Static documentation rebuilt by current pkgdown

6 files changed, 186 insertions, 46 deletions

diff --git a/docs/reference/FOCUS_2006.html b/docs/reference/FOCUS_2006.html
index 2c9d327..ca9b5ce 100644
--- a/docs/reference/FOCUS_2006.html
+++ b/docs/reference/FOCUS_2006.html
@@ -18,12 +18,21 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
-
+  
+  
+<meta property="og:title" content="Example gmkin workspace for Datasets C and D from the FOCUS Kinetics report — FOCUS_2006" />
+
+<meta property="og:description" content="An gmkinws object with data taken from FOCUS (2006), Appendix
+  3. This is the the workspace that is loaded into gmkin by
+  default." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,10 +60,25 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Reference</a>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
 </li>
 <li>
-  <a href="../articles/index.html">Articles</a>
+  <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu">
+    <li>
+      <a href="../articles/gmkin_manual.html">Manual for gmkin</a>
+    </li>
+  </ul>
 </li>
 <li>
   <a href="../news/index.html">News</a>
@@ -96,16 +120,16 @@
   Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
   Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
   EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
-  <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p>
+  <a href='http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p>
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'>  <span class='fu'>not_run</span>({
-    <span class='fu'>save</span>(<span class='no'>FOCUS_2006</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"FOCUS_2006.RData"</span>)
-    <span class='co'># Now you can load the file "FOCUS_2006.RData" from gmkin,</span>
-    <span class='co'># restoring the workspace that is loaded at startup.</span>
+    <pre class="examples"><div class='input'>  </div><span class='co'># NOT RUN {</span>
+  <span class='fu'>save</span>(<span class='no'>FOCUS_2006</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"FOCUS_2006.RData"</span>)
+  <span class='co'># Now you can load the file "FOCUS_2006.RData" from gmkin,</span>
+  <span class='co'># restoring the workspace that is loaded at startup.</span>
 
-})</div></pre>
+<span class='co'># }</span></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
@@ -127,7 +151,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/FOCUS_2006_Z.html b/docs/reference/FOCUS_2006_Z.html
index dff1b0e..4eff2a7 100644
--- a/docs/reference/FOCUS_2006_Z.html
+++ b/docs/reference/FOCUS_2006_Z.html
@@ -18,12 +18,19 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="Example gmkin workspace for Dataset Z from the FOCUS Kinetics report — FOCUS_2006_Z" />
 
+<meta property="og:description" content="Data taken from FOCUS (2006), Appendix 7, p. 350." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,10 +58,25 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Reference</a>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
 </li>
 <li>
-  <a href="../articles/index.html">Articles</a>
+  <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu">
+    <li>
+      <a href="../articles/gmkin_manual.html">Manual for gmkin</a>
+    </li>
+  </ul>
 </li>
 <li>
   <a href="../news/index.html">News</a>
@@ -94,15 +116,15 @@
   Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
   Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
   EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
-  <a href = 'http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p>
+  <a href='http://focus.jrc.ec.europa.eu/dk'>http://focus.jrc.ec.europa.eu/dk</a></p>
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'>  <span class='fu'>not_run</span>({
-    <span class='fu'>save</span>(<span class='no'>FOCUS_2006_Z</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"FOCUS_2006_Z.RData"</span>)
-    <span class='co'># Now you can load the file "FOCUS_2006_Z.RData" from gmkin</span>
+    <pre class="examples"><div class='input'>  </div><span class='co'># NOT RUN {</span>
+  <span class='fu'>save</span>(<span class='no'>FOCUS_2006_Z</span>, <span class='kw'>file</span> <span class='kw'>=</span> <span class='st'>"FOCUS_2006_Z.RData"</span>)
+  <span class='co'># Now you can load the file "FOCUS_2006_Z.RData" from gmkin</span>
 
-})</div></pre>
+<span class='co'># }</span></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
@@ -124,7 +146,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/UBA_model_gallery.html b/docs/reference/UBA_model_gallery.html
index 74fc20b..4157743 100644
--- a/docs/reference/UBA_model_gallery.html
+++ b/docs/reference/UBA_model_gallery.html
@@ -18,12 +18,24 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="A collection of some standard kinetic models — UBA_model_gallery" />
 
+<meta property="og:description" content="The UBA model gallery contains predefined kinetic models for some common use
+  cases, with metabolites named as in the commonly used PELMO degradation
+  scheme (Jene 1998).  Please use the model gallery of the gmkin
+  GUI to see their definitions.  The models use the topology of the models
+  defined by Michael Klein (2010) for DegKinManager, with the exception of the
+  kinetic sorption model." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,10 +63,25 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Reference</a>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
 </li>
 <li>
-  <a href="../articles/index.html">Articles</a>
+  <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu">
+    <li>
+      <a href="../articles/gmkin_manual.html">Manual for gmkin</a>
+    </li>
+  </ul>
 </li>
 <li>
   <a href="../news/index.html">News</a>
@@ -125,7 +152,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/gmkin.html b/docs/reference/gmkin.html
index 961372e..75548cb 100644
--- a/docs/reference/gmkin.html
+++ b/docs/reference/gmkin.html
@@ -18,12 +18,21 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
-
+  
+  
+<meta property="og:title" content="Start a graphical user interface (GUI) based on the <code>gWidgetsWWW2</code> toolkit. — gmkin" />
+
+<meta property="og:description" content="This function starts a browser based GUI. Please visit the 
+  github page of gWidgetsWWW2 
+  for an explanation how this toolkit works." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,10 +60,25 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Reference</a>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
 </li>
 <li>
-  <a href="../articles/index.html">Articles</a>
+  <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu">
+    <li>
+      <a href="../articles/gmkin_manual.html">Manual for gmkin</a>
+    </li>
+  </ul>
 </li>
 <li>
   <a href="../news/index.html">News</a>
@@ -79,7 +103,7 @@
 
     
     <p>This function starts a browser based GUI. Please visit the 
-  <a href = 'http://github.com/jverzani/gWidgetsWWW2'>github page of gWidgetsWWW2</a> 
+  <a href='http://github.com/jverzani/gWidgetsWWW2'>github page of gWidgetsWWW2</a> 
   for an explanation how this toolkit works.</p>
     
 
@@ -107,19 +131,21 @@
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'>  <span class='co'>## Not run: gmkin() # Start the gmkin GUI</span>
-  <span class='fu'>not_run</span>({
-      <span class='no'>g</span> <span class='kw'>&lt;-</span> <span class='fu'>gmkin</span>()
-
-      <span class='co'># Only for debugging or other advanced usage:</span>
-      <span class='no'>session</span> <span class='kw'>&lt;-</span> <span class='kw'>gmkin</span><span class='kw'>:::</span><span class='fu'>get_current_session</span>(<span class='no'>g</span>)
-      <span class='no'>session</span>$<span class='no'>p.df</span>
-      <span class='no'>session</span>$<span class='no'>ds.df</span>
-      <span class='no'>session</span>$<span class='no'>ds.cur</span>
-      <span class='no'>session</span>$<span class='no'>m.cur</span>
-      <span class='no'>session</span>$<span class='no'>ws</span>
-
-})</div></pre>
+    <pre class="examples"><div class='input'>  </div><span class='co'># NOT RUN {</span>
+<span class='fu'>gmkin</span>()
+<span class='co'># }</span><div class='input'> # Start the gmkin GUI
+  </div><span class='co'># NOT RUN {</span>
+    <span class='no'>g</span> <span class='kw'>&lt;-</span> <span class='fu'>gmkin</span>()
+
+    <span class='co'># Only for debugging or other advanced usage:</span>
+    <span class='no'>session</span> <span class='kw'>&lt;-</span> <span class='kw pkg'>gmkin</span><span class='kw ns'>:::</span><span class='fu'>get_current_session</span>(<span class='no'>g</span>)
+    <span class='no'>session</span>$<span class='no'>p.df</span>
+    <span class='no'>session</span>$<span class='no'>ds.df</span>
+    <span class='no'>session</span>$<span class='no'>ds.cur</span>
+    <span class='no'>session</span>$<span class='no'>m.cur</span>
+    <span class='no'>session</span>$<span class='no'>ws</span>
+
+<span class='co'># }</span></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
@@ -144,7 +170,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/gmkinws.html b/docs/reference/gmkinws.html
index 28f6014..2c1f509 100644
--- a/docs/reference/gmkinws.html
+++ b/docs/reference/gmkinws.html
@@ -18,12 +18,19 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
+  
+  
+<meta property="og:title" content="A workspace class for gmkin — gmkinws" />
 
+<meta property="og:description" content="Datasets, models and fits are stored in lists." />
+<meta name="twitter:card" content="summary" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,10 +58,25 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Reference</a>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
 </li>
 <li>
-  <a href="../articles/index.html">Articles</a>
+  <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu">
+    <li>
+      <a href="../articles/gmkin_manual.html">Manual for gmkin</a>
+    </li>
+  </ul>
 </li>
 <li>
   <a href="../news/index.html">News</a>
@@ -118,7 +140,7 @@ by the names used in the models contained in field m</p></dd>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 6f21a01..3fd068b 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -18,12 +18,16 @@
 <!-- Font Awesome icons -->
 <link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
 
+<!-- clipboard.js -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
 <script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
-
+  
+  
+<meta property="og:title" content="Function reference" />
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -51,10 +55,25 @@
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
-  <a href="../reference/index.html">Reference</a>
+  <a href="../index.html">
+    <span class="fa fa-home fa-lg"></span>
+     
+  </a>
 </li>
 <li>
-  <a href="../articles/index.html">Articles</a>
+  <a href="../reference/index.html">Reference</a>
+</li>
+<li class="dropdown">
+  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
+    Articles
+     
+    <span class="caret"></span>
+  </a>
+  <ul class="dropdown-menu" role="menu">
+    <li>
+      <a href="../articles/gmkin_manual.html">Manual for gmkin</a>
+    </li>
+  </ul>
 </li>
 <li>
   <a href="../news/index.html">News</a>
@@ -145,7 +164,7 @@
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+  <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p>
 </div>
 
       </footer>