From ae13a2e7f373f697cdfb6acb7ae042d6e27d8967 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Fri, 24 Mar 2017 15:22:07 +0100
Subject: Add pkgdown docu, change package build directory
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+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Plot dose-response models</h1>
+ </div>
+
+
+ <p>Produce graphics of dose-response data and dose-response relationships
+ either combined or separately, for one or more substances.</p>
+
+
+ <pre><span class='fu'>drplot</span>(<span class='no'>drresults</span>, <span class='no'>data</span>, <span class='no'>dtype</span>, <span class='no'>alpha</span>, <span class='no'>ctype</span>, <span class='no'>path</span>,
+ <span class='no'>fileprefix</span>, <span class='no'>overlay</span>, <span class='no'>xlim</span>, <span class='no'>ylim</span>, <span class='no'>xlab</span>, <span class='no'>ylab</span>, <span class='no'>axes</span>, <span class='no'>frame.plot</span>, <span class='no'>postscript</span>,
+ <span class='no'>pdf</span>, <span class='no'>png</span>, <span class='no'>bw</span>, <span class='no'>pointsize</span>, <span class='no'>colors</span>, <span class='no'>ltys</span>, <span class='no'>pchs</span>, <span class='no'>devoff</span>, <span class='no'>lpos</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>drresults</th>
+ <td><p>A data frame as returned from <code><a href='drfit.html'>drfit</a></code>.</p></td>
+ </tr>
+ <tr>
+ <th>data</th>
+ <td><p>A data frame as returned from <code><a href='drdata.html'>drdata</a></code>. The data frame has to
+ contain at least a factor called "substance", a vector called "unit"
+ containing the unit used for the dose, a column "response" with the
+ response values of the test system normalized between 0 and 1, a column
+ "dose" with the numeric dose values and a factor called "dosefactor"
+ containing the dose as a factor.</p></td>
+ </tr>
+ <tr>
+ <th>dtype</th>
+ <td><p>A string describing if the raw data should be plotted ("raw"), or an error
+ bar should be constructed from the standard deviations of the responses at
+ each dose level ("std", default value) or from the confidence intervals
+ ("conf"). If you don't want to see the data, set it to "none".</p></td>
+ </tr>
+ <tr>
+ <th>alpha</th>
+ <td><p>The confidence level, defaulting to 0.95, only used if dtype "conf" has been
+ chosen.</p></td>
+ </tr>
+ <tr>
+ <th>ctype</th>
+ <td><p>This argument decides if horizontal lines are drawn to show the scatter of
+ the control values (dose = 0), if there are more than three of them.
+ Defaults to "none", further allowed values are "std" and "conf" for
+ displaying the standard deviation of the controls or the confidence
+ interval for the mean of the controls.</p></td>
+ </tr>
+ <tr>
+ <th>path</th>
+ <td><p>The path where graphic files should be put if any are produced. Defaults
+ to "./" i.e. the current working directory of R.</p></td>
+ </tr>
+ <tr>
+ <th>fileprefix</th>
+ <td><p>A string which will form the beginning of each filename, if graphic files
+ are created. Defaults to "drplot".</p></td>
+ </tr>
+ <tr>
+ <th>overlay</th>
+ <td><p>If TRUE, all output will be put into one graph, otherwise a separate graph
+ will be created for each substance.</p></td>
+ </tr>
+ <tr>
+ <th>xlim</th>
+ <td><p>The plot limits (min,max) on the dose axis.</p></td>
+ </tr>
+ <tr>
+ <th>ylim</th>
+ <td><p>The plot limits (min,max) on the response axis.</p></td>
+ </tr>
+ <tr>
+ <th>xlab</th>
+ <td><p>The axis title for the x axis. Defaults to "Concentration in" <code>unit</code>.</p></td>
+ </tr>
+ <tr>
+ <th>ylab</th>
+ <td><p>The axis title for the y axis. Defaults to "Normalized response".</p></td>
+ </tr>
+ <tr>
+ <th>axes</th>
+ <td><p>Specifies if axes should be drawn. Default is TRUE, as in
+ <code>plot.default</code></p></td>
+ </tr>
+ <tr>
+ <th>frame.plot</th>
+ <td><p>Specifies if the plot should be framed. Default is TRUE, as in
+ <code>plot.default</code></p></td>
+ </tr>
+ <tr>
+ <th>postscript</th>
+ <td><p>If TRUE, (a) postscript graph(s) will be created. Otherwise, and if
+ the pdf and png arguments are also FALSE, graphics will be
+ displayed with a screen graphics device.</p></td>
+ </tr>
+ <tr>
+ <th>pdf</th>
+ <td><p>If TRUE, (a) pdf graph(s) will be created. Otherwise, and if
+ the postscript, and png arguments are also FALSE, graphics will be
+ displayed with a screen graphics device.</p></td>
+ </tr>
+ <tr>
+ <th>png</th>
+ <td><p>If TRUE, (a) png graph(s) will be created. Otherwise, and if the
+ postscript and pdf arguments are also FALSE, graphics will be displayed
+ with a screen graphics device.</p></td>
+ </tr>
+ <tr>
+ <th>bw</th>
+ <td><p>A boolean deciding if the plots will be black and white or not. Default
+ is TRUE.</p></td>
+ </tr>
+ <tr>
+ <th>pointsize</th>
+ <td><p>The pointsize used for pdf, png and postscript graphics.</p></td>
+ </tr>
+ <tr>
+ <th>colors</th>
+ <td><p>This is a vector of colors, defaulting to 1:8, used for plotting the data.</p></td>
+ </tr>
+ <tr>
+ <th>ltys</th>
+ <td><p>This is a vector of line types for the dose-response models, defaulting to 1:8.</p></td>
+ </tr>
+ <tr>
+ <th>pchs</th>
+ <td><p>This is a vector of character types for the data. The default uses built-in
+ characters 1:n with n being the number of substances for which data are plotted
+ for overlays, or always 1 when no overlay plot is generated.</p></td>
+ </tr>
+ <tr>
+ <th>lpos</th>
+ <td><p>An optional argument defaulting to "topright" specifying the position
+ of the legend by being passed to the legend function. See the help for the
+ legend function for all possiblities.</p></td>
+ </tr>
+ <tr>
+ <th>devoff</th>
+ <td><p>If set to FALSE, the device will not be closed after creation of an overlay
+ pdf, png or postscript graph, so texts and other elements can
+ be added.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p></p>
+<dt>results</dt><dd><p>You will get plots of data and/or the fitted dose-response curves, on the
+ screen and/or as postscript/pdf/png files, depending on the parameters.</p></dd>
+
+
+ <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
+
+ <p>There is a demo for each dataset that can be accessed by
+ <code>demo(dataset)</code></p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>antifoul</span>)
+<span class='no'>r</span> <span class='kw'><-</span> <span class='fu'><a href='drfit.html'>drfit</a></span>(<span class='no'>antifoul</span>)</div><div class='output co'>#> <span class='message'></span>
+#> <span class='message'>TBT: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'></span>
+#> <span class='message'>Zn Pyrithion: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='input'><span class='co'>## Not run: drplot(r,antifoul)</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="#note">Note</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>
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