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/drplot.html
parent: cd9d3e214233b0a6862200f60bf70a4214bc2115 (diff)
1 files changed, 268 insertions, 0 deletions
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+  <a href="../reference/index.html">Reference</a>
+</li>
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+      
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+      <div class="row">
+  <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'>&lt;-</span> <span class='fu'><a href='drfit.html'>drfit</a></span>(<span class='no'>antifoul</span>)</div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>TBT: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>Zn Pyrithion: Fitting data...</span></div><div class='output co'>#&gt; <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>
+
+      </footer>
+   </div>
+
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+</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/drplot.html
parent	cd9d3e214233b0a6862200f60bf70a4214bc2115 (diff)