Static documentation rebuilt by pkgdown

6 files changed, 191 insertions, 91 deletions

diff --git a/docs/reference/FOCUS_2006.html b/docs/reference/FOCUS_2006.html
index ca9b5ce..93153ad 100644
--- a/docs/reference/FOCUS_2006.html
+++ b/docs/reference/FOCUS_2006.html
@@ -21,18 +21,24 @@
 <!-- clipboard.js -->
 <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
-  
-  
+
+
+
 <meta property="og:title" content="Example gmkin workspace for Datasets C and D from the FOCUS Kinetics report — FOCUS_2006" />
 
 <meta property="og:description" content="An gmkinws object with data taken from FOCUS (2006), Appendix
   3. This is the the workspace that is loaded into gmkin by
   default." />
 <meta name="twitter:card" content="summary" />
+
+
+
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -55,8 +61,12 @@
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
-      <a class="navbar-brand" href="../index.html">gmkin</a>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">gmkin</a>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.6.8</span>
+      </span>
     </div>
+
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
@@ -81,13 +91,14 @@
   </ul>
 </li>
 <li>
-  <a href="../news/index.html">News</a>
+  <a href="../news/index.html">Changelog</a>
 </li>
       </ul>
       
       <ul class="nav navbar-nav navbar-right">
         
       </ul>
+      
     </div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
@@ -95,17 +106,21 @@
       
       </header>
 
-      <div class="row">
+<div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Example gmkin workspace for Datasets C and D from the FOCUS Kinetics report</h1>
+    
+    <div class="hidden name"><code>FOCUS_2006.Rd</code></div>
     </div>
 
+    <div class="ref-description">
     
     <p>An <code><a href='gmkinws.html'>gmkinws</a></code> object with data taken from FOCUS (2006), Appendix
   3. This is the the workspace that is loaded into <code><a href='gmkin.html'>gmkin</a></code> by
   default.</p>
     
+    </div>
 
     <pre class="usage"><span class='no'>FOCUS_2006</span></pre>
         
@@ -157,5 +172,8 @@
       </footer>
    </div>
 
+  
+
   </body>
 </html>
+
diff --git a/docs/reference/FOCUS_2006_Z.html b/docs/reference/FOCUS_2006_Z.html
index 4eff2a7..ee01417 100644
--- a/docs/reference/FOCUS_2006_Z.html
+++ b/docs/reference/FOCUS_2006_Z.html
@@ -21,16 +21,22 @@
 <!-- clipboard.js -->
 <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
-  
-  
+
+
+
 <meta property="og:title" content="Example gmkin workspace for Dataset Z from the FOCUS Kinetics report — FOCUS_2006_Z" />
 
 <meta property="og:description" content="Data taken from FOCUS (2006), Appendix 7, p. 350." />
 <meta name="twitter:card" content="summary" />
+
+
+
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -53,8 +59,12 @@
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
-      <a class="navbar-brand" href="../index.html">gmkin</a>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">gmkin</a>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.6.8</span>
+      </span>
     </div>
+
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
@@ -79,13 +89,14 @@
   </ul>
 </li>
 <li>
-  <a href="../news/index.html">News</a>
+  <a href="../news/index.html">Changelog</a>
 </li>
       </ul>
       
       <ul class="nav navbar-nav navbar-right">
         
       </ul>
+      
     </div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
@@ -93,15 +104,19 @@
       
       </header>
 
-      <div class="row">
+<div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Example gmkin workspace for Dataset Z from the FOCUS Kinetics report</h1>
+    
+    <div class="hidden name"><code>FOCUS_2006_Z.Rd</code></div>
     </div>
 
+    <div class="ref-description">
     
     <p>Data taken from FOCUS (2006), Appendix 7, p. 350.</p>
     
+    </div>
 
     <pre class="usage"><span class='no'>FOCUS_2006_Z</span></pre>
         
@@ -152,5 +167,8 @@
       </footer>
    </div>
 
+  
+
   </body>
 </html>
+
diff --git a/docs/reference/UBA_model_gallery.html b/docs/reference/UBA_model_gallery.html
index 4157743..00f84ae 100644
--- a/docs/reference/UBA_model_gallery.html
+++ b/docs/reference/UBA_model_gallery.html
@@ -21,12 +21,15 @@
 <!-- clipboard.js -->
 <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
-  
-  
+
+
+
 <meta property="og:title" content="A collection of some standard kinetic models — UBA_model_gallery" />
 
 <meta property="og:description" content="The UBA model gallery contains predefined kinetic models for some common use
@@ -36,6 +39,9 @@
   defined by Michael Klein (2010) for DegKinManager, with the exception of the
   kinetic sorption model." />
 <meta name="twitter:card" content="summary" />
+
+
+
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -58,8 +64,12 @@
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
-      <a class="navbar-brand" href="../index.html">gmkin</a>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">gmkin</a>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.6.8</span>
+      </span>
     </div>
+
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
@@ -84,13 +94,14 @@
   </ul>
 </li>
 <li>
-  <a href="../news/index.html">News</a>
+  <a href="../news/index.html">Changelog</a>
 </li>
       </ul>
       
       <ul class="nav navbar-nav navbar-right">
         
       </ul>
+      
     </div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
@@ -98,12 +109,15 @@
       
       </header>
 
-      <div class="row">
+<div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>A collection of some standard kinetic models</h1>
+    
+    <div class="hidden name"><code>UBA_model_gallery.Rd</code></div>
     </div>
 
+    <div class="ref-description">
     
     <p>The UBA model gallery contains predefined kinetic models for some common use
   cases, with metabolites named as in the commonly used PELMO degradation
@@ -112,6 +126,7 @@
   defined by Michael Klein (2010) for DegKinManager, with the exception of the
   kinetic sorption model.</p>
     
+    </div>
 
     <pre class="usage"><span class='fu'>data</span>(<span class='st'>"UBA_model_gallery"</span>)</pre>
         
@@ -158,5 +173,8 @@
       </footer>
    </div>
 
+  
+
   </body>
 </html>
+
diff --git a/docs/reference/gmkin.html b/docs/reference/gmkin.html
index 75548cb..70c2d07 100644
--- a/docs/reference/gmkin.html
+++ b/docs/reference/gmkin.html
@@ -21,18 +21,24 @@
 <!-- clipboard.js -->
 <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
-  
-  
+
+
+
 <meta property="og:title" content="Start a graphical user interface (GUI) based on the <code>gWidgetsWWW2</code> toolkit. — gmkin" />
 
 <meta property="og:description" content="This function starts a browser based GUI. Please visit the 
   github page of gWidgetsWWW2 
   for an explanation how this toolkit works." />
 <meta name="twitter:card" content="summary" />
+
+
+
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -55,8 +61,12 @@
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
-      <a class="navbar-brand" href="../index.html">gmkin</a>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">gmkin</a>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.6.8</span>
+      </span>
     </div>
+
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
@@ -81,13 +91,14 @@
   </ul>
 </li>
 <li>
-  <a href="../news/index.html">News</a>
+  <a href="../news/index.html">Changelog</a>
 </li>
       </ul>
       
       <ul class="nav navbar-nav navbar-right">
         
       </ul>
+      
     </div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
@@ -95,21 +106,25 @@
       
       </header>
 
-      <div class="row">
+<div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Start a graphical user interface (GUI) based on the <code>gWidgetsWWW2</code> toolkit.</h1>
+    
+    <div class="hidden name"><code>gmkin.Rd</code></div>
     </div>
 
+    <div class="ref-description">
     
     <p>This function starts a browser based GUI. Please visit the 
   <a href='http://github.com/jverzani/gWidgetsWWW2'>github page of gWidgetsWWW2</a> 
   for an explanation how this toolkit works.</p>
     
+    </div>
 
     <pre class="usage"><span class='fu'>gmkin</span>(<span class='no'>script_name</span>, <span class='kw'>show.log</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</pre>
     
-    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
@@ -176,5 +191,8 @@
       </footer>
    </div>
 
+  
+
   </body>
 </html>
+
diff --git a/docs/reference/gmkinws.html b/docs/reference/gmkinws.html
index 2c1f509..e0fee8b 100644
--- a/docs/reference/gmkinws.html
+++ b/docs/reference/gmkinws.html
@@ -21,16 +21,22 @@
 <!-- clipboard.js -->
 <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
-  
-  
+
+
+
 <meta property="og:title" content="A workspace class for gmkin — gmkinws" />
 
 <meta property="og:description" content="Datasets, models and fits are stored in lists." />
 <meta name="twitter:card" content="summary" />
+
+
+
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -53,8 +59,12 @@
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
-      <a class="navbar-brand" href="../index.html">gmkin</a>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">gmkin</a>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.6.8</span>
+      </span>
     </div>
+
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
@@ -79,13 +89,14 @@
   </ul>
 </li>
 <li>
-  <a href="../news/index.html">News</a>
+  <a href="../news/index.html">Changelog</a>
 </li>
       </ul>
       
       <ul class="nav navbar-nav navbar-right">
         
       </ul>
+      
     </div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
@@ -93,15 +104,19 @@
       
       </header>
 
-      <div class="row">
+<div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>A workspace class for gmkin</h1>
+    
+    <div class="hidden name"><code>gmkinws.Rd</code></div>
     </div>
 
+    <div class="ref-description">
     
     <p>Datasets, models and fits are stored in lists.</p>
     
+    </div>
 
     <pre class="usage"><span class='no'>gmkinws</span></pre>
         
@@ -146,5 +161,8 @@ by the names used in the models contained in field m</p></dd>
       </footer>
    </div>
 
+  
+
   </body>
 </html>
+
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 3fd068b..1b9bd74 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -21,13 +21,19 @@
 <!-- clipboard.js -->
 <script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script>
 
+<!-- sticky kit -->
+<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script>
+
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
-<script src="../jquery.sticky-kit.min.js"></script>
 <script src="../pkgdown.js"></script>
-  
-  
+
+
+
 <meta property="og:title" content="Function reference" />
+
+
+
 <!-- mathjax -->
 <script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
 
@@ -50,8 +56,12 @@
         <span class="icon-bar"></span>
         <span class="icon-bar"></span>
       </button>
-      <a class="navbar-brand" href="../index.html">gmkin</a>
+      <span class="navbar-brand">
+        <a class="navbar-link" href="../index.html">gmkin</a>
+        <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.6.8</span>
+      </span>
     </div>
+
     <div id="navbar" class="navbar-collapse collapse">
       <ul class="nav navbar-nav">
         <li>
@@ -76,13 +86,14 @@
   </ul>
 </li>
 <li>
-  <a href="../news/index.html">News</a>
+  <a href="../news/index.html">Changelog</a>
 </li>
       </ul>
       
       <ul class="nav navbar-nav navbar-right">
         
       </ul>
+      
     </div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
@@ -90,64 +101,60 @@
       
       </header>
 
-      <div class="row">
-  <div class="col-md-9">
+<div class="row">
+  <div class="contents col-md-9">
     <div class="page-header">
-      <h1>
-        Reference
-        <small>version&nbsp;0.6.8</small>
-      </h1>
+      <h1>Reference</h1>
     </div>
 
-    <div class="contents">
-      <table class="ref-index">
-
-      <colgroup>
-        <col class="alias" />
-        <col class="title" />
-      </colgroup>
-
-      <tbody>
-        <tr>
-          <th colspan="2">
-            <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-            <p class="section-desc"></p>
-          </th>
-        </tr>
-        <tr>
-          <!--  -->
-          <td>
-            <p><code><a href="FOCUS_2006_Z.html">FOCUS_2006_Z</a></code> </p>
-          </td>
-          <td><p>Example gmkin workspace for Dataset Z from the FOCUS Kinetics report</p></td>
-        </tr><tr>
-          <!--  -->
-          <td>
-            <p><code><a href="FOCUS_2006.html">FOCUS_2006</a></code> </p>
-          </td>
-          <td><p>Example gmkin workspace for Datasets C and D from the FOCUS Kinetics report</p></td>
-        </tr><tr>
-          <!--  -->
-          <td>
-            <p><code><a href="gmkin.html">gmkin</a></code> </p>
-          </td>
-          <td><p>Start a graphical user interface (GUI) based on the <code>gWidgetsWWW2</code> toolkit.</p></td>
-        </tr><tr>
-          <!--  -->
-          <td>
-            <p><code><a href="gmkinws.html">gmkinws</a></code> </p>
-          </td>
-          <td><p>A workspace class for gmkin</p></td>
-        </tr><tr>
-          <!--  -->
-          <td>
-            <p><code><a href="UBA_model_gallery.html">data</a></code> </p>
-          </td>
-          <td><p>A collection of some standard kinetic models</p></td>
-        </tr>
-      </tbody>
-      </table>
-    </div>
+    <table class="ref-index">
+
+    <colgroup>
+      
+      <col class="alias" />
+      <col class="title" />
+    </colgroup>
+
+    <tbody>
+      <tr>
+        <th colspan="2">
+          <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
+          <p class="section-desc"></p>
+        </th>
+      </tr>
+      <tr>
+        
+        <td>
+          <p><code><a href="FOCUS_2006.html">FOCUS_2006</a></code> </p>
+        </td>
+        <td><p>Example gmkin workspace for Datasets C and D from the FOCUS Kinetics report</p></td>
+      </tr><tr>
+        
+        <td>
+          <p><code><a href="FOCUS_2006_Z.html">FOCUS_2006_Z</a></code> </p>
+        </td>
+        <td><p>Example gmkin workspace for Dataset Z from the FOCUS Kinetics report</p></td>
+      </tr><tr>
+        
+        <td>
+          <p><code><a href="UBA_model_gallery.html">UBA_model_gallery</a></code> </p>
+        </td>
+        <td><p>A collection of some standard kinetic models</p></td>
+      </tr><tr>
+        
+        <td>
+          <p><code><a href="gmkin.html">gmkin()</a></code> </p>
+        </td>
+        <td><p>Start a graphical user interface (GUI) based on the <code>gWidgetsWWW2</code> toolkit.</p></td>
+      </tr><tr>
+        
+        <td>
+          <p><code><a href="gmkinws.html">gmkinws</a></code> </p>
+        </td>
+        <td><p>A workspace class for gmkin</p></td>
+      </tr>
+    </tbody>
+    </table>
   </div>
 
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
@@ -170,5 +177,8 @@
       </footer>
    </div>
 
+  
+
   </body>
 </html>
+