Maintenance prompted by email from CRAN

- Fix an improper use of 'packageVersion' - Update .Rbuildignore - Fix a link in the README - Static documentation rebuilt by pkgdown::build_site()
author: Johannes Ranke <jranke@uni-bremen.de> 2023-07-21 08:24:12 +0200
committer: Johannes Ranke <jranke@uni-bremen.de> 2023-07-21 08:32:32 +0200
commit: d04bac001217855b4e9a1490a35bef3325441b55 (patch)
tree: 26bf1a06d038c796c2dbce21e5867088c555ee06 /docs/reference/checksubstance.html
parent: 0bc79f02e99d719be5dbb96ed1591d46c8373c9f (diff)
1 files changed, 81 insertions, 156 deletions
diff --git a/docs/reference/checksubstance.html b/docs/reference/checksubstance.html
index 39bcd4a..54c5be6 100644
--- a/docs/reference/checksubstance.html
+++ b/docs/reference/checksubstance.html
@@ -1,65 +1,13 @@
-<!-- Generated by pkgdown: do not edit by hand -->
 <!DOCTYPE html>
-<html lang="en">
-  <head>
-  <meta charset="utf-8">
-<meta http-equiv="X-UA-Compatible" content="IE=edge">
-<meta name="viewport" content="width=device-width, initial-scale=1.0">
-
-<title>Check raw data for a specified substance — checksubstance • drfit</title>
-
-
-<!-- jquery -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
-<!-- Bootstrap -->
-
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
-
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
-
-<!-- Font Awesome icons -->
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
-
-<!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
-
-<!-- headroom.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
-
-<!-- pkgdown -->
-<link href="../pkgdown.css" rel="stylesheet">
-<script src="../pkgdown.js"></script>
-
-
-
-
-<meta property="og:title" content="Check raw data for a specified substance — checksubstance" />
-<meta property="og:description" content="Report metadata for a specified substance from a specified database, and plot
-  the data." />
-<meta name="twitter:card" content="summary" />
-
-
-
-
-<!-- mathjax -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script>
-
-<!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Check raw data for a specified substance — checksubstance • drfit</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Check raw data for a specified substance — checksubstance"><meta property="og:description" content="Report metadata for a specified substance from a specified database, and plot
+  the data."><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></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>
+<![endif]--></head><body data-spy="scroll" data-target="#toc">
+    
 
-  <body>
     <div class="container template-reference-topic">
-      <header>
-      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+      <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" aria-expanded="false">
@@ -70,35 +18,21 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">drfit</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.3</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.7.4</span>
       </span>
     </div>
 
     <div id="navbar" class="navbar-collapse collapse">
-      <ul class="nav navbar-nav">
-        <li>
-  <a href="../index.html">
-    <span class="fas fa fas fa-home fa-lg"></span>
-     
-  </a>
-</li>
-<li>
+      <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 -->
+      </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse -->
   </div><!--/.container -->
 </div><!--/.navbar -->
 
       
 
-      </header>
-
-<div class="row">
+      </header><div class="row">
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Check raw data for a specified substance</h1>
@@ -111,104 +45,95 @@
   the data.</p>
     </div>
 
-    <pre class="usage"><span class='fu'>checksubstance</span>(<span class='no'>substance</span>,
-    <span class='kw'>db</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"cytotox"</span>, <span class='st'>"enzymes"</span>, <span class='st'>"ecotox"</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. Matching is not 
-    case-sensitive.</p></td>
-    </tr>
-    <tr>
-      <th>db</th>
-      <td><p>The database to be used. Currently, the databases "cytotox" and "enzymes"
+    <div id="ref-usage">
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">checksubstance</span><span class="op">(</span><span class="va">substance</span>, </span>
+<span>    db <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"cytotox"</span>, <span class="st">"enzymes"</span>, <span class="st">"ecotox"</span><span class="op">)</span>, </span>
+<span>    experimentator <span class="op">=</span> <span class="st">"%"</span>,</span>
+<span>    celltype <span class="op">=</span> <span class="st">"%"</span>, enzymetype <span class="op">=</span> <span class="st">"%"</span>, organism <span class="op">=</span> <span class="st">"%"</span>,</span>
+<span>    endpoint <span class="op">=</span> <span class="st">"%"</span>,</span>
+<span>    whereClause <span class="op">=</span> <span class="st">"1"</span>, ok <span class="op">=</span> <span class="st">"%"</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div id="arguments">
+    <h2>Arguments</h2>
+    <dl><dt>substance</dt>
+<dd><p>The name of the substance identifying it within the database. Matching is not 
+    case-sensitive.</p></dd>
+
+  <dt>db</dt>
+<dd><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
+    "cytotox").</p></dd>
+
+  <dt>experimentator</dt>
+<dd><p>The name of the experimentator whose data is to be used. Default is "%",
+    which means that data from all experimentators are shown.</p></dd>
+
+  <dt>celltype</dt>
+<dd><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='kw'>if</span> (<span class='fl'>FALSE</span>) <span class='fu'>checksubstance</span>(<span class='st'>"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>
+    displayed.</p></dd>
+
+  <dt>enzymetype</dt>
+<dd><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></dd>
+
+  <dt>organism</dt>
+<dd><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></dd>
 
+  <dt>endpoint</dt>
+<dd><p>The endpoint that should be used for selecting the data. Only important if
+    the database "ecotox" is used. Defaults to "%".</p></dd>
+
+  <dt>whereClause</dt>
+<dd><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></dd>
+
+  <dt>ok</dt>
+<dd><p>With the default value "%", all data in the database is retrieved for the
+    specified substance.</p></dd>
+
+</dl></div>
+    <div id="value">
+    <h2>Value</h2>
+    
+
+<p>The function lists a report and shows one graph.</p>
+    </div>
+    <div id="author">
     <h2>Author</h2>
     <p>Johannes Ranke
-  <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a></p>
+  <a href="mailto:jranke@uni-bremen.de">jranke@uni-bremen.de</a></p>
+    </div>
+
+    <div id="ref-examples">
+    <h2>Examples</h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Check substance IM14 BF4 in the cytotox database</span></span></span>
+<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="fu">checksubstance</span><span class="op">(</span><span class="st">"IM14 BF4"</span><span class="op">)</span></span></span>
+</code></pre></div>
+    </div>
   </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
+    </nav></div>
 </div>
 
 
-      <footer>
-      <div class="copyright">
-  <p>Developed by Johannes Ranke.</p>
+      <footer><div class="copyright">
+  <p></p><p>Developed by Johannes Ranke.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
-      </footer>
-   </div>
+      </footer></div>
 
   
 
 
-  </body>
-</html>
+  
 
+  </body></html>
author	Johannes Ranke <jranke@uni-bremen.de>	2023-07-21 08:24:12 +0200
committer	Johannes Ranke <jranke@uni-bremen.de>	2023-07-21 08:32:32 +0200
commit	d04bac001217855b4e9a1490a35bef3325441b55 (patch)
tree	26bf1a06d038c796c2dbce21e5867088c555ee06 /docs/reference/checksubstance.html
parent	0bc79f02e99d719be5dbb96ed1591d46c8373c9f (diff)