Static documentation rebuilt by pkgdown

author: Johannes Ranke <jranke@uni-bremen.de> 2017-10-13 09:34:15 +0200
committer: Johannes Ranke <jranke@uni-bremen.de> 2017-10-13 09:34:15 +0200
commit: 28425283bdeb34fac01d1eeb9c8dd40f987934ea (patch)
tree: ddabdcd7a60d9ee7f6a34f604ee4cb38d7ed6dc7 /docs/reference
parent: e3fa7ea27ccdf98e751642dea7315ce6076ad004 (diff)
6 files changed, 127 insertions, 106 deletions
diff --git a/docs/reference/FOCUS_2006.html b/docs/reference/FOCUS_2006.html
index cc367ce..2c9d327 100644
--- a/docs/reference/FOCUS_2006.html
+++ b/docs/reference/FOCUS_2006.html
@@ -6,8 +6,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-<title>
- — FOCUS_2006 • gmkin</title>
+<title>Example gmkin workspace for Datasets C and D from the FOCUS Kinetics report — FOCUS_2006 • gmkin</title>
 
 <!-- jquery -->
 <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -26,12 +25,14 @@
 <script src="../pkgdown.js"></script>
 
 <!-- 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>
@@ -73,8 +74,7 @@
       <div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
-    <h1>
-</h1>
+    <h1>Example gmkin workspace for Datasets C and D from the FOCUS Kinetics report</h1>
     </div>
 
     
@@ -83,7 +83,7 @@
   default.</p>
     
 
-    <pre><span class='no'>FOCUS_2006</span></pre>
+    <pre class="usage"><span class='no'>FOCUS_2006</span></pre>
         
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
@@ -100,12 +100,12 @@
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'>  <span class='co'>## Not run: ------------------------------------</span>
-<span class='co'>#   save(FOCUS_2006, file = "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>
-<span class='co'>#   </span>
-<span class='co'>## ---------------------------------------------</span></div></pre>
+    <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>
+
+})</div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
diff --git a/docs/reference/FOCUS_2006_Z.html b/docs/reference/FOCUS_2006_Z.html
index e7ed542..dff1b0e 100644
--- a/docs/reference/FOCUS_2006_Z.html
+++ b/docs/reference/FOCUS_2006_Z.html
@@ -6,8 +6,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-<title>
- — FOCUS_2006_Z • gmkin</title>
+<title>Example gmkin workspace for Dataset Z from the FOCUS Kinetics report — FOCUS_2006_Z • gmkin</title>
 
 <!-- jquery -->
 <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -26,12 +25,14 @@
 <script src="../pkgdown.js"></script>
 
 <!-- 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>
@@ -73,15 +74,14 @@
       <div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
-    <h1>
-</h1>
+    <h1>Example gmkin workspace for Dataset Z from the FOCUS Kinetics report</h1>
     </div>
 
     
     <p>Data taken from FOCUS (2006), Appendix 7, p. 350.</p>
     
 
-    <pre><span class='no'>FOCUS_2006_Z</span></pre>
+    <pre class="usage"><span class='no'>FOCUS_2006_Z</span></pre>
         
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
@@ -98,11 +98,11 @@
     
 
     <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
-    <pre class="examples"><div class='input'>  <span class='co'>## Not run: ------------------------------------</span>
-<span class='co'>#   save(FOCUS_2006_Z, file = "FOCUS_2006_Z.RData")</span>
-<span class='co'>#   # Now you can load the file "FOCUS_2006_Z.RData" from gmkin</span>
-<span class='co'>#   </span>
-<span class='co'>## ---------------------------------------------</span></div></pre>
+    <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>
+
+})</div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
diff --git a/docs/reference/UBA_model_gallery.html b/docs/reference/UBA_model_gallery.html
index 4c7f639..74fc20b 100644
--- a/docs/reference/UBA_model_gallery.html
+++ b/docs/reference/UBA_model_gallery.html
@@ -6,8 +6,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-<title>
- — UBA_model_gallery • gmkin</title>
+<title>A collection of some standard kinetic models — UBA_model_gallery • gmkin</title>
 
 <!-- jquery -->
 <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -26,12 +25,14 @@
 <script src="../pkgdown.js"></script>
 
 <!-- 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>
@@ -73,8 +74,7 @@
       <div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
-    <h1>
-</h1>
+    <h1>A collection of some standard kinetic models</h1>
     </div>
 
     
@@ -86,7 +86,7 @@
   kinetic sorption model.</p>
     
 
-    <pre><span class='fu'>data</span>(<span class='st'>"UBA_model_gallery"</span>)</pre>
+    <pre class="usage"><span class='fu'>data</span>(<span class='st'>"UBA_model_gallery"</span>)</pre>
         
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
@@ -97,7 +97,7 @@
     <p>Klein M (2010) Calculation of rates constants according to FOCUS degradation
   kinetics using DegKinManager and ModelMaker. Project report of UBA project
   FKZ 360 03 048</p>
-    <p>Jene B (1998) PELMO 3.00 Manual extension, Staatliche Lehr- und
+<p>Jene B (1998) PELMO 3.00 Manual extension, Staatliche Lehr- und
   Forschungsanstalt für Landwirtschaft, Weinbau und Gartenbau, D-67435
   Neustadt/Wstr.</p>
     
diff --git a/docs/reference/gmkin.html b/docs/reference/gmkin.html
index d65deb2..961372e 100644
--- a/docs/reference/gmkin.html
+++ b/docs/reference/gmkin.html
@@ -6,8 +6,7 @@
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-<title>
- — gmkin • gmkin</title>
+<title>Start a graphical user interface (GUI) based on the <code>gWidgetsWWW2</code> toolkit. — gmkin • gmkin</title>
 
 <!-- jquery -->
 <script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
@@ -26,12 +25,14 @@
 <script src="../pkgdown.js"></script>
 
 <!-- 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>
@@ -73,31 +74,31 @@
       <div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
-    <h1>
-</h1>
+    <h1>Start a graphical user interface (GUI) based on the <code>gWidgetsWWW2</code> toolkit.</h1>
     </div>
 
     
     <p>This function starts a browser based GUI. Please visit the 
-  <a href = 'github page of gWidgetsWWW2'>http://github.com/jverzani/gWidgetsWWW2</a> 
+  <a href = 'http://github.com/jverzani/gWidgetsWWW2'>github page of gWidgetsWWW2</a> 
   for an explanation how this toolkit works.</p>
     
 
-    <pre><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>
+    <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>
-    <dl class="dl-horizontal">
-      <dt>script_name</dt>
-      <dd>
-    During development, a script name with a local working version
+    <table class="ref-arguments">
+    <colgroup><col class="name" /><col class="desc" /></colgroup>
+    <tr>
+      <th>script_name</th>
+      <td><p>During development, a script name with a local working version
     of gmkin can be passed. Defaults to the location of the gmkin.R script
-    shipped with the package.
-  </dd>
-      <dt>show.log</dt>
-      <dd>
-    During development, it may be useful to see the log of the Rook apps.
-  </dd>
-    </dl>
+    shipped with the package.</p></td>
+    </tr>
+    <tr>
+      <th>show.log</th>
+      <td><p>During development, it may be useful to see the log of the Rook apps.</p></td>
+    </tr>
+    </table>
     
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
 
@@ -107,18 +108,18 @@
 
     <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='co'>## Not run: ------------------------------------</span>
-<span class='co'>#     g &lt;- gmkin()</span>
-<span class='co'># </span>
-<span class='co'>#     # Only for debugging or other advanced usage:</span>
-<span class='co'>#     session &lt;- gmkin:::get_current_session(g)</span>
-<span class='co'>#     session$p.df</span>
-<span class='co'>#     session$ds.df</span>
-<span class='co'>#     session$ds.cur</span>
-<span class='co'>#     session$m.cur</span>
-<span class='co'>#     session$ws</span>
-<span class='co'>#   </span>
-<span class='co'>## --------------------------------------------- </span></div></pre>
+  <span class='fu'>not_run</span>({
+      <span class='no'>g</span> <span class='kw'>&lt;-</span> <span class='fu'>gmkin</span>()
+
+      <span class='co'># Only for debugging or other advanced usage:</span>
+      <span class='no'>session</span> <span class='kw'>&lt;-</span> <span class='kw'>gmkin</span><span class='kw'>:::</span><span class='fu'>get_current_session</span>(<span class='no'>g</span>)
+      <span class='no'>session</span>$<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>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
     <h2>Contents</h2>
diff --git a/docs/reference/gmkinws.html b/docs/reference/gmkinws.html
index b276453..28f6014 100644
--- a/docs/reference/gmkinws.html
+++ b/docs/reference/gmkinws.html
@@ -25,12 +25,14 @@
 <script src="../pkgdown.js"></script>
 
 <!-- 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>
@@ -79,7 +81,7 @@
     <p>Datasets, models and fits are stored in lists.</p>
     
 
-    <pre><span class='no'>gmkinws</span></pre>
+    <pre class="usage"><span class='no'>gmkinws</span></pre>
         
     <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
 
@@ -87,14 +89,14 @@
     
     <h2 class="hasAnchor" id="fields"><a class="anchor" href="#fields"></a>Fields</h2>
 
-    <p></p>
-    <p><dl class='dl-horizontal'>
-<dt><code>observed</code></dt><dd>Names of the observed variables in the datasets, named
-by the names used in the models contained in field m</dd></p>
-    <p><dt><code>ds</code></dt><dd>A list of datasets compatible with mkinfit (long format)</dd></p>
-    <p><dt><code>m</code></dt><dd>A list of mkinmod models</dd></p>
-    <p><dt><code>f</code></dt><dd>A list of mkinfit objects</dd>
-</dl></p>
+    
+    <dl class='dl-horizontal'>
+<dt><code>observed</code></dt><dd><p>Names of the observed variables in the datasets, named
+by the names used in the models contained in field m</p></dd>
+    <dt><code>ds</code></dt><dd><p>A list of datasets compatible with mkinfit (long format)</p></dd>
+    <dt><code>m</code></dt><dd><p>A list of mkinmod models</p></dd>
+    <dt><code>f</code></dt><dd><p>A list of mkinfit objects</p></dd>
+</dl>
     
 
   </div>
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 2d2bce1..6f21a01 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -25,12 +25,14 @@
 <script src="../pkgdown.js"></script>
 
 <!-- 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>
@@ -72,44 +74,60 @@
       <div class="row">
   <div class="col-md-9">
     <div class="page-header">
-      <h1>Function reference</h1>
-      <h4>version&nbsp;0.6.8</h4>
+      <h1>
+        Reference
+        <small>version&nbsp;0.6.8</small>
+      </h1>
     </div>
 
     <div class="contents">
-      <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
-      <p class="section-desc"></p>
-
-      
-      <p><a href="FOCUS_2006_Z.html">
-</a></p>
-      <ul>
-        <li><code><a href="FOCUS_2006_Z.html">FOCUS_2006_Z</a></code></li>
-      </ul>
-      
-      <p><a href="FOCUS_2006.html">
-</a></p>
-      <ul>
-        <li><code><a href="FOCUS_2006.html">FOCUS_2006</a></code></li>
-      </ul>
-      
-      <p><a href="gmkin.html">
-</a></p>
-      <ul>
-        <li><code><a href="gmkin.html">gmkin</a></code></li>
-      </ul>
-      
-      <p><a href="gmkinws.html">A workspace class for gmkin</a></p>
-      <ul>
-        <li><code><a href="gmkinws.html">gmkinws</a></code></li>
-      </ul>
-      
-      <p><a href="UBA_model_gallery.html">
-</a></p>
-      <ul>
-        <li><code><a href="UBA_model_gallery.html">UBA_model_gallery</a></code></li>
-      </ul>
-    
+      <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>
   </div>
author	Johannes Ranke <jranke@uni-bremen.de>	2017-10-13 09:34:15 +0200
committer	Johannes Ranke <jranke@uni-bremen.de>	2017-10-13 09:34:15 +0200
commit	28425283bdeb34fac01d1eeb9c8dd40f987934ea (patch)
tree	ddabdcd7a60d9ee7f6a34f604ee4cb38d7ed6dc7 /docs/reference
parent	e3fa7ea27ccdf98e751642dea7315ce6076ad004 (diff)