Rebuild static documentation with current pkdown

author: Johannes Ranke <jranke@uni-bremen.de> 2018-03-01 09:48:02 +0100
committer: Johannes Ranke <jranke@uni-bremen.de> 2018-03-01 09:48:02 +0100
commit: 4bd4606c76dfc152547e0f5899a98494a4290d33 (patch)
tree: 36978d1bc83fcf56b1302181ce8367a60d6c156d
parent: 3f82707cd1e974848185b1141c69734e2573594d (diff)
16 files changed, 550 insertions, 182 deletions
diff --git a/ChangeLog b/ChangeLog
index fcd9305..ec197d8 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,9 @@
+commit 3f82707cd1e974848185b1141c69734e2573594d
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2017-06-13 16:05:39 +0200
+
+    Make grConvert optional as it vanished on Windows
+
 commit f5b36dc73e7778091a08eaed51fd9d4f8677fbc1
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Date:   2017-03-17 21:19:14 +0100
diff --git a/DESCRIPTION b/DESCRIPTION
index eb8cc73..05af50c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,14 +2,15 @@ Package: chents
 Type: Package
 Title: Chemical Entities as R Objects
 Version: 0.2-6
-Date: 2017-06-13
+Date: 2018-02-27
 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), 
                     email = "jranke@uni-bremen.de"))
 Description: Utilities for dealing with chemical entities and associated
     data as R objects. If Python and RDKit (> 2015.03) are installed and
     configured for use with 'PythonInR', some basic chemoinformatics functions
     like the calculation of molecular weight and plotting of chemical
-    structures in R graphics are available.
+    structures in R graphics are available. For plotting, you need
+    grConvert (https://sjp.co.nz/projects/grconvert) which is not on CRAN.
 Imports:
     webchem,
     R6,
diff --git a/docs/authors.html b/docs/authors.html
index 9f174b2..7e1fe6b 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -18,19 +18,25 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="pkgdown.css" rel="stylesheet">
 <script src="jquery.sticky-kit.min.js"></script>
 <script src="pkgdown.js"></script>
-
+  
+  
+<meta property="og:title" content="Authors" />
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]-->
+
+
   </head>
 
   <body>
@@ -49,6 +55,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="reference/index.html">Reference</a>
 </li>
       </ul>
@@ -71,7 +83,7 @@
 
     <ul class="list-unstyled">
       <li>
-        <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright&nbsp;holder.
+        <p><strong>Johannes Ranke</strong>. Author, maintainer, copyright holder. 
         </p>
       </li>
     </ul>
@@ -87,7 +99,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/index.html b/docs/index.html
index 991bab9..f16ddf7 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -8,8 +8,16 @@
 <title>Chemical Entities as R Objects • chents</title>
 <!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
 <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
-<!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
-<script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><!-- mathjax --><script src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
+<!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script><!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
+<script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><meta property="og:title" content="Chemical Entities as R Objects">
+<meta property="og:description" content="Utilities for dealing with chemical entities and associated
+    data as R objects. If Python and RDKit (&gt; 2015.03) are installed and
+    configured for use with 'PythonInR', some basic chemoinformatics functions
+    like the calculation of molecular weight and plotting of chemical
+    structures in R graphics are available. For plotting, you need
+    grConvert (https://sjp.co.nz/projects/grconvert) which is not on CRAN.">
+<meta name="twitter:card" content="summary">
+<!-- mathjax --><script src="https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]-->
@@ -29,6 +37,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
 <li>
+  <a href="index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="reference/index.html">Reference</a>
 </li>
       </ul>
@@ -45,7 +59,7 @@
   <div class="contents col-md-9">
     <div id="chents" class="section level1">
 <div class="page-header"><h1 class="hasAnchor">
-<a href="#chents" class="anchor"> </a>chents</h1></div>
+<a href="#chents" class="anchor"></a>chents</h1></div>
 <p>The R package <strong>chents</strong> provides some utilities for working with chemical entities in R, made available under the GNU public license. This means:</p>
 <div class="sourceCode"><pre class="sourceCode R"><code class="sourceCode r">This program is free software:<span class="st"> </span>you can redistribute it and/or modify it under
 the terms of the GNU General Public License as published by the Free Software
@@ -61,7 +75,7 @@ You should have received a copy of the GNU General Public License along with
 this program. If not, see &lt;http:<span class="er">//</span>www.gnu.org/licenses/<span class="er">&gt;</span></code></pre></div>
 <div id="features" class="section level2">
 <h2 class="hasAnchor">
-<a href="#features" class="anchor"> </a>Features</h2>
+<a href="#features" class="anchor"></a>Features</h2>
 <ul>
 <li>Some chemical information is retrieved from the PubChem website using the webchem package</li>
 <li>If PythonInR is installed and configured, and RDKit is available via PythonInR, some additional chemical information is computed and a 2D graph can be plotted</li>
@@ -77,7 +91,7 @@ this program. If not, see &lt;http:<span class="er">//</span>www.gnu.org/license
 <p>GPL</p>
 <h2>Developers</h2>
 <ul class="list-unstyled">
-<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small> </li>
+<li>Johannes Ranke <br><small class="roles"> Author, maintainer, copyright holder </small>  </li>
 </ul>
 </div>
 </div>
@@ -88,7 +102,7 @@ this program. If not, see &lt;http:<span class="er">//</span>www.gnu.org/license
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/pkgdown.css b/docs/pkgdown.css
index fd7b0ba..181fe63 100644
--- a/docs/pkgdown.css
+++ b/docs/pkgdown.css
@@ -34,13 +34,14 @@ img.icon {
   float: right;
 }
 
-/* Section anchors ---------------------------------*/
-
-.hasAnchor {
-  margin-left: -30px;
+img {
+  max-width: 100%;
 }
 
+/* Section anchors ---------------------------------*/
+
 a.anchor {
+  margin-left: -30px;
   display:inline-block;
   width: 30px;
   height: 30px;
@@ -56,6 +57,13 @@ a.anchor {
   visibility: visible;
 }
 
+@media (max-width: 767px) {
+  .hasAnchor:hover a.anchor {
+    visibility: hidden;
+  }
+}
+
+
 /* Fixes for fixed navbar --------------------------*/
 
 .contents h1, .contents h2, .contents h3, .contents h4 {
@@ -63,6 +71,17 @@ a.anchor {
   margin-top: -60px;
 }
 
+/* Static header placement on mobile devices */
+@media (max-width: 767px) {
+  .navbar-fixed-top {
+    position: absolute;
+  }
+  .navbar {
+    padding: 0;
+  }
+}
+
+
 /* Sidebar --------------------------*/
 
 #sidebar {
@@ -81,33 +100,95 @@ a.anchor {
   margin-bottom: 0.5em;
 }
 
+.orcid {
+  height: 16px;
+  vertical-align: middle;
+}
+
+/* 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%;}
+.ref-index .title {width: 60%;}
+
+.ref-index .alias {width: 40%;}
+.ref-index .title {width: 60%;}
+
+.ref-arguments th {text-align: right; padding-right: 10px;}
+.ref-arguments th, .ref-arguments td {vertical-align: top;}
+.ref-arguments .name {width: 20%;}
+.ref-arguments .desc {width: 80%;}
+
+/* Nice scrolling for wide elements --------------------------------------- */
+
+table {
+  display: block;
+  overflow: auto;
+}
+
 /* Syntax highlighting ---------------------------------------------------- */
 
-code {
-  background-color: #f7f7f7;
-  color: #333;
+pre {
+  word-wrap: normal;
+  word-break: normal;
+  border: 1px solid #eee;
 }
-code a {
-  color: #375f84;
+
+pre, code {
+  background-color: #f8f8f8;
+  color: #333;
 }
 
-.warning { color: red; }
-.message { font-weight: bolder; }
-.error   { color: red; font-weight: bolder; }
+pre code {
+  overflow: auto;
+  word-wrap: normal;
+  white-space: pre;
+}
 
-.fl,.number {color:rgb(21,20,181);}
-.fu,.functioncall {color:#264D66 ;}
-.ch,.st,.string {color:#375D81 ;}
-.kw,.keyword {color:black;}
-.argument {color:#264D66 ;}
-.co,.comment {color: #777;}
-.formalargs {color: #264D66;}
-.eqformalargs {color:#264D66;}
-.slot {font-style:italic;}
-.symbol {color:black ;}
-.prompt {color:black ;}
+pre .img {
+  margin: 5px 0;
+}
 
-pre img {
+pre .img img {
   background-color: #fff;
   display: block;
+  height: auto;
+}
+
+code a, pre a {
+  color: #375f84;
+}
+
+a.sourceLine:hover {
+  text-decoration: none;
+}
+
+.fl      {color: #1514b5;}
+.fu      {color: #000000;} /* function */
+.ch,.st  {color: #036a07;} /* string */
+.kw      {color: #264D66;} /* keyword */
+.co      {color: #888888;} /* comment */
+
+.message { color: black;   font-weight: bolder;}
+.error   { color: orange;  font-weight: bolder;}
+.warning { color: #6A0366; font-weight: bolder;}
+
+/* Clipboard --------------------------*/
+
+.hasCopyButton {
+  position: relative;
+}
+
+.btn-copy-ex {
+  position: absolute;
+  right: 0;
+  top: 0;
+  visibility: hidden;
+}
+
+.hasCopyButton:hover button.btn-copy-ex {
+  visibility: visible;
 }
diff --git a/docs/pkgdown.js b/docs/pkgdown.js
index c8b38c4..64b20df 100644
--- a/docs/pkgdown.js
+++ b/docs/pkgdown.js
@@ -1,8 +1,94 @@
 $(function() {
-  $("#sidebar").stick_in_parent({offset_top: 40});
+
+  $("#sidebar")
+    .stick_in_parent({offset_top: 40})
+    .on('sticky_kit:bottom', function(e) {
+      $(this).parent().css('position', 'static');
+    })
+    .on('sticky_kit:unbottom', function(e) {
+      $(this).parent().css('position', 'relative');
+    });
+
   $('body').scrollspy({
     target: '#sidebar',
     offset: 60
   });
 
+  var cur_path = paths(location.pathname);
+  $("#navbar ul li a").each(function(index, value) {
+    if (value.text == "Home")
+      return;
+    if (value.getAttribute("href") === "#")
+      return;
+
+    var path = paths(value.pathname);
+    if (is_prefix(cur_path, path)) {
+      // Add class to parent <li>, and enclosing <li> if in dropdown
+      var menu_anchor = $(value);
+      menu_anchor.parent().addClass("active");
+      menu_anchor.closest("li.dropdown").addClass("active");
+    }
+  });
 });
+
+function paths(pathname) {
+  var pieces = pathname.split("/");
+  pieces.shift(); // always starts with /
+
+  var end = pieces[pieces.length - 1];
+  if (end === "index.html" || end === "")
+    pieces.pop();
+  return(pieces);
+}
+
+function is_prefix(needle, haystack) {
+  if (needle.length > haystack.lengh)
+    return(false);
+
+  for (var i = 0; i < haystack.length; i++) {
+    if (needle[i] != haystack[i])
+      return(false);
+  }
+
+  return(true);
+}
+
+/* Clipboard --------------------------*/
+
+function changeTooltipMessage(element, msg) {
+  var tooltipOriginalTitle=element.getAttribute('data-original-title');
+  element.setAttribute('data-original-title', msg);
+  $(element).tooltip('show');
+  element.setAttribute('data-original-title', tooltipOriginalTitle);
+}
+
+if(Clipboard.isSupported()) {
+  $(document).ready(function() {
+    var copyButton = "<button type='button' class='btn btn-primary btn-copy-ex' type = 'submit' title='Copy to clipboard' aria-hidden='true' data-toggle='tooltip' data-placement='left auto' data-trigger='hover' data-clipboard-copy><i class='fa fa-copy' aria-hidden='true'></i></button>";
+
+    $(".examples").addClass("hasCopyButton");
+
+    // Insert copy buttons:
+    $(copyButton).prependTo(".hasCopyButton");
+
+    // Initialize tooltips:
+    $('.btn-copy-ex').tooltip({container: 'body'});
+
+    // Initialize clipboard:
+    var clipboardBtnCopies = new Clipboard('[data-clipboard-copy]', {
+      text: function(trigger) {
+        return trigger.parentNode.textContent;
+      }
+    });
+
+    clipboardBtnCopies.on('success', function(e) {
+      changeTooltipMessage(e.trigger, 'Copied!');
+      e.clearSelection();
+    });
+
+    clipboardBtnCopies.on('error', function() {
+      changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy');
+    });
+  });
+}
+
diff --git a/docs/reference/chent-1.png b/docs/reference/chent-1.png
new file mode 100644
index 0000000..8731cf1
--- /dev/null
+++ b/docs/reference/chent-1.png
diff --git a/docs/reference/chent.html b/docs/reference/chent.html
index 15c4d10..ef683ef 100644
--- a/docs/reference/chent.html
+++ b/docs/reference/chent.html
@@ -18,19 +18,30 @@
 <!-- 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="An R6 class for chemical entities with associated data — chent" />
 
+<meta property="og:description" content="The class is initialised with an identifier. Chemical information is retrieved from
+the internet. Additionally, it can be generated using RDKit if RDKit and its
+python bindings are installed and configured for use with PythonInR." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]-->
+
+
   </head>
 
   <body>
@@ -49,6 +60,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -75,7 +92,7 @@ the internet. Additionally, it can be generated using RDKit if RDKit and its
 python bindings are installed and configured for use with PythonInR.</p>
     
 
-    <pre><span class='no'>chent</span></pre>
+    <pre class="usage"><span class='no'>chent</span></pre>
         
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
@@ -83,52 +100,52 @@ python bindings are installed and configured for use with PythonInR.</p>
     
     <h2 class="hasAnchor" id="fields"><a class="anchor" href="#fields"></a>Fields</h2>
 
-    <p></p>
-    <p><dl class='dl-horizontal'>
-<dt><code>identifier</code></dt><dd>The identifier that was used to initiate the object, with attribute &#39;source&#39;</dd></p>
-    <p><dt><code>inchikey</code></dt><dd>InChI Key, with attribute &#39;source&#39;</dd></p>
-    <p><dt><code>smiles</code></dt><dd>SMILES code, with attribute &#39;source&#39;</dd></p>
-    <p><dt><code>mw</code></dt><dd>Molecular weight, with attribute &#39;source&#39;</dd></p>
-    <p><dt><code>pubchem</code></dt><dd>List of information retreived from PubChem</dd></p>
-    <p><dt><code>rdkit</code></dt><dd>List of information obtained with RDKit, if installed and
-configured for use with PythonInR</dd></p>
-    <p><dt><code>svg</code></dt><dd>SVG code</dd></p>
-    <p><dt><code>Picture</code></dt><dd>Graph as a <code>picture</code> object obtained using grImport</dd></p>
-    <p><dt><code>Pict_font_size</code></dt><dd>Font size as extracted from the intermediate PostScript file</dd></p>
-    <p><dt><code>pdf_height</code></dt><dd>Height of the MediaBox in the pdf after cropping</dd></p>
-    <p><dt><code>chyaml</code></dt><dd>List of information obtained from a YAML file</dd></p>
-    <p><dt><code>degradation</code></dt><dd>List of degradation endpoints</dd>
-</dl></p>
+    
+    <dl class='dl-horizontal'>
+<dt><code>identifier</code></dt><dd><p>The identifier that was used to initiate the object, with attribute 'source'</p></dd>
+    <dt><code>inchikey</code></dt><dd><p>InChI Key, with attribute 'source'</p></dd>
+    <dt><code>smiles</code></dt><dd><p>SMILES code, with attribute 'source'</p></dd>
+    <dt><code>mw</code></dt><dd><p>Molecular weight, with attribute 'source'</p></dd>
+    <dt><code>pubchem</code></dt><dd><p>List of information retreived from PubChem</p></dd>
+    <dt><code>rdkit</code></dt><dd><p>List of information obtained with RDKit, if installed and
+configured for use with PythonInR</p></dd>
+    <dt><code>svg</code></dt><dd><p>SVG code</p></dd>
+    <dt><code>Picture</code></dt><dd><p>Graph as a <code>picture</code> object obtained using grImport</p></dd>
+    <dt><code>Pict_font_size</code></dt><dd><p>Font size as extracted from the intermediate PostScript file</p></dd>
+    <dt><code>pdf_height</code></dt><dd><p>Height of the MediaBox in the pdf after cropping</p></dd>
+    <dt><code>chyaml</code></dt><dd><p>List of information obtained from a YAML file</p></dd>
+    <dt><code>degradation</code></dt><dd><p>List of degradation endpoints</p></dd>
+</dl>
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
     <pre class="examples"><div class='input'><span class='no'>oct</span> <span class='kw'>&lt;-</span> <span class='no'>chent</span>$<span class='fu'>new</span>(<span class='st'>"1-octanol"</span>, <span class='kw'>smiles</span> <span class='kw'>=</span> <span class='st'>"CCCCCCCCO"</span>)</div><div class='output co'>#&gt; <span class='message'>PubChem:</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</span></div><div class='output co'>#&gt; <span class='message'></span>
-#&gt; <span class='message'>Initialize Python Version 3.4.2 (default, Oct  8 2014, 10:47:48) </span>
-#&gt; <span class='message'>[GCC 4.9.1]</span></div><div class='output co'>#&gt; <span class='message'>Trying to get chemical information from RDKit using user SMILES</span>
-#&gt; <span class='message'>CCCCCCCCO</span></div><div class='output co'>#&gt; <span class='message'>Did not find chyaml file ./1-octanol.yaml</span></div><div class='input'><span class='fu'>print</span>(<span class='no'>oct</span>)</div><div class='output co'>#&gt; &lt;chent&gt;
+#&gt; <span class='message'>Initialize Python Version 2.7.13 (default, Nov 24 2017, 17:33:09) </span>
+#&gt; <span class='message'>[GCC 6.3.0 20170516]</span></div><div class='output co'>#&gt; <span class='message'>Trying to get chemical information from RDKit using user SMILES</span>
+#&gt; <span class='message'>CCCCCCCCO</span></div><div class='output co'>#&gt; <span class='message'>Loading required namespace: grConvert</span></div><div class='output co'>#&gt; <span class='message'>Did not find chyaml file ./1-octanol.yaml</span></div><div class='input'><span class='fu'>print</span>(<span class='no'>oct</span>)</div><div class='output co'>#&gt; &lt;chent&gt;
 #&gt; Identifier $identifier 1-octanol 
 #&gt; InChI Key $inchikey KBPLFHHGFOOTCA-UHFFFAOYSA-N 
 #&gt; SMILES string $smiles:
 #&gt;              user PubChem_Canonical 
-#&gt;       &quot;CCCCCCCCO&quot;       &quot;CCCCCCCCO&quot; 
+#&gt;       "CCCCCCCCO"       "CCCCCCCCO" 
 #&gt; Molecular weight $mw: 130.2 
 #&gt; PubChem synonyms (up to 10):
-#&gt;  [1] &quot;957&quot;              &quot;1-octanol&quot;        &quot;Octan-1-ol&quot;       &quot;octanol&quot;         
-#&gt;  [5] &quot;Octyl alcohol&quot;    &quot;N-octanol&quot;        &quot;Capryl alcohol&quot;   &quot;n-Octyl alcohol&quot; 
-#&gt;  [9] &quot;111-87-5&quot;         &quot;caprylic alcohol&quot;</div><div class='input'><span class='fu'>plot</span>(<span class='no'>oct</span>)</div><div class='input'><span class='no'>caffeine</span> <span class='kw'>&lt;-</span> <span class='no'>chent</span>$<span class='fu'>new</span>(<span class='st'>"caffeine"</span>)</div><div class='output co'>#&gt; <span class='message'>PubChem:</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</span></div><div class='output co'>#&gt; <span class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span>
+#&gt;  [1] "957"              "1-octanol"        "Octan-1-ol"       "octanol"         
+#&gt;  [5] "Octyl alcohol"    "N-octanol"        "111-87-5"         "Capryl alcohol"  
+#&gt;  [9] "caprylic alcohol" "n-Octyl alcohol" </div><div class='input'><span class='fu'>plot</span>(<span class='no'>oct</span>)</div><div class='input'><span class='no'>caffeine</span> <span class='kw'>&lt;-</span> <span class='no'>chent</span>$<span class='fu'>new</span>(<span class='st'>"caffeine"</span>)</div><div class='output co'>#&gt; <span class='message'>PubChem:</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/cids/JSON</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/property/MolecularFormula,MolecularWeight,CanonicalSMILES,IsomericSMILES,InChI,InChIKey,IUPACName,XLogP,TPSA,Complexity,Charge,HBondDonorCount,HBondAcceptorCount/JSON</span></div><div class='output co'>#&gt; <span class='message'>https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/synonyms/JSON</span></div><div class='output co'>#&gt; <span class='message'>Trying to get chemical information from RDKit using PubChem_Canonical SMILES</span>
 #&gt; <span class='message'>CN1C=NC2=C1C(=O)N(C(=O)N2C)C</span></div><div class='output co'>#&gt; <span class='message'>Did not find chyaml file ./caffeine.yaml</span></div><div class='input'><span class='fu'>print</span>(<span class='no'>caffeine</span>)</div><div class='output co'>#&gt; &lt;chent&gt;
 #&gt; Identifier $identifier caffeine 
 #&gt; InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N 
 #&gt; SMILES string $smiles:
 #&gt;              PubChem_Canonical 
-#&gt; &quot;CN1C=NC2=C1C(=O)N(C(=O)N2C)C&quot; 
+#&gt; "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" 
 #&gt; Molecular weight $mw: 194.2 
 #&gt; PubChem synonyms (up to 10):
-#&gt;  [1] &quot;2519&quot;                    &quot;caffeine&quot;               
-#&gt;  [3] &quot;Guaranine&quot;               &quot;1,3,7-Trimethylxanthine&quot;
-#&gt;  [5] &quot;Methyltheobromine&quot;       &quot;Cafeina&quot;                
-#&gt;  [7] &quot;Thein&quot;                   &quot;Koffein&quot;                
-#&gt;  [9] &quot;Mateina&quot;                 &quot;Theine&quot;                 </div><div class='input'><span class='fu'>plot</span>(<span class='no'>caffeine</span>)</div><img src='chent-22.png' alt='' width='540' height='400' /></pre>
+#&gt;  [1] "2519"                    "caffeine"               
+#&gt;  [3] "1,3,7-Trimethylxanthine" "58-08-2"                
+#&gt;  [5] "Guaranine"               "Thein"                  
+#&gt;  [7] "Cafeina"                 "Methyltheobromine"      
+#&gt;  [9] "Koffein"                 "Mateina"                </div><div class='input'><span class='fu'>plot</span>(<span class='no'>caffeine</span>)</div><div class='img'><img src='chent-1.png' alt='' width='700' height='432.632880098887' /></div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
@@ -150,7 +167,7 @@ configured for use with PythonInR</dd></p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/draw_svg.chent.html b/docs/reference/draw_svg.chent.html
index 2cc3804..5342eca 100644
--- a/docs/reference/draw_svg.chent.html
+++ b/docs/reference/draw_svg.chent.html
@@ -18,19 +18,28 @@
 <!-- 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="Draw SVG graph from a chent object using RDKit — draw_svg.chent" />
 
+<meta property="og:description" content="Draw SVG graph from a chent object using RDKit" />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]-->
+
+
   </head>
 
   <body>
@@ -49,6 +58,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -73,22 +88,33 @@
     <p>Draw SVG graph from a chent object using RDKit</p>
     
 
-    <pre><span class='fu'>draw_svg.chent</span>(<span class='no'>x</span>, <span class='kw'>width</span> <span class='kw'>=</span> <span class='fl'>300</span>, <span class='kw'>height</span> <span class='kw'>=</span> <span class='fl'>150</span>,
+    <pre class="usage"><span class='fu'>draw_svg.chent</span>(<span class='no'>x</span>, <span class='kw'>width</span> <span class='kw'>=</span> <span class='fl'>300</span>, <span class='kw'>height</span> <span class='kw'>=</span> <span class='fl'>150</span>,
   <span class='kw'>filename</span> <span class='kw'>=</span> <span class='fu'>paste0</span>(<span class='fu'>names</span>(<span class='no'>x</span>$<span class='no'>identifier</span>), <span class='st'>".svg"</span>), <span class='kw'>subdir</span> <span class='kw'>=</span> <span class='st'>"svg"</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
-    <dl class="dl-horizontal">
-      <dt>x</dt>
-      <dd>The chent object to be plotted</dd>
-      <dt>width</dt>
-      <dd>The desired width in pixels</dd>
-      <dt>height</dt>
-      <dd>The desired height in pixels</dd>
-      <dt>filename</dt>
-      <dd>The filename</dd>
-      <dt>subdir</dt>
-      <dd>The path to which the file should be written</dd>
-    </dl>
+    <table class="ref-arguments">
+    <colgroup><col class="name" /><col class="desc" /></colgroup>
+    <tr>
+      <th>x</th>
+      <td><p>The chent object to be plotted</p></td>
+    </tr>
+    <tr>
+      <th>width</th>
+      <td><p>The desired width in pixels</p></td>
+    </tr>
+    <tr>
+      <th>height</th>
+      <td><p>The desired height in pixels</p></td>
+    </tr>
+    <tr>
+      <th>filename</th>
+      <td><p>The filename</p></td>
+    </tr>
+    <tr>
+      <th>subdir</th>
+      <td><p>The path to which the file should be written</p></td>
+    </tr>
+    </table>
     
 
   </div>
@@ -107,7 +133,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 52967a5..29771c9 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -18,19 +18,25 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
-
+  
+  
+<meta property="og:title" content="Function reference" />
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]-->
+
+
   </head>
 
   <body>
@@ -49,6 +55,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -66,50 +78,72 @@
       <div class="row">
   <div class="col-md-9">
     <div class="page-header">
-      <h1>Function reference</h1>
-      <h4>version&nbsp;0.2-6</h4>
+      <h1>
+        Reference
+        <small>version&nbsp;0.2-6</small>
+      </h1>
     </div>
 
     <div class="contents">
-      <h2 id="section-r-class-definitions-and-methods" class="hasAnchor"><a href="#section-r-class-definitions-and-methods" class="anchor"></a>R6 Class definitions and methods</h2>
-      <p class="section-desc"></p>
-
-      
-      <p><a href="chent.html">An R6 class for chemical entities with associated data</a></p>
-      <ul>
-        <li><code><a href="chent.html">chent</a></code></li>
-      </ul>
-      
-      <p><a href="draw_svg.chent.html">Draw SVG graph from a chent object using RDKit</a></p>
-      <ul>
-        <li><code><a href="draw_svg.chent.html">draw_svg.chent</a></code></li>
-      </ul>
-      
-      <p><a href="plot.chent.html">Plot method for chent objects</a></p>
-      <ul>
-        <li><code><a href="plot.chent.html">plot.chent</a></code></li>
-      </ul>
-      
-      <p><a href="print.chent.html">Printing method for chent objects</a></p>
-      <ul>
-        <li><code><a href="print.chent.html">print.chent</a></code></li>
-      </ul>
-      
-      <p><a href="pai.html">An R6 class for pesticidal active ingredients and associated data</a></p>
-      <ul>
-        <li><code><a href="pai.html">pai</a></code></li>
-      </ul>
-      
-      <p><a href="print.pai.html">Printing method for pai objects (pesticidal active ingredients)</a></p>
-      <ul>
-        <li><code><a href="print.pai.html">print.pai</a></code></li>
-      </ul>
-      
-      <p><a href="pp.html">R6 class for holding a product with at least one active ingredient</a></p>
-      <ul>
-        <li><code><a href="pp.html">pp</a></code></li>
-      </ul>
-    
+      <table class="ref-index">
+
+      <colgroup>
+        <col class="alias" />
+        <col class="title" />
+      </colgroup>
+
+      <tbody>
+        <tr>
+          <th colspan="2">
+            <h2 id="section-r-class-definitions-and-methods" class="hasAnchor"><a href="#section-r-class-definitions-and-methods" class="anchor"></a>R6 Class definitions and methods</h2>
+            <p class="section-desc"></p>
+          </th>
+        </tr>
+        <tr>
+          <!--  -->
+          <td>
+            <p><code><a href="chent.html">chent</a></code> </p>
+          </td>
+          <td><p>An R6 class for chemical entities with associated data</p></td>
+        </tr><tr>
+          <!--  -->
+          <td>
+            <p><code><a href="draw_svg.chent.html">draw_svg.chent</a></code> </p>
+          </td>
+          <td><p>Draw SVG graph from a chent object using RDKit</p></td>
+        </tr><tr>
+          <!--  -->
+          <td>
+            <p><code><a href="plot.chent.html">plot</a></code> </p>
+          </td>
+          <td><p>Plot method for chent objects</p></td>
+        </tr><tr>
+          <!--  -->
+          <td>
+            <p><code><a href="print.chent.html">print</a></code> </p>
+          </td>
+          <td><p>Printing method for chent objects</p></td>
+        </tr><tr>
+          <!--  -->
+          <td>
+            <p><code><a href="pai.html">pai</a></code> </p>
+          </td>
+          <td><p>An R6 class for pesticidal active ingredients and associated data</p></td>
+        </tr><tr>
+          <!--  -->
+          <td>
+            <p><code><a href="print.pai.html">print</a></code> </p>
+          </td>
+          <td><p>Printing method for pai objects (pesticidal active ingredients)</p></td>
+        </tr><tr>
+          <!--  -->
+          <td>
+            <p><code><a href="pp.html">pp</a></code> </p>
+          </td>
+          <td><p>R6 class for holding a product with at least one active ingredient</p></td>
+        </tr>
+      </tbody>
+      </table>
     </div>
   </div>
 
@@ -127,7 +161,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/pai.html b/docs/reference/pai.html
index 4c143a1..30a5b77 100644
--- a/docs/reference/pai.html
+++ b/docs/reference/pai.html
@@ -18,19 +18,29 @@
 <!-- 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="An R6 class for pesticidal active ingredients and associated data — pai" />
 
+<meta property="og:description" content="The class is initialised with an identifier which is generally an ISO common name.
+Additional chemical information is retrieved from the internet if available." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]-->
+
+
   </head>
 
   <body>
@@ -49,6 +59,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -74,7 +90,7 @@
 Additional chemical information is retrieved from the internet if available.</p>
     
 
-    <pre><span class='no'>pai</span></pre>
+    <pre class="usage"><span class='no'>pai</span></pre>
         
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
@@ -82,11 +98,11 @@ Additional chemical information is retrieved from the internet if available.</p>
     
     <h2 class="hasAnchor" id="fields"><a class="anchor" href="#fields"></a>Fields</h2>
 
-    <p></p>
-    <p><dl class='dl-horizontal'>
-<dt><code>iso</code></dt><dd>ISO common name according to ISO 1750 as retreived from www.alanwood.net/pesticides</dd></p>
-    <p><dt><code>alanwood</code></dt><dd>List of information retreived from www.alanwood.net/pesticides</dd>
-</dl></p>
+    
+    <dl class='dl-horizontal'>
+<dt><code>iso</code></dt><dd><p>ISO common name according to ISO 1750 as retreived from www.alanwood.net/pesticides</p></dd>
+    <dt><code>alanwood</code></dt><dd><p>List of information retreived from www.alanwood.net/pesticides</p></dd>
+</dl>
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
@@ -97,11 +113,11 @@ Additional chemical information is retrieved from the internet if available.</p>
 #&gt; InChI Key $inchikey MXWJVTOOROXGIU-UHFFFAOYSA-N 
 #&gt; SMILES string $smiles:
 #&gt;            PubChem_Canonical 
-#&gt; &quot;CCNC1=NC(=NC(=N1)Cl)NC(C)C&quot; 
+#&gt; "CCNC1=NC(=NC(=N1)Cl)NC(C)C" 
 #&gt; Molecular weight $mw: 215.7 
 #&gt; PubChem synonyms (up to 10):
-#&gt;  [1] &quot;2256&quot;         &quot;atrazine&quot;     &quot;1912-24-9&quot;    &quot;Atranex&quot;      &quot;Fenatrol&quot;    
-#&gt;  [6] &quot;Atred&quot;        &quot;Oleogesaprim&quot; &quot;Atazinax&quot;     &quot;Atrasine&quot;     &quot;Chromozin&quot;   </div></pre>
+#&gt;  [1] "2256"         "atrazine"     "1912-24-9"    "Gesaprim"     "Chromozin"   
+#&gt;  [6] "Oleogesaprim" "Aktikon"      "Argezin"      "Atazinax"     "Atranex"     </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
@@ -123,7 +139,7 @@ Additional chemical information is retrieved from the internet if available.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/plot.chent-1.png b/docs/reference/plot.chent-1.png
new file mode 100644
index 0000000..8731cf1
--- /dev/null
+++ b/docs/reference/plot.chent-1.png
diff --git a/docs/reference/plot.chent.html b/docs/reference/plot.chent.html
index 3cc23d9..cc3b96b 100644
--- a/docs/reference/plot.chent.html
+++ b/docs/reference/plot.chent.html
@@ -18,19 +18,28 @@
 <!-- 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="Plot method for chent objects — plot.chent" />
 
+<meta property="og:description" content="Plot method for chent objects" />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]-->
+
+
   </head>
 
   <body>
@@ -49,6 +58,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -73,16 +88,21 @@
     <p>Plot method for chent objects</p>
     
 
-    <pre><span class='co'># S3 method for chent</span>
+    <pre class="usage"><span class='co'># S3 method for chent</span>
 <span class='fu'>plot</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
-    <dl class="dl-horizontal">
-      <dt>x</dt>
-      <dd>The chent object to be plotted</dd>
-      <dt>...</dt>
-      <dd>Further arguments passed to <code>grid.picture</code></dd>
-    </dl>
+    <table class="ref-arguments">
+    <colgroup><col class="name" /><col class="desc" /></colgroup>
+    <tr>
+      <th>x</th>
+      <td><p>The chent object to be plotted</p></td>
+    </tr>
+    <tr>
+      <th>...</th>
+      <td><p>Further arguments passed to <code>grid.picture</code></p></td>
+    </tr>
+    </table>
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
@@ -92,14 +112,14 @@
 #&gt; InChI Key $inchikey RYYVLZVUVIJVGH-UHFFFAOYSA-N 
 #&gt; SMILES string $smiles:
 #&gt;              PubChem_Canonical 
-#&gt; &quot;CN1C=NC2=C1C(=O)N(C(=O)N2C)C&quot; 
+#&gt; "CN1C=NC2=C1C(=O)N(C(=O)N2C)C" 
 #&gt; Molecular weight $mw: 194.2 
 #&gt; PubChem synonyms (up to 10):
-#&gt;  [1] &quot;2519&quot;                    &quot;caffeine&quot;               
-#&gt;  [3] &quot;Guaranine&quot;               &quot;1,3,7-Trimethylxanthine&quot;
-#&gt;  [5] &quot;Methyltheobromine&quot;       &quot;Cafeina&quot;                
-#&gt;  [7] &quot;Thein&quot;                   &quot;Koffein&quot;                
-#&gt;  [9] &quot;Mateina&quot;                 &quot;Theine&quot;                 </div><div class='input'><span class='fu'>plot</span>(<span class='no'>caffeine</span>)</div><img src='plot.chent-11.png' alt='' width='540' height='400' /></pre>
+#&gt;  [1] "2519"                    "caffeine"               
+#&gt;  [3] "1,3,7-Trimethylxanthine" "58-08-2"                
+#&gt;  [5] "Guaranine"               "Thein"                  
+#&gt;  [7] "Cafeina"                 "Methyltheobromine"      
+#&gt;  [9] "Koffein"                 "Mateina"                </div><div class='input'><span class='fu'>plot</span>(<span class='no'>caffeine</span>)</div><div class='img'><img src='plot.chent-1.png' alt='' width='700' height='432.632880098887' /></div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
@@ -118,7 +138,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/pp.html b/docs/reference/pp.html
index 4569a6f..538b885 100644
--- a/docs/reference/pp.html
+++ b/docs/reference/pp.html
@@ -18,19 +18,28 @@
 <!-- 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="R6 class for holding a product with at least one active ingredient — pp" />
 
+<meta property="og:description" content="An R6 class for holding information about a product with at least one active ingredient" />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]-->
+
+
   </head>
 
   <body>
@@ -49,6 +58,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -73,7 +88,7 @@
     <p>An R6 class for holding information about a product with at least one active ingredient</p>
     
 
-    <pre><span class='no'>pp</span></pre>
+    <pre class="usage"><span class='no'>pp</span></pre>
         
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
@@ -81,13 +96,13 @@
     
     <h2 class="hasAnchor" id="fields"><a class="anchor" href="#fields"></a>Fields</h2>
 
-    <p></p>
-    <p><dl class='dl-horizontal'>
-<dt><code>name</code></dt><dd>The name of the product</dd></p>
-    <p><dt><code>ais</code></dt><dd>A list of active ingredients</dd></p>
-    <p><dt><code>concentrations</code></dt><dd>The concentration of the ais</dd></p>
-    <p><dt><code>concentration_units</code></dt><dd>Defaults to g/L</dd>
-</dl></p>
+    
+    <dl class='dl-horizontal'>
+<dt><code>name</code></dt><dd><p>The name of the product</p></dd>
+    <dt><code>ais</code></dt><dd><p>A list of active ingredients</p></dd>
+    <dt><code>concentrations</code></dt><dd><p>The concentration of the ais</p></dd>
+    <dt><code>concentration_units</code></dt><dd><p>Defaults to g/L</p></dd>
+</dl>
     
 
   </div>
@@ -109,7 +124,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/print.chent.html b/docs/reference/print.chent.html
index 29b215a..81fde0d 100644
--- a/docs/reference/print.chent.html
+++ b/docs/reference/print.chent.html
@@ -18,19 +18,28 @@
 <!-- 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="Printing method for chent objects — print.chent" />
 
+<meta property="og:description" content="Printing method for chent objects" />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]-->
+
+
   </head>
 
   <body>
@@ -49,6 +58,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -73,16 +88,21 @@
     <p>Printing method for chent objects</p>
     
 
-    <pre><span class='co'># S3 method for chent</span>
+    <pre class="usage"><span class='co'># S3 method for chent</span>
 <span class='fu'>print</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
-    <dl class="dl-horizontal">
-      <dt>x</dt>
-      <dd>The chent object to be printed</dd>
-      <dt>...</dt>
-      <dd>Further arguments for compatibility with the S3 method</dd>
-    </dl>
+    <table class="ref-arguments">
+    <colgroup><col class="name" /><col class="desc" /></colgroup>
+    <tr>
+      <th>x</th>
+      <td><p>The chent object to be printed</p></td>
+    </tr>
+    <tr>
+      <th>...</th>
+      <td><p>Further arguments for compatibility with the S3 method</p></td>
+    </tr>
+    </table>
     
 
   </div>
@@ -101,7 +121,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/print.pai.html b/docs/reference/print.pai.html
index d2da6b8..08966de 100644
--- a/docs/reference/print.pai.html
+++ b/docs/reference/print.pai.html
@@ -18,19 +18,28 @@
 <!-- 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="Printing method for pai objects (pesticidal active ingredients) — print.pai" />
 
+<meta property="og:description" content="Printing method for pai objects (pesticidal active ingredients)" />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
-<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
 <!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]-->
+
+
   </head>
 
   <body>
@@ -49,6 +58,12 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
+</li>
+<li>
   <a href="../reference/index.html">Reference</a>
 </li>
       </ul>
@@ -73,16 +88,21 @@
     <p>Printing method for pai objects (pesticidal active ingredients)</p>
     
 
-    <pre><span class='co'># S3 method for pai</span>
+    <pre class="usage"><span class='co'># S3 method for pai</span>
 <span class='fu'>print</span>(<span class='no'>x</span>, <span class='no'>...</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
-    <dl class="dl-horizontal">
-      <dt>x</dt>
-      <dd>The chent object to be printed</dd>
-      <dt>...</dt>
-      <dd>Further arguments for compatibility with the S3 method</dd>
-    </dl>
+    <table class="ref-arguments">
+    <colgroup><col class="name" /><col class="desc" /></colgroup>
+    <tr>
+      <th>x</th>
+      <td><p>The chent object to be printed</p></td>
+    </tr>
+    <tr>
+      <th>...</th>
+      <td><p>Further arguments for compatibility with the S3 method</p></td>
+    </tr>
+    </table>
     
 
   </div>
@@ -101,7 +121,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
author	Johannes Ranke <jranke@uni-bremen.de>	2018-03-01 09:48:02 +0100
committer	Johannes Ranke <jranke@uni-bremen.de>	2018-03-01 09:48:02 +0100
commit	4bd4606c76dfc152547e0f5899a98494a4290d33 (patch)
tree	36978d1bc83fcf56b1302181ce8367a60d6c156d
parent	3f82707cd1e974848185b1141c69734e2573594d (diff)