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- - - </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"> @@ -69,35 +17,21 @@ </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>Get dose-response data via RODBC</h1> @@ -109,75 +43,67 @@ <p>Get dose-response data from an adequate ODBC data source</p> </div> - <pre class="usage"><span class='fu'>drdata</span>(<span class='no'>substances</span>, <span class='kw'>experimentator</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"cytotox"</span>, - <span class='kw'>celltype</span> <span class='kw'>=</span> <span class='st'>"IPC-81"</span>, <span class='kw'>enzymetype</span> <span class='kw'>=</span> <span class='st'>"AChE"</span>, <span class='kw'>organism</span> <span class='kw'>=</span> <span class='st'>"Vibrio fischeri"</span>, - <span class='kw'>endpoint</span> <span class='kw'>=</span> <span class='st'>"Luminescence"</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'>"'ok','no fit'"</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>substances</th> - <td><p>A string or an array of strings with the substance names for - which dose-response data is to be retrieved. Matching is case-sensitive.</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 retrieved.</p></td> - </tr> - <tr> - <th>db</th> - <td><p>The database to be used. Currently, the databases "cytotox", "enzymes" + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">drdata</span><span class="op">(</span><span class="va">substances</span>, experimentator <span class="op">=</span> <span class="st">"%"</span>, db <span class="op">=</span> <span class="st">"cytotox"</span>, </span> +<span> celltype <span class="op">=</span> <span class="st">"IPC-81"</span>, enzymetype <span class="op">=</span> <span class="st">"AChE"</span>, organism <span class="op">=</span> <span class="st">"Vibrio fischeri"</span>,</span> +<span> endpoint <span class="op">=</span> <span class="st">"Luminescence"</span>,</span> +<span> whereClause <span class="op">=</span> <span class="st">"1"</span>, ok <span class="op">=</span> <span class="st">"'ok','no fit'"</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>substances</dt> +<dd><p>A string or an array of strings with the substance names for + which dose-response data is to be retrieved. Matching is case-sensitive.</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 retrieved.</p></dd> + + <dt>db</dt> +<dd><p>The database to be used. Currently, the databases "cytotox", "enzymes" and "ecotox" of the UFT Department of Bioorganic Chemistry are - supported (default is "cytotox").</p></td> - </tr> - <tr> - <th>celltype</th> - <td><p>Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are - supported.</p></td> - </tr> - <tr> - <th>enzymetype</th> - <td><p>Currently, only data for AChE, GR and GST are supported.</p></td> - </tr> - <tr> - <th>organism</th> - <td><p>The organism that was exposed to the chemical. Only important if the database - "ecotox" is used. Defaults to "Vibrio fischeri".</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 "Luminescence".</p></td> - </tr> - <tr> - <th>whereClause</th> - <td><p>With this argument, additional conditions for the SQL query can be set, + supported (default is "cytotox").</p></dd> + + <dt>celltype</dt> +<dd><p>Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are + supported.</p></dd> + + <dt>enzymetype</dt> +<dd><p>Currently, only data for AChE, GR and GST are supported.</p></dd> + + <dt>organism</dt> +<dd><p>The organism that was exposed to the chemical. Only important if the database + "ecotox" is used. Defaults to "Vibrio fischeri".</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 "Luminescence".</p></dd> + + <dt>whereClause</dt> +<dd><p>With this argument, additional conditions for the SQL query can be set, e.g. "plate != 710" (i.e. "Do not retrieve data for 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 "'ok','no fit'", only data that has been checked and + default is 1 (in SQL syntax this means TRUE).</p></dd> + + <dt>ok</dt> +<dd><p>With the default value "'ok','no fit'", only data that has been checked and set to "ok" or "no fit" in the database is retrieved. The argument "no fit" will result in not using the data for fitting, but it will be plotted. Another sensible argument would be "'ok','no fit','?'", in order to - additionally retrieve data which has not yet been checked.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + additionally retrieve data which has not yet been checked.</p></dd> - <p></p> -<dt>data</dt><dd><p>A data frame with a factor describing the dose levels, the numeric dose +</dl></div> + <div id="value"> + <h2>Value</h2> + <dl><dt>data</dt> +<dd><p>A data frame with a factor describing the dose levels, the numeric dose levels and a numeric column describing the response, as well as the entries for plate, experimentator, performed (date of test performance), celltype, unit (of the dose/concentration), and for the ok field in the database.</p></dd> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - +</dl></div> + <div id="details"> + <h2>Details</h2> <p>The function is currently only used for retrieving data from the mysql database "cytotox" of the UFT Department of Bioorganic Chemistry. Access to this database is limited to UFT staff. Additionally to the @@ -186,66 +112,45 @@ myODBC. Then, under Unix, you can use iodbc or unixodbc for setting up the respective data source with data source name (DSN) "cytotox". For my setting using unixodbc, I am using the file <code class="file">/etc/odbcinst.ini</code> - containing:</p><table class='table'> -<tr><td>[MySQL]</td><td></td><td></td></tr> -<tr><td>Description</td><td>=</td><td>MySQL driver for ODBC</td></tr> -<tr><td>Driver</td><td>=</td><td>/usr/local/lib/libmyodbc.so</td></tr> -<tr><td>Setup</td><td>=</td><td>/usr/lib/odbc/libodbcmyS.so</td></tr> -</table> -<p>and the file <code class="file">/etc/odbc.ini</code> containing:</p><table class='table'> -<tr><td>[cytotox]</td><td></td><td></td></tr> -<tr><td>Description</td><td>=</td><td>Cytotoxicity database of the department of bioorganic chemistry, UFT Bremen</td></tr> -<tr><td>Driver</td><td>=</td><td>MySQL</td></tr> -<tr><td>Trace</td><td>=</td><td>Yes</td></tr> -<tr><td>TraceFile</td><td>=</td><td>/tmp/odbc.log</td></tr> -<tr><td>Database</td><td>=</td><td>cytotox</td></tr> -<tr><td>Server</td><td>=</td><td>eckehaat</td></tr> -<tr><td>Port</td><td>=</td><td>3306</td></tr> -</table> - - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='kw'>if</span> (<span class='fl'>FALSE</span>) { - - <span class='co'># Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81</span> - <span class='co'># cells</span> - <span class='fu'>drdata</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"TBT"</span>, <span class='st'>"ZnPT2"</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="#details">Details</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - + containing:</p><table class="table table"><tr><td>[MySQL]</td><td></td><td></td></tr><tr><td>Description</td><td>=</td><td>MySQL driver for ODBC</td></tr><tr><td>Driver</td><td>=</td><td>/usr/local/lib/libmyodbc.so</td></tr><tr><td>Setup</td><td>=</td><td>/usr/lib/odbc/libodbcmyS.so</td></tr></table><p>and the file <code class="file">/etc/odbc.ini</code> containing:</p><table class="table table"><tr><td>[cytotox]</td><td></td><td></td></tr><tr><td>Description</td><td>=</td><td>Cytotoxicity database of the department of bioorganic chemistry, UFT Bremen</td></tr><tr><td>Driver</td><td>=</td><td>MySQL</td></tr><tr><td>Trace</td><td>=</td><td>Yes</td></tr><tr><td>TraceFile</td><td>=</td><td>/tmp/odbc.log</td></tr><tr><td>Database</td><td>=</td><td>cytotox</td></tr><tr><td>Server</td><td>=</td><td>eckehaat</td></tr><tr><td>Port</td><td>=</td><td>3306</td></tr></table></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="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81</span></span></span> +<span class="r-in"><span> <span class="co"># cells</span></span></span> +<span class="r-in"><span> <span class="fu">drdata</span><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">"TBT"</span>, <span class="st">"ZnPT2"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><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> |