Add pkgdown docu, change package build directory

author: Johannes Ranke <jranke@uni-bremen.de> 2017-03-24 15:22:07 +0100
committer: Johannes Ranke <jranke@uni-bremen.de> 2017-03-24 15:22:07 +0100
commit: ae13a2e7f373f697cdfb6acb7ae042d6e27d8967 (patch)
tree: 61bc66f752a81e9d50becf173d138ca9dfa80778 /docs/reference/checksubstance.html
parent: cd9d3e214233b0a6862200f60bf70a4214bc2115 (diff)
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+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
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+  <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+<title>Check raw data for a specified substance — checksubstance • drfit</title>
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+  </head>
+
+  <body>
+    <div class="container template-reference-topic">
+      <header>
+      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+  <div class="container">
+    <div class="navbar-header">
+      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+        <span class="icon-bar"></span>
+        <span class="icon-bar"></span>
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+    <div id="navbar" class="navbar-collapse collapse">
+      <ul class="nav navbar-nav">
+        <li>
+  <a href="../reference/index.html">Reference</a>
+</li>
+      </ul>
+      
+      <ul class="nav navbar-nav navbar-right">
+        
+      </ul>
+    </div><!--/.nav-collapse -->
+  </div><!--/.container -->
+</div><!--/.navbar -->
+
+      
+      </header>
+
+      <div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Check raw data for a specified substance</h1>
+    </div>
+
+    
+    <p>Report metadata for a specified substance from a specified database, and plot
+  the data.</p>
+    
+
+    <pre><span class='fu'>checksubstance</span>(<span class='no'>substance</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"cytotox"</span>, <span class='kw'>experimentator</span> <span class='kw'>=</span> <span class='st'>"%"</span>,
+    <span class='kw'>celltype</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>enzymetype</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>organism</span> <span class='kw'>=</span> <span class='st'>"%"</span>,
+    <span class='kw'>endpoint</span> <span class='kw'>=</span> <span class='st'>"%"</span>,
+    <span class='kw'>whereClause</span> <span class='kw'>=</span> <span class='st'>"1"</span>, <span class='kw'>ok</span> <span class='kw'>=</span> <span class='st'>"%"</span>)</pre>
+    
+    <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>
+      <th>substance</th>
+      <td><p>The name of the substance identifying it within the database.</p></td>
+    </tr>
+    <tr>
+      <th>db</th>
+      <td><p>The database to be used. Currently, the databases "cytotox" and "enzymes"
+    of the UFT Department of Bioorganic Chemistry are supported (default is
+    "cytotox").</p></td>
+    </tr>
+    <tr>
+      <th>experimentator</th>
+      <td><p>The name of the experimentator whose data is to be used. Default is "%",
+    which means that data from all experimentators are shown.</p></td>
+    </tr>
+    <tr>
+      <th>celltype</th>
+      <td><p>Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are
+    supported.  Default is "%", i.e. data for any cell type will be
+    displayed.</p></td>
+    </tr>
+    <tr>
+      <th>enzymetype</th>
+      <td><p>Currently, only data for AChE, GR and GST are supported. The default value
+    is "%", i.e. data for any enzyme type will be displayed.</p></td>
+    </tr>
+    <tr>
+      <th>organism</th>
+      <td><p>The latin name of the tested organism, if the ecotox db was selected. The
+    default value is "%", i.e. data for any organism will be displayed.</p></td>
+    </tr>
+    <tr>
+      <th>endpoint</th>
+      <td><p>The endpoint that should be used for selecting the data. Only important if
+    the database "ecotox" is used. Defaults to "%".</p></td>
+    </tr>
+    <tr>
+      <th>whereClause</th>
+      <td><p>With this argument, additional conditions for the SQL query can be set, 
+    e.g. "plate != 710". The default is 1 (in SQL syntax this means TRUE).</p></td>
+    </tr>
+    <tr>
+      <th>ok</th>
+      <td><p>With the default value "%", all data in the database is retrieved for the 
+    specified substance.</p></td>
+    </tr>
+    </table>
+    
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p>The function lists a report and shows one graph.</p>
+    
+
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><div class='input'><span class='co'># Check substance IM14 BF4 in the cytotox database</span>
+<span class='co'>## Not run: checksubstance("IM14 BF4")</span></div></pre>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+    <h2>Contents</h2>
+    <ul class="nav nav-pills nav-stacked">
+      <li><a href="#arguments">Arguments</a></li>
+      
+      <li><a href="#value">Value</a></li>
+      
+      <li><a href="#examples">Examples</a></li>
+    </ul>
+
+    <h2>Author</h2>
+    
+  Johannes Ranke 
+  <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> 
+  <a href = 'http://www.uft.uni-bremen.de/chemie/ranke'>http://www.uft.uni-bremen.de/chemie/ranke</a>
+
+  </div>
+</div>
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+      </footer>
+   </div>
+
+  </body>
+</html>
author	Johannes Ranke <jranke@uni-bremen.de>	2017-03-24 15:22:07 +0100
committer	Johannes Ranke <jranke@uni-bremen.de>	2017-03-24 15:22:07 +0100
commit	ae13a2e7f373f697cdfb6acb7ae042d6e27d8967 (patch)
tree	61bc66f752a81e9d50becf173d138ca9dfa80778 /docs/reference/checksubstance.html
parent	cd9d3e214233b0a6862200f60bf70a4214bc2115 (diff)