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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"> @@ -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>Plot dose-response models</h1> @@ -111,191 +45,172 @@ either combined or separately, for one or more substances.</p> </div> - <pre class="usage"><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 + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">drplot</span><span class="op">(</span><span class="va">drresults</span>, <span class="va">data</span>, <span class="va">dtype</span>, <span class="va">alpha</span>, <span class="va">ctype</span>, <span class="va">path</span>,</span> +<span> <span class="va">fileprefix</span>, <span class="va">overlay</span>, <span class="va">xlim</span>, <span class="va">ylim</span>, <span class="va">xlab</span>, <span class="va">ylab</span>, <span class="va">axes</span>, <span class="va">frame.plot</span>, <span class="va">postscript</span>,</span> +<span> <span class="va">pdf</span>, <span class="va">png</span>, <span class="va">bw</span>, <span class="va">pointsize</span>, <span class="va">colors</span>, <span class="va">ltys</span>, <span class="va">pchs</span>, <span class="va">devoff</span>, <span class="va">lpos</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>drresults</dt> +<dd><p>A data frame as returned from <code><a href="drfit.html">drfit</a></code>.</p></dd> + + <dt>data</dt> +<dd><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 + containing the dose as a factor.</p></dd> + + <dt>dtype</dt> +<dd><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 + ("conf"). If you don't want to see the data, set it to "none".</p></dd> + + <dt>alpha</dt> +<dd><p>The confidence level, defaulting to 0.95, only used if dtype "conf" has been + chosen.</p></dd> + + <dt>ctype</dt> +<dd><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><a href='https://rdrr.io/r/graphics/plot.default.html'>plot.default</a></code></p></td> - </tr> - <tr> - <th>frame.plot</th> - <td><p>Specifies if the plot should be framed. Default is TRUE, as in - <code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot.default</a></code></p></td> - </tr> - <tr> - <th>postscript</th> - <td><p>If TRUE, (a) postscript graph(s) will be created. Otherwise, and if + interval for the mean of the controls.</p></dd> + + <dt>path</dt> +<dd><p>The path where graphic files should be put if any are produced. Defaults + to "./" i.e. the current working directory of R.</p></dd> + + <dt>fileprefix</dt> +<dd><p>A string which will form the beginning of each filename, if graphic files + are created. Defaults to "drplot".</p></dd> + + <dt>overlay</dt> +<dd><p>If TRUE, all output will be put into one graph, otherwise a separate graph + will be created for each substance.</p></dd> + + <dt>xlim</dt> +<dd><p>The plot limits (min,max) on the dose axis.</p></dd> + + <dt>ylim</dt> +<dd><p>The plot limits (min,max) on the response axis.</p></dd> + + <dt>xlab</dt> +<dd><p>The axis title for the x axis. Defaults to "Concentration in" <code>unit</code>.</p></dd> + + <dt>ylab</dt> +<dd><p>The axis title for the y axis. Defaults to "Normalized response".</p></dd> + + <dt>axes</dt> +<dd><p>Specifies if axes should be drawn. Default is TRUE, as in + <code><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot.default</a></code></p></dd> + + <dt>frame.plot</dt> +<dd><p>Specifies if the plot should be framed. Default is TRUE, as in + <code><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot.default</a></code></p></dd> + + <dt>postscript</dt> +<dd><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 + displayed with a screen graphics device.</p></dd> + + <dt>pdf</dt> +<dd><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 + displayed with a screen graphics device.</p></dd> + + <dt>png</dt> +<dd><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 + with a screen graphics device.</p></dd> + + <dt>bw</dt> +<dd><p>A boolean deciding if the plots will be black and white or not. Default + is TRUE.</p></dd> + + <dt>pointsize</dt> +<dd><p>The pointsize used for pdf, png and postscript graphics.</p></dd> + + <dt>colors</dt> +<dd><p>This is a vector of colors, defaulting to 1:8, used for plotting the data.</p></dd> + + <dt>ltys</dt> +<dd><p>This is a vector of line types for the dose-response models, defaulting to 1:8.</p></dd> + + <dt>pchs</dt> +<dd><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 + for overlays, or always 1 when no overlay plot is generated.</p></dd> + + <dt>lpos</dt> +<dd><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> + legend function for all possiblities.</p></dd> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + <dt>devoff</dt> +<dd><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></dd> - <p></p> -<dt>results</dt><dd><p>You will get plots of data and/or the fitted dose-response curves, on the +</dl></div> + <div id="value"> + <h2>Value</h2> + <dl><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> - +</dl></div> + <div id="note"> + <h2>Note</h2> <p>There is a demo for each dataset that can be accessed by - <code><a href='https://rdrr.io/r/utils/demo.html'>demo(dataset)</a></code></p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></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='fu'>drplot</span>(<span class='no'>r</span>,<span class='no'>antifoul</span>)</div><div class='img'><img src='drplot-1.png' alt='' width='700' height='433' /></div><div class='img'><img src='drplot-2.png' alt='' width='700' height='433' /></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> - + <code>demo(dataset)</code></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="fu"><a href="https://rdrr.io/r/utils/data.html" class="external-link">data</a></span><span class="op">(</span><span class="va">antifoul</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">r</span> <span class="op"><-</span> <span class="fu"><a href="drfit.html">drfit</a></span><span class="op">(</span><span class="va">antifoul</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> TBT: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> Zn Pyrithion: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</span> +<span class="r-in"><span><span class="fu">drplot</span><span class="op">(</span><span class="va">r</span>,<span class="va">antifoul</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="drplot-1.png" alt="" width="700" height="433"></span> +<span class="r-plt img"><img src="drplot-2.png" alt="" width="700" height="433"></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> |