Adapt to mkin 1.0.x, rebuild docsv.0.6.11

1 files changed, 34 insertions, 25 deletions

diff --git a/docs/index.html b/docs/index.html
index 6936d50..229d914 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -6,21 +6,21 @@
 <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://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">
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-<!-- 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><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
+<!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous">
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="bootstrap-toc.css">
+<script src="bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
+<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" 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://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]-->
 </head>
-<body>
+<body data-spy="scroll" data-target="#toc">
     <div class="container template-home">
       <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
   <div class="container">
@@ -33,7 +33,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">gmkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.10</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.11</span>
       </span>
     </div>
 
@@ -41,7 +41,7 @@
       <ul class="nav navbar-nav">
 <li>
   <a href="index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
+    <span class="fas fa-home fa-lg"></span>
      
   </a>
 </li>
@@ -64,7 +64,14 @@
   <a href="news/index.html">Changelog</a>
 </li>
       </ul>
-<ul class="nav navbar-nav navbar-right"></ul>
+<ul class="nav navbar-nav navbar-right">
+<li>
+  <a href="http://github.com/jranke/gmkin/">
+    <span class="fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
+      </ul>
 </div>
 <!--/.nav-collapse -->
   </div>
@@ -96,14 +103,14 @@
 <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" title="1">update.packages()</a></code></pre></div>
+<div class="sourceCode" id="cb1"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true"></a>update.packages()</span></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" title="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"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true"></a>install.packages(<span class="st">"drat"</span>)</span></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" title="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"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true"></a><span class="kw">drat::</span>addRepo(<span class="st">"jranke"</span>)</span></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" title="1">install.packages(<span class="st">"gmkin"</span>)</a></code></pre></div>
+<div class="sourceCode" id="cb4"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true"></a>install.packages(<span class="st">"gmkin"</span>)</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><img src="gmkin_screenshot.png" alt="gmkin screenshot"></p>
 </div>
@@ -112,8 +119,8 @@
 <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" title="1">require(gmkin)</a>
-<a class="sourceLine" id="cb5-2" title="2">gmkin()</a></code></pre></div>
+<div class="sourceCode" id="cb5"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true"></a>require(gmkin)</span>
+<span id="cb5-2"><a href="#cb5-2" aria-hidden="true"></a>gmkin()</span></code></pre></div>
 <p>You may also want to adapt the browser that R starts (using e.g. <code><a href="https://rdrr.io/r/base/options.html">options(browser="/usr/bin/firefox")</a></code> on linux, or setting the default browser on Windows).</p>
 </div>
 <div id="documentation" class="section level2">
@@ -140,9 +147,9 @@
 <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" 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>
+<div class="sourceCode" id="cb6"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true"></a>require(devtools)</span>
+<span id="cb6-2"><a href="#cb6-2" aria-hidden="true"></a>install_github(<span class="st">"jverzani/gWidgetsWWW2"</span>, quick = TRUE)</span>
+<span id="cb6-3"><a href="#cb6-3" aria-hidden="true"></a>install_github(<span class="st">"jranke/gmkin"</span>, quick = TRUE)</span></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>
@@ -150,11 +157,11 @@
 <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" 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>
+<div class="sourceCode" id="cb7"><pre class="sourceCode s"><code class="sourceCode gnuassembler"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true"></a>require(gmkin)</span>
+<span id="cb7-2"><a href="#cb7-2" aria-hidden="true"></a>gmkin()</span>
+<span id="cb7-3"><a href="#cb7-3" aria-hidden="true"></a>while (TRUE) {</span>
+<span id="cb7-4"><a href="#cb7-4" aria-hidden="true"></a>  Sys.sleep(<span class="dv">10</span>)</span>
+<span id="cb7-5"><a href="#cb7-5" aria-hidden="true"></a>}</span></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">
@@ -166,10 +173,12 @@
 </div>
   </div>
 
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
     <div class="links">
 <h2>Links</h2>
 <ul class="list-unstyled">
+<li>Browse source code at <br><a href="http://github.com/jranke/gmkin/">http://​github.com/​jranke/​gmkin/​</a>
+</li>
 <li>Report a bug at <br><a href="http://github.com/jranke/gmkin/issues">http://​github.com/​jranke/​gmkin/​issues</a>
 </li>
 </ul>
@@ -197,7 +206,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
 </div>
 
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