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diff --git a/docs/reference/drplot.html b/docs/reference/drplot.html new file mode 100644 index 0000000..eff1338 --- /dev/null +++ b/docs/reference/drplot.html @@ -0,0 +1,268 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html> + <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>Plot dose-response models — drplot • drfit</title> + +<!-- jquery --> +<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script> +<!-- Bootstrap --> + +<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> +<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script> + +<!-- Font Awesome icons --> +<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous"> + + +<!-- pkgdown --> +<link href="../pkgdown.css" rel="stylesheet"> +<script src="../jquery.sticky-kit.min.js"></script> +<script src="../pkgdown.js"></script> + +<!-- mathjax --> +<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></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> + + <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> + <span class="icon-bar"></span> + </button> + <a class="navbar-brand" href="../index.html">drfit</a> + </div> + <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>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> + + </footer> + </div> + + </body> +</html> |