 
@@ -75,7 +76,7 @@
       <h1>Manual for gmkin</h1>
                         <h4 class="author">Johannes Ranke</h4>
             
-            <h4 class="date">2018-09-13</h4>
+            <h4 class="date">2019-03-14</h4>
       
       
       <div class="hidden name"><code>gmkin_manual.Rmd</code></div>
@@ -94,11 +95,11 @@
 <h2 class="hasAnchor">
 <a href="#starting-gmkin" class="anchor"></a>Starting gmkin</h2>
 <p>As gmkin is an R package, you need to start R and load the gmkin package before you can run gmkin. The latter can be achieved by entering the command</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw">library</span>(gmkin)</a></code></pre></div>
+<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/library">library</a></span>(gmkin)</a></code></pre></div>
 <p>into the R console. This will also load the packages that gmkin depends on, most notably gWidgetsWWW2 and mkin. Loading the package only has to be done once after you have started R.</p>
 <p>Before you start gmkin, you should make sure that R is using the working directory that you would like to keep your gmkin project file(s) in. If you use the standard R GUI application on windows, you can change the working directory from the File menu (‘File’ -&gt; ‘Change dir…’).</p>
 <p>Once you are sure that the working directory is what you want it to be, gmkin can be started by entering the R command</p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1"><span class="kw"><a href="../reference/gmkin.html">gmkin</a></span>()</a></code></pre></div>
+<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" title="1"><span class="kw"><a href="../reference/gmkin.html">gmkin</a></span>()</a></code></pre></div>
 <p>This will cause the default browser to start up or, if it is already running, to pop up and open a new tab for displaying the gmkin user interface.</p>
 <p>In the R console, you should see a message that the httpd help server is started, if it wasn’t already started before.</p>
 <p>In the browser, you should see something like the screenshot below.</p>
@@ -160,9 +161,9 @@
 <a href="#importing-data-from-text-files" class="anchor"></a>Importing data from text files</h3>
 <p>In case you want to work with a larger dataset that is already available as a computer file e.g. in a spreadsheet application, you can export these data as a tab separated or comma separated text file and import it using the “Browse” and “Upload” buttons in the dataset editor.</p>
 <p>As an example, we can create a text file from one of the datasets shipped with the mkin package using the following R command:</p>
-<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw">write.table</span>(schaefer07_complex_case, <span class="dt">sep =</span> <span class="st">","</span>, <span class="dt">dec =</span> <span class="st">"."</span>, </a>
-<a class="sourceLine" id="cb3-2" data-line-number="2">            <span class="dt">row.names =</span> <span class="ot">FALSE</span>, <span class="dt">quote =</span> <span class="ot">FALSE</span>, </a>
-<a class="sourceLine" id="cb3-3" data-line-number="3">            <span class="dt">file =</span> <span class="st">"schaefer07.csv"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/write.table">write.table</a></span>(schaefer07_complex_case, <span class="dt">sep =</span> <span class="st">","</span>, <span class="dt">dec =</span> <span class="st">"."</span>,</a>
+<a class="sourceLine" id="cb3-2" title="2">            <span class="dt">row.names =</span> <span class="ot">FALSE</span>, <span class="dt">quote =</span> <span class="ot">FALSE</span>,</a>
+<a class="sourceLine" id="cb3-3" title="3">            <span class="dt">file =</span> <span class="st">"schaefer07.csv"</span>)</a></code></pre></div>
 <p>This produces a text file with comma separated values in the current working directory of R.</p>
 <p>Loading this text file into gmkin using the “Browse” and “Upload” buttons</p>
 <div class="figure">
@@ -241,23 +242,23 @@
 <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" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1">Model cost at call  <span class="dv">1</span> <span class="op">:</span><span class="st">  </span><span class="fl">15156.12</span> </a>
-<a class="sourceLine" id="cb4-2" data-line-number="2">Model cost at call  <span class="dv">3</span> <span class="op">:</span><span class="st">  </span><span class="fl">15156.12</span> </a>
-<a class="sourceLine" id="cb4-3" data-line-number="3">Model cost at call  <span class="dv">7</span> <span class="op">:</span><span class="st">  </span><span class="fl">14220.79</span> </a>
-<a class="sourceLine" id="cb4-4" data-line-number="4">Model cost at call  <span class="dv">8</span> <span class="op">:</span><span class="st">  </span><span class="fl">14220.79</span> </a>
-<a class="sourceLine" id="cb4-5" data-line-number="5">Model cost at call  <span class="dv">11</span> <span class="op">:</span><span class="st">  </span><span class="fl">14220.79</span> </a>
-<a class="sourceLine" id="cb4-6" data-line-number="6">Model cost at call  <span class="dv">12</span> <span class="op">:</span><span class="st">  </span><span class="fl">3349.268</span> </a>
-<a class="sourceLine" id="cb4-7" data-line-number="7">Model cost at call  <span class="dv">15</span> <span class="op">:</span><span class="st">  </span><span class="fl">3349.268</span> </a>
-<a class="sourceLine" id="cb4-8" data-line-number="8">Model cost at call  <span class="dv">17</span> <span class="op">:</span><span class="st">  </span><span class="fl">788.6367</span> </a>
-<a class="sourceLine" id="cb4-9" data-line-number="9">Model cost at call  <span class="dv">18</span> <span class="op">:</span><span class="st">  </span><span class="fl">788.6366</span> </a>
-<a class="sourceLine" id="cb4-10" data-line-number="10">Model cost at call  <span class="dv">22</span> <span class="op">:</span><span class="st">  </span><span class="fl">374.0575</span> </a>
-<a class="sourceLine" id="cb4-11" data-line-number="11">Model cost at call  <span class="dv">23</span> <span class="op">:</span><span class="st">  </span><span class="fl">374.0575</span> </a>
-<a class="sourceLine" id="cb4-12" data-line-number="12">Model cost at call  <span class="dv">27</span> <span class="op">:</span><span class="st">  </span><span class="fl">371.2135</span> </a>
-<a class="sourceLine" id="cb4-13" data-line-number="13">Model cost at call  <span class="dv">28</span> <span class="op">:</span><span class="st">  </span><span class="fl">371.2135</span> </a>
-<a class="sourceLine" id="cb4-14" data-line-number="14">Model cost at call  <span class="dv">32</span> <span class="op">:</span><span class="st">  </span><span class="fl">371.2134</span> </a>
-<a class="sourceLine" id="cb4-15" data-line-number="15">Model cost at call  <span class="dv">36</span> <span class="op">:</span><span class="st">  </span><span class="fl">371.2134</span> </a>
-<a class="sourceLine" id="cb4-16" data-line-number="16">Model cost at call  <span class="dv">37</span> <span class="op">:</span><span class="st">  </span><span class="fl">371.2134</span> </a>
-<a class="sourceLine" id="cb4-17" data-line-number="17">Optimisation by method Port successfully terminated.</a></code></pre></div>
+<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1">Model cost at call  <span class="dv">1</span> <span class="op">:</span><span class="st">  </span><span class="fl">15156.12</span></a>
+<a class="sourceLine" id="cb4-2" title="2">Model cost at call  <span class="dv">3</span> <span class="op">:</span><span class="st">  </span><span class="fl">15156.12</span></a>
+<a class="sourceLine" id="cb4-3" title="3">Model cost at call  <span class="dv">7</span> <span class="op">:</span><span class="st">  </span><span class="fl">14220.79</span></a>
+<a class="sourceLine" id="cb4-4" title="4">Model cost at call  <span class="dv">8</span> <span class="op">:</span><span class="st">  </span><span class="fl">14220.79</span></a>
+<a class="sourceLine" id="cb4-5" title="5">Model cost at call  <span class="dv">11</span> <span class="op">:</span><span class="st">  </span><span class="fl">14220.79</span></a>
+<a class="sourceLine" id="cb4-6" title="6">Model cost at call  <span class="dv">12</span> <span class="op">:</span><span class="st">  </span><span class="fl">3349.268</span></a>
+<a class="sourceLine" id="cb4-7" title="7">Model cost at call  <span class="dv">15</span> <span class="op">:</span><span class="st">  </span><span class="fl">3349.268</span></a>
+<a class="sourceLine" id="cb4-8" title="8">Model cost at call  <span class="dv">17</span> <span class="op">:</span><span class="st">  </span><span class="fl">788.6367</span></a>
+<a class="sourceLine" id="cb4-9" title="9">Model cost at call  <span class="dv">18</span> <span class="op">:</span><span class="st">  </span><span class="fl">788.6366</span></a>
+<a class="sourceLine" id="cb4-10" title="10">Model cost at call  <span class="dv">22</span> <span class="op">:</span><span class="st">  </span><span class="fl">374.0575</span></a>
+<a class="sourceLine" id="cb4-11" title="11">Model cost at call  <span class="dv">23</span> <span class="op">:</span><span class="st">  </span><span class="fl">374.0575</span></a>
+<a class="sourceLine" id="cb4-12" title="12">Model cost at call  <span class="dv">27</span> <span class="op">:</span><span class="st">  </span><span class="fl">371.2135</span></a>
+<a class="sourceLine" id="cb4-13" title="13">Model cost at call  <span class="dv">28</span> <span class="op">:</span><span class="st">  </span><span class="fl">371.2135</span></a>
+<a class="sourceLine" id="cb4-14" title="14">Model cost at call  <span class="dv">32</span> <span class="op">:</span><span class="st">  </span><span class="fl">371.2134</span></a>
+<a class="sourceLine" id="cb4-15" title="15">Model cost at call  <span class="dv">36</span> <span class="op">:</span><span class="st">  </span><span class="fl">371.2134</span></a>
+<a class="sourceLine" id="cb4-16" title="16">Model cost at call  <span class="dv">37</span> <span class="op">:</span><span class="st">  </span><span class="fl">371.2134</span></a>
+<a class="sourceLine" id="cb4-17" title="17">Optimisation by method Port successfully terminated.</a></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>
 <div class="figure">
@@ -281,7 +282,7 @@
 <h3 class="hasAnchor">
 <a href="#confidence-interval-plots" class="anchor"></a>Confidence interval plots</h3>
 <p>Whenever a new fit has been configured or a run of a fit has been completed, the plotting area is updated with the abovementioned plot of the data and the current model solution.</p>
-<p>In addition, a confidence interval plot is shown below this conventional plot. In case a fit has been run and confidence intervals were successfully calculated for the fit (i.e. if the model was not overparameterised and no other problems occurred), the confidence intervals are graphically displayed as bars as shown below.</p>
+<p>In addition, a confidence interval plot is shown below this conventional plot. In case a fit has been run and confidence intervals were successfully calculated for the fit ( i.e. if the model was not overparameterised and no other problems occurred), the confidence intervals are graphically displayed as bars as shown below.</p>
 <div class="figure">
 <img src="img/confidence.png" alt="confidence"><p class="caption">confidence</p>
 </div>
@@ -290,7 +291,7 @@
 <div id="howtos" class="section level2">
 <h2 class="hasAnchor">
 <a href="#howtos" class="anchor"></a>Howtos</h2>
-<p>The following sections show step by step descriptions of how to perform certain tasks using gmkin. In principle, this should be necessary as the GUI was designed to be largely self-explanatory. Nevertheless may help a beginner to understand how to use gmkin. At the same time, the gmkin author uses them as test cases to make sure that the most important functionality is not broken before releasing a new version.</p>
+<p>The following sections show step by step descriptions of how to perform certain tasks using gmkin. In principle, this should not be necessary as the GUI was designed to be largely self-explanatory. Nevertheless it may help a beginner to understand how to use gmkin. At the same time, the gmkin author uses them as test cases to make sure that the most important functionality is not broken before releasing a new version.</p>
 <div id="use-a-model-and-a-dataset-from-a-built-in-workspace" class="section level3">
 <h3 class="hasAnchor">
 <a href="#use-a-model-and-a-dataset-from-a-built-in-workspace" class="anchor"></a>1. Use a model and a dataset from a built-in workspace</h3>
@@ -399,9 +400,8 @@
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-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
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diff --git a/docs/articles/index.html b/docs/articles/index.html
index 66f320b..bb2278b 100644
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@@ -1,6 +1,6 @@
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@@ -9,17 +9,17 @@
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 <script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
@@ -35,7 +35,8 @@
 
 
 <!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -51,14 +52,15 @@
       <div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
     <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
       <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">0.6.9</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.9</span>
       </span>
     </div>
 
@@ -124,9 +126,8 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
 </div>
-
       </footer>
    </div>
 
diff --git a/docs/authors.html b/docs/authors.html
index bd814b3..85ee6e1 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -1,6 +1,6 @@
 <!-- Generated by pkgdown: do not edit by hand -->
 <!DOCTYPE html>
-<html>
+<html lang="en">
   <head>
   <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
 <title>Authors • gmkin</title>
 
 <!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" 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">
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+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" 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">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" 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>
@@ -35,7 +35,8 @@
 
 
 <!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -51,14 +52,15 @@
       <div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
     <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
       <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">0.6.9</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.9</span>
       </span>
     </div>
 
@@ -133,9 +135,8 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
 </div>
-
       </footer>
    </div>
 
diff --git a/docs/index.html b/docs/index.html
index 0df4c29..a9c7511 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -1,20 +1,20 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
 <head>
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
 <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1.0">
 <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><!-- 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">
+<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous">
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" crossorigin="anonymous">
+<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" 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.">
 <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]>
+<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></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]-->
@@ -24,14 +24,15 @@
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
     <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
       <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">0.6.9</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.9</span>
       </span>
     </div>
 
@@ -73,7 +74,7 @@
       
       </header><div class="row">
   <div class="contents col-md-9">
-    <div id="gmkin" class="section level1">
+<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>
@@ -93,15 +94,15 @@
 <h3 class="hasAnchor">
 <a href="#installing-gmkin-and-gwidgetswww2" class="anchor"></a>Installing gmkin and gWidgetsWWW2</h3>
 <p>Windows and Linux users running R 3.1.0 or later can make use of my drat package repository on github. Before installing gmkin, you should update your R packages already installed, e.g. by starting R, and pasting the command</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><a class="sourceLine" id="cb1-1" data-line-number="1">update.packages()</a></code></pre></div>
+<div class="sourceCode" id="cb1"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><a class="sourceLine" id="cb1-1" title="1">update.packages()</a></code></pre></div>
 <p>or similar, depending on your R installation.</p>
 <p>For installing gmkin or upgrading to the latest released version, please install the drat package</p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><a class="sourceLine" id="cb2-1" data-line-number="1">install.packages(<span class="st">"drat"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb2"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><a class="sourceLine" id="cb2-1" title="1">install.packages(<span class="st">"drat"</span>)</a></code></pre></div>
 <p>add my repository</p>
-<div class="sourceCode" id="cb3"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw">drat::</span>addRepo(<span class="st">"jranke"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb3"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><a class="sourceLine" id="cb3-1" title="1"><span class="kw">drat::</span>addRepo(<span class="st">"jranke"</span>)</a></code></pre></div>
 <p>and install as usual</p>
-<div class="sourceCode" id="cb4"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><a class="sourceLine" id="cb4-1" data-line-number="1">install.packages(<span class="st">"gmkin"</span>)</a></code></pre></div>
-<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>
+<div class="sourceCode" id="cb4"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><a class="sourceLine" id="cb4-1" title="1">install.packages(<span class="st">"gmkin"</span>)</a></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><img src="gmkin_screenshot.png" alt="gmkin screenshot"></p>
 </div>
 </div>
@@ -109,9 +110,9 @@
 <h2 class="hasAnchor">
 <a href="#usage" class="anchor"></a>Usage</h2>
 <p>Without further preparation, you can start the GUI by starting R and pasting the following commands into the R terminal (R console on Windows):</p>
-<div class="sourceCode" id="cb5"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><a class="sourceLine" id="cb5-1" data-line-number="1">require(gmkin)</a>
-<a class="sourceLine" id="cb5-2" data-line-number="2">gmkin()</a></code></pre></div>
-<p>You may also want to adapt the browser that R starts (using e.g. <code>options(browser="/usr/bin/firefox")</code> on linux, or setting the default browser on Windows).</p>
+<div class="sourceCode" id="cb5"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><a class="sourceLine" id="cb5-1" title="1">require(gmkin)</a>
+<a class="sourceLine" id="cb5-2" title="2">gmkin()</a></code></pre></div>
+<p>You may also want to adapt the browser that R starts (using e.g. <code><a href="https://www.rdocumentation.org/packages/base/topics/options">options(browser="/usr/bin/firefox")</a></code> on linux, or setting the default browser on Windows).</p>
 </div>
 <div id="documentation" class="section level2">
 <h2 class="hasAnchor">
@@ -137,9 +138,9 @@
 <h3 class="hasAnchor">
 <a href="#installation-using-the-devtools-package" class="anchor"></a>Installation using the devtools package</h3>
 <p>Users of the <code>devtools</code> package can also install gWidgetsWWW2 and gmkin directly from the respective github repositories:</p>
-<div class="sourceCode" id="cb6"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><a class="sourceLine" id="cb6-1" data-line-number="1">require(devtools)</a>
-<a class="sourceLine" id="cb6-2" data-line-number="2">install_github(<span class="st">"jverzani/gWidgetsWWW2"</span>, quick = TRUE)</a>
-<a class="sourceLine" id="cb6-3" data-line-number="3">install_github(<span class="st">"jranke/gmkin"</span>, quick = TRUE)</a></code></pre></div>
+<div class="sourceCode" id="cb6"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><a class="sourceLine" id="cb6-1" title="1">require(devtools)</a>
+<a class="sourceLine" id="cb6-2" title="2">install_github(<span class="st">"jverzani/gWidgetsWWW2"</span>, quick = TRUE)</a>
+<a class="sourceLine" id="cb6-3" title="3">install_github(<span class="st">"jranke/gmkin"</span>, quick = TRUE)</a></code></pre></div>
 <p>Installing gWidgetsWWW2 in this way yields a lot of warnings concerning overly long path names (see Notes on gWidgetsWWW2 above). Using <code>quick = TRUE</code> skips docs, multiple-architecture builds, demos, and vignettes, to make installation as fast and painless as possible.</p>
 </div>
 </div>
@@ -147,11 +148,11 @@
 <h2 class="hasAnchor">
 <a href="#simplifying-the-start-of-gmkin-under-windows" class="anchor"></a>Simplifying the start of gmkin under Windows</h2>
 <p>You can put the commands</p>
-<div class="sourceCode" id="cb7"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><a class="sourceLine" id="cb7-1" data-line-number="1">require(gmkin)</a>
-<a class="sourceLine" id="cb7-2" data-line-number="2">gmkin()</a>
-<a class="sourceLine" id="cb7-3" data-line-number="3">while (TRUE) {</a>
-<a class="sourceLine" id="cb7-4" data-line-number="4">  Sys.sleep(<span class="dv">10</span>)</a>
-<a class="sourceLine" id="cb7-5" data-line-number="5">}</a></code></pre></div>
+<div class="sourceCode" id="cb7"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><a class="sourceLine" id="cb7-1" title="1">require(gmkin)</a>
+<a class="sourceLine" id="cb7-2" title="2">gmkin()</a>
+<a class="sourceLine" id="cb7-3" title="3">while (TRUE) {</a>
+<a class="sourceLine" id="cb7-4" title="4">  Sys.sleep(<span class="dv">10</span>)</a>
+<a class="sourceLine" id="cb7-5" title="5">}</a></code></pre></div>
 <p>into an R script (e.g. under <code>C:\Users\&lt;your username&gt;\AppData\Roaming\gmkin_start.R</code>), and create a Windows shortcut, e.g. on the Desktop, with the target <code>"C:\Program Files\R\R-3.x.y\bin\R.exe" --slave -f c:\Users\&lt;your username&gt;\AppData\Roaming\gmkin_start.R</code>, where R.x.y is the version of R that you would like to use with gmkin. This will start a non-interactive R console that runs the gmkin GUI. In the properties dialogue of the shortcut, you can also set the working directory in which it starts gmkin. Thanks to Jonas Klein of the Umweltbundesamt for the trick with using Sys.sleep in a while loop and for suggesting the AppData directory for the start script.</p>
 </div>
 <div id="acknowledgements" class="section level2">
@@ -162,7 +163,7 @@
 </div>
   </div>
 
-  <div class="col-md-3" id="sidebar">
+  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <div class="links">
 <h2>Links</h2>
 <ul class="list-unstyled">
@@ -187,15 +188,13 @@
   </div>
 </div>
 
-
       <footer><div class="copyright">
   <p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
 </div>
-
       </footer>
 </div>
 
diff --git a/docs/news/index.html b/docs/news/index.html
index d8cce8c..5055106 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -1,6 +1,6 @@
 <!-- Generated by pkgdown: do not edit by hand -->
 <!DOCTYPE html>
-<html>
+<html lang="en">
   <head>
   <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
 <title>Changelog • gmkin</title>
 
 <!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" 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>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" 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">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" 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>
@@ -35,7 +35,8 @@
 
 
 <!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -51,14 +52,15 @@
       <div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
     <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
       <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">0.6.9</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.9</span>
       </span>
     </div>
 
@@ -126,9 +128,8 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
 </div>
-
       </footer>
    </div>
 
diff --git a/docs/pkgdown.css b/docs/pkgdown.css
index 6ca2f37..c03fb08 100644
--- a/docs/pkgdown.css
+++ b/docs/pkgdown.css
@@ -58,9 +58,14 @@ img {
   max-width: 100%;
 }
 
+/* Fix bug in bootstrap (only seen in firefox) */
+summary {
+  display: list-item;
+}
+
 /* Typographic tweaking ---------------------------------*/
 
-.contents h1.page-header {
+.contents .page-header {
   margin-top: calc(-60px + 1em);
 }
 
@@ -136,10 +141,9 @@ a.anchor {
 .ref-index th {font-weight: normal;}
 
 .ref-index td {vertical-align: top;}
+.ref-index .icon {width: 40px;}
 .ref-index .alias {width: 40%;}
-.ref-index .title {width: 60%;}
-
-.ref-index .alias {width: 40%;}
+.ref-index-icons .alias {width: calc(40% - 40px);}
 .ref-index .title {width: 60%;}
 
 .ref-arguments th {text-align: right; padding-right: 10px;}
diff --git a/docs/pkgdown.js b/docs/pkgdown.js
index de9bd72..eb7e83d 100644
--- a/docs/pkgdown.js
+++ b/docs/pkgdown.js
@@ -25,9 +25,13 @@
     for (var i = 0; i < links.length; i++) {
       if (links[i].getAttribute("href") === "#")
         continue;
-      var path = paths(links[i].pathname);
+      // Ignore external links
+      if (links[i].host !== location.host)
+        continue;
+
+      var nav_path = paths(links[i].pathname);
 
-      var length = prefix_length(cur_path, path);
+      var length = prefix_length(nav_path, cur_path);
       if (length > max_length) {
         max_length = length;
         pos = i;
@@ -52,13 +56,14 @@
     return(pieces);
   }
 
+  // Returns -1 if not found
   function prefix_length(needle, haystack) {
     if (needle.length > haystack.length)
-      return(0);
+      return(-1);
 
     // Special case for length-0 haystack, since for loop won't run
     if (haystack.length === 0) {
-      return(needle.length === 0 ? 1 : 0);
+      return(needle.length === 0 ? 0 : -1);
     }
 
     for (var i = 0; i < haystack.length; i++) {
@@ -78,9 +83,9 @@
     element.setAttribute('data-original-title', tooltipOriginalTitle);
   }
 
-  if(Clipboard.isSupported()) {
+  if(ClipboardJS.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>";
+      var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-label='Copy to clipboard' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy'></i></button>";
 
       $(".examples, div.sourceCode").addClass("hasCopyButton");
 
@@ -91,7 +96,7 @@
       $('.btn-copy-ex').tooltip({container: 'body'});
 
       // Initialize clipboard:
-      var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      var clipboardBtnCopies = new ClipboardJS('[data-clipboard-copy]', {
         text: function(trigger) {
           return trigger.parentNode.textContent;
         }
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index d836be5..b60ebd0 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,5 +1,5 @@
 pandoc: 2.2.1
-pkgdown: 1.1.0
+pkgdown: 1.3.0.9000
 pkgdown_sha: ~
 articles:
   gmkin_manual: gmkin_manual.html
diff --git a/docs/reference/FOCUS_2006.html b/docs/reference/FOCUS_2006.html
index 4a96697..57bb310 100644
--- a/docs/reference/FOCUS_2006.html
+++ b/docs/reference/FOCUS_2006.html
@@ -1,6 +1,6 @@
 <!-- Generated by pkgdown: do not edit by hand -->
 <!DOCTYPE html>
-<html>
+<html lang="en">
   <head>
   <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
 <title>Example gmkin workspace for Datasets C and D from the FOCUS Kinetics report — FOCUS_2006 • gmkin</title>
 
 <!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" 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>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" 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">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" 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>
@@ -40,7 +40,8 @@
 
 
 <!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -56,14 +57,15 @@
       <div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
     <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
       <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">0.6.9</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.9</span>
       </span>
     </div>
 
@@ -140,7 +142,7 @@
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <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='fu'><a href='https://www.rdocumentation.org/packages/base/topics/save'>save</a></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>
 
@@ -166,9 +168,8 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
 </div>
-
       </footer>
    </div>
 
diff --git a/docs/reference/FOCUS_2006_Z.html b/docs/reference/FOCUS_2006_Z.html
index 8a1cc24..e3309c7 100644
--- a/docs/reference/FOCUS_2006_Z.html
+++ b/docs/reference/FOCUS_2006_Z.html
@@ -1,6 +1,6 @@
 <!-- Generated by pkgdown: do not edit by hand -->
 <!DOCTYPE html>
-<html>
+<html lang="en">
   <head>
   <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
 <title>Example gmkin workspace for Dataset Z from the FOCUS Kinetics report — FOCUS_2006_Z • gmkin</title>
 
 <!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" 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>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" 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">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" 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>
@@ -38,7 +38,8 @@
 
 
 <!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -54,14 +55,15 @@
       <div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
     <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
       <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">0.6.9</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.9</span>
       </span>
     </div>
 
@@ -136,7 +138,7 @@
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <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='fu'><a href='https://www.rdocumentation.org/packages/base/topics/save'>save</a></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>
 
 <span class='co'># }</span></pre>
@@ -161,9 +163,8 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
 </div>
-
       </footer>
    </div>
 
diff --git a/docs/reference/UBA_model_gallery.html b/docs/reference/UBA_model_gallery.html
index a7e6f59..3cf9e12 100644
--- a/docs/reference/UBA_model_gallery.html
+++ b/docs/reference/UBA_model_gallery.html
@@ -1,6 +1,6 @@
 <!-- Generated by pkgdown: do not edit by hand -->
 <!DOCTYPE html>
-<html>
+<html lang="en">
   <head>
   <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
 <title>A collection of some standard kinetic models — UBA_model_gallery • gmkin</title>
 
 <!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" 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>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" 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">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
 
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@@ -43,7 +43,8 @@
 
 
 <!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -59,14 +60,15 @@
       <div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
     <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
       <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">0.6.9</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.9</span>
       </span>
     </div>
 
@@ -128,7 +130,7 @@
     
     </div>
 
-    <pre class="usage"><span class='fu'>data</span>(<span class='st'>"UBA_model_gallery"</span>)</pre>
+    <pre class="usage"><span class='fu'><a href='https://www.rdocumentation.org/packages/utils/topics/data'>data</a></span>(<span class='st'>"UBA_model_gallery"</span>)</pre>
         
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
@@ -145,7 +147,7 @@
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>UBA_model_gallery</span>)</div></pre>
+    <pre class="examples"><div class='input'><span class='fu'><a href='https://www.rdocumentation.org/packages/utils/topics/data'>data</a></span>(<span class='no'>UBA_model_gallery</span>)</div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
@@ -167,9 +169,8 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
 </div>
-
       </footer>
    </div>
 
diff --git a/docs/reference/gmkin.html b/docs/reference/gmkin.html
index 21961bb..8740e7d 100644
--- a/docs/reference/gmkin.html
+++ b/docs/reference/gmkin.html
@@ -1,6 +1,6 @@
 <!-- Generated by pkgdown: do not edit by hand -->
 <!DOCTYPE html>
-<html>
+<html lang="en">
   <head>
   <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
 <title>Start a graphical user interface (GUI) based on the <code>gWidgetsWWW2</code> toolkit. — gmkin • gmkin</title>
 
 <!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
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-<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>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" 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">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" 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>
@@ -40,7 +40,8 @@
 
 
 <!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -56,14 +57,15 @@
       <div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
     <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
       <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">0.6.9</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.9</span>
       </span>
     </div>
 
@@ -173,9 +175,7 @@
     </ul>
 
     <h2>Author</h2>
-    
-  Johannes Ranke
-
+    <p>Johannes Ranke</p>
   </div>
 </div>
 
@@ -185,9 +185,8 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
 </div>
-
       </footer>
    </div>
 
diff --git a/docs/reference/gmkinws.html b/docs/reference/gmkinws.html
index 7355823..d2f667f 100644
--- a/docs/reference/gmkinws.html
+++ b/docs/reference/gmkinws.html
@@ -1,6 +1,6 @@
 <!-- Generated by pkgdown: do not edit by hand -->
 <!DOCTYPE html>
-<html>
+<html lang="en">
   <head>
   <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
 <title>A workspace class for gmkin — gmkinws • gmkin</title>
 
 <!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" 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>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" 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">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" 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>
@@ -38,7 +38,8 @@
 
 
 <!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -54,14 +55,15 @@
       <div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
     <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
       <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">0.6.9</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.9</span>
       </span>
     </div>
 
@@ -155,9 +157,8 @@ by the names used in the models contained in field m</p></dd>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
 </div>
-
       </footer>
    </div>
 
diff --git a/docs/reference/index.html b/docs/reference/index.html
index f0a6712..cc279d2 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -1,6 +1,6 @@
 <!-- Generated by pkgdown: do not edit by hand -->
 <!DOCTYPE html>
-<html>
+<html lang="en">
   <head>
   <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
@@ -9,17 +9,17 @@
 <title>Function reference • gmkin</title>
 
 <!-- jquery -->
-<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" 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>
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" 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">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css" integrity="sha256-eZrrJcwDc/3uDhsdt61sL2oOBY362qM3lon1gyExkL0=" 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>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" 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>
@@ -35,7 +35,8 @@
 
 
 <!-- mathjax -->
-<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
@@ -51,14 +52,15 @@
       <div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
     <div class="navbar-header">
-      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
+        <span class="sr-only">Toggle navigation</span>
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
       <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">0.6.9</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.9</span>
       </span>
     </div>
 
@@ -171,9 +173,8 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.3.0.9000.</p>
 </div>
-
       </footer>
    </div>
author	Johannes Ranke <jranke@uni-bremen.de>	2019-03-14 15:25:49 +0100
committer	Johannes Ranke <jranke@uni-bremen.de>	2019-03-14 15:25:49 +0100
commit	0e9109db089217fea76cb5481db2ed5f3f861f03 (patch)
tree	a4c692e73aef34a9506f2d22b516d06a601ad8b4 /docs
parent	63c27ce7f02c1fc03a1777d924c6fd2b25318963 (diff)