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- - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body data-spy="scroll" data-target="#toc"> <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"> @@ -73,19 +18,12 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">chemCal</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.2.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.2.3</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <ul class="nav navbar-nav"><li> <a href="../articles/chemCal.html">Get started</a> </li> <li> @@ -94,25 +32,19 @@ <li> <a href="../news/index.html">Changelog</a> </li> - </ul> - <ul class="nav navbar-nav navbar-right"> - <li> - <a href="https://github.com/jranke/chemCal/"> + </ul><ul class="nav navbar-nav navbar-right"><li> + <a href="https://github.com/jranke/chemCal/" class="external-link"> <span class="fab fa-github fa-lg"></span> </a> </li> - </ul> - - </div><!--/.nav-collapse --> + </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 calibration graphs from univariate linear models</h1> @@ -125,102 +57,88 @@ as confidence, and, for unweighted regression, prediction bands.</p> </div> - <pre class="usage"><span class='fu'>calplot</span><span class='op'>(</span><span class='va'>object</span>, xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"auto"</span>, <span class='st'>"auto"</span><span class='op'>)</span>, ylim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"auto"</span>, <span class='st'>"auto"</span><span class='op'>)</span>, - xlab <span class='op'>=</span> <span class='st'>"Concentration"</span>, ylab <span class='op'>=</span> <span class='st'>"Response"</span>, legend_x <span class='op'>=</span> <span class='st'>"auto"</span>, - alpha<span class='op'>=</span><span class='fl'>0.05</span>, varfunc <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</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>object</th> - <td><p>A univariate model object of class <code><a href='https://rdrr.io/r/stats/lm.html'>lm</a></code> or - <code><a href='https://rdrr.io/pkg/MASS/man/rlm.html'>rlm</a></code> - with model formula <code>y ~ x</code> or <code>y ~ x - 1</code>.</p></td> - </tr> - <tr> - <th>xlim</th> - <td><p>The limits of the plot on the x axis.</p></td> - </tr> - <tr> - <th>ylim</th> - <td><p>The limits of the plot on the y axis.</p></td> - </tr> - <tr> - <th>xlab</th> - <td><p>The label of the x axis.</p></td> - </tr> - <tr> - <th>ylab</th> - <td><p>The label of the y axis.</p></td> - </tr> - <tr> - <th>legend_x</th> - <td><p>An optional numeric value for adjusting the x coordinate of the legend.</p></td> - </tr> - <tr> - <th>alpha</th> - <td><p>The error tolerance level for the confidence and prediction bands. Note that this - includes both tails of the Gaussian distribution, unlike the alpha and beta parameters - used in <code><a href='lod.html'>lod</a></code> (see note below).</p></td> - </tr> - <tr> - <th>varfunc</th> - <td><p>The variance function for generating the weights in the model. - Currently, this argument is ignored (see note below).</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="fu">calplot</span><span class="op">(</span><span class="va">object</span>, xlim <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">"auto"</span>, <span class="st">"auto"</span><span class="op">)</span>, ylim <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">"auto"</span>, <span class="st">"auto"</span><span class="op">)</span>, + xlab <span class="op">=</span> <span class="st">"Concentration"</span>, ylab <span class="op">=</span> <span class="st">"Response"</span>, legend_x <span class="op">=</span> <span class="st">"auto"</span>, + alpha<span class="op">=</span><span class="fl">0.05</span>, varfunc <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></code></pre></div> + </div> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>object</dt> +<dd><p>A univariate model object of class <code><a href="https://rdrr.io/r/stats/lm.html" class="external-link">lm</a></code> or + <code><a href="https://rdrr.io/pkg/MASS/man/rlm.html" class="external-link">rlm</a></code> + with model formula <code>y ~ x</code> or <code>y ~ x - 1</code>.</p></dd> +<dt>xlim</dt> +<dd><p>The limits of the plot on the x axis.</p></dd> +<dt>ylim</dt> +<dd><p>The limits of the plot on the y axis.</p></dd> +<dt>xlab</dt> +<dd><p>The label of the x axis.</p></dd> +<dt>ylab</dt> +<dd><p>The label of the y axis.</p></dd> +<dt>legend_x</dt> +<dd><p>An optional numeric value for adjusting the x coordinate of the legend.</p></dd> +<dt>alpha</dt> +<dd><p>The error tolerance level for the confidence and prediction bands. Note that this + includes both tails of the Gaussian distribution, unlike the alpha and beta parameters + used in <code><a href="lod.html">lod</a></code> (see note below).</p></dd> +<dt>varfunc</dt> +<dd><p>The variance function for generating the weights in the model. + Currently, this argument is ignored (see note below).</p></dd> +</dl></div> + <div id="value"> + <h2>Value</h2> <p>A plot of the calibration data, of your fitted model as well as lines showing the confidence limits. Prediction limits are only shown for models from unweighted regression.</p> - <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> - + </div> + <div id="note"> + <h2>Note</h2> <p>Prediction bands for models from weighted linear regression require weights for the data, for which responses should be predicted. Prediction intervals using weights e.g. from a variance function are currently not supported by - the internally used function <code><a href='https://rdrr.io/r/stats/predict.lm.html'>predict.lm</a></code>, therefore, + the internally used function <code><a href="https://rdrr.io/r/stats/predict.lm.html" class="external-link">predict.lm</a></code>, therefore, <code>calplot</code> does not draw prediction bands for such models.</p> <p>It is possible to compare the <code>calplot</code> prediction bands with the - <code><a href='lod.html'>lod</a></code> values if the <code><a href='lod.html'>lod()</a></code> alpha and beta parameters are + <code><a href="lod.html">lod</a></code> values if the <code><a href="lod.html">lod()</a></code> alpha and beta parameters are half the value of the <code>calplot()</code> alpha parameter.</p> - <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> - + </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> - <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='op'>(</span><span class='va'>massart97ex3</span><span class='op'>)</span> -<span class='va'>m</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/lm.html'>lm</a></span><span class='op'>(</span><span class='va'>y</span> <span class='op'>~</span> <span class='va'>x</span>, data <span class='op'>=</span> <span class='va'>massart97ex3</span><span class='op'>)</span> -<span class='fu'>calplot</span><span class='op'>(</span><span class='va'>m</span><span class='op'>)</span> -</div><div class='img'><img src='calplot.lm-1.png' alt='' width='700' height='433' /></div></pre> + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><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">massart97ex3</span><span class="op">)</span></span> +<span class="r-in"><span class="va">m</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/stats/lm.html" class="external-link">lm</a></span><span class="op">(</span><span class="va">y</span> <span class="op">~</span> <span class="va">x</span>, data <span class="op">=</span> <span class="va">massart97ex3</span><span class="op">)</span></span> +<span class="r-in"><span class="fu">calplot</span><span class="op">(</span><span class="va">m</span><span class="op">)</span></span> +<span class="r-plt img"><img src="calplot.lm-1.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> + <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> 1.6.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> |