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authorJohannes Ranke <jranke@uni-bremen.de>2017-03-24 15:22:07 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2017-03-24 15:22:07 +0100
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+ <h1>Fit dose-response models</h1>
+ </div>
+
+
+ <p>Fit dose-response relationships to dose-response data and calculate
+ biometric results for (eco)toxicity evaluation</p>
+
+
+ <pre><span class='fu'>drfit</span>(<span class='no'>data</span>, <span class='kw'>startlogED50</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>chooseone</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>probit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>logit</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+ <span class='kw'>weibull</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>linlogit</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>level</span> <span class='kw'>=</span> <span class='fl'>0.95</span>, <span class='kw'>linlogitWrong</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
+ <span class='kw'>allWrong</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>ps0</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>ls0</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>ws0</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>b0</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>f0</span> <span class='kw'>=</span> <span class='fl'>0</span>,
+ <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+ <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>EDx.tolerance</span> <span class='kw'>=</span> <span class='fl'>1e-4</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>data</th>
+ <td><p>A data frame containing dose-response data. The data frame has to contain
+ at least a factor called &#8220;substance&#8221;, a numeric vector &#8220;dose&#8221;
+ with the dose values, a vector called &#8220;unit&#8221; containing the unit
+ used for the dose and a numeric vector &#8220;response&#8221; with the response
+ values of the test system normalized between 0 and 1. Such a data frame can
+ be easily obtained if a compliant RODBC data source is available for use in
+ conjunction with the function <code><a href='drdata.html'>drdata</a></code>.</p>
+<p>If there is a column called &#8220;ok&#8221; and it is set to &#8220;no fit&#8221; in
+ a specific line, then the corresponding data point will be excluded from
+ the fitting procedure, although it will be plotted.</p></td>
+ </tr>
+ <tr>
+ <th>startlogED50</th>
+ <td><p>Especially for the linlogit model, a suitable log10 of the ED50 has to be
+ given by the user, since it is not correctly estimated for data showing
+ hormesis with the default estimation method.</p></td>
+ </tr>
+ <tr>
+ <th>probit</th>
+ <td><p>A boolean defining if cumulative density curves of normal distributions
+ <code>pnorm</code> are fitted against the decadic logarithm of the dose.
+ Default ist TRUE.</p></td>
+ </tr>
+ <tr>
+ <th>logit</th>
+ <td><p>A boolean defining if cumulative density curves of logistic distributions
+ <code>plogis</code> are fitted to the decadic logarithm of the dose.
+ Default is FALSE.</p></td>
+ </tr>
+ <tr>
+ <th>weibull</th>
+ <td><p>A boolean defining if the cumulative density curves of weibull distributions
+ (<code>pweibull</code> with additionall location parameter and scale=1)
+ are fitted to the decadic logarithm of the dose. Default is FALSE.
+ Note that the weibull distribution is fitted here to the log transformed doses
+ which appears to be an uncommon approach.</p></td>
+ </tr>
+ <tr>
+ <th>linlogit</th>
+ <td><p>A boolean defining if the linear-logistic function
+ <code><a href='linlogitf.html'>linlogitf</a></code> as defined by van Ewijk and Hoekstra 1993 is
+ fitted to the data. Default is FALSE.</p></td>
+ </tr>
+ <tr>
+ <th>level</th>
+ <td><p>The level for the confidence interval listed for the log ED50.</p></td>
+ </tr>
+ <tr>
+ <th>linlogitWrong</th>
+ <td><p>An optional vector containing the names of the substances for which the
+ linlogit function produces a wrong fit.</p></td>
+ </tr>
+ <tr>
+ <th>allWrong</th>
+ <td><p>An optional vector containing the names of the substances for which all
+ functions produce a wrong fit.</p></td>
+ </tr>
+ <tr>
+ <th>chooseone</th>
+ <td><p>If TRUE (default), the models are tried in the order linlogit, probit,
+ logit, weibull, and the first model that produces a valid fit is used.
+ If FALSE, all models that are set to TRUE and that can be fitted will be
+ reported.</p></td>
+ </tr>
+ <tr>
+ <th>ps0</th>
+ <td><p>If the probit model is fitted, <code>ps0</code> gives the possibility to adjust
+ the starting value for the scale parameter of <code>pnorm</code>.</p></td>
+ </tr>
+ <tr>
+ <th>ls0</th>
+ <td><p>If the logit model is fitted, <code>ls0</code> gives the possibility to adjust
+ the starting value for the scale parameter of <code>plogis</code>.</p></td>
+ </tr>
+ <tr>
+ <th>ws0</th>
+ <td><p>If the weibull model is fitted, <code>ws0</code> gives the possibility to adjust
+ the starting value for the shape parameter of <code>pweibull</code>.</p></td>
+ </tr>
+ <tr>
+ <th>b0,f0</th>
+ <td><p>If the linearlogistic model is fitted, <code>b0</code> and <code>f0</code> give the
+ possibility to adjust the starting values for the parameters b and f.</p></td>
+ </tr>
+ <tr>
+ <th>showED50</th>
+ <td><p>If set to TRUE, the ED50 and its confidence interval on the original dose
+ scale (not log scale) is included in the output.</p></td>
+ </tr>
+ <tr>
+ <th>EDx</th>
+ <td><p>A vector of inhibition values x in percent for which the corresponding doses
+ EDx should be reported.</p></td>
+ </tr>
+ <tr>
+ <th>EDx.tolerance</th>
+ <td><p>Tolerance of the effect level, expressed on the response scale from 0 to 1.</p></td>
+ </tr>
+ </table>
+
+ <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+ <p>A dataframe with the attribute <code>models</code> holding a list of the fitted
+ dose-response models of class <code>nls</code>. The dataframe has at least
+ one line for each substance.</p>
+<p>For the &#8220;linlogit&#8221;, &#8220;logit&#8221; and &#8220;probit&#8221; models, the
+ parameter <code>a</code> that is reported coincides with the logED50, i.e the
+ logED50 is one of the model parameters that is being fitted. Therefore,
+ a confidence interval for the confidence level <code>level</code> is calculated
+ using the <code>confint.nls</code> function and listed.
+
+ The following variables are in the dataframe:</p>
+<dt>Substance</dt><dd><p>The name of the substance</p></dd>
+ <dt>ndl</dt><dd><p>The number of dose levels in the raw data</p></dd>
+ <dt>n</dt><dd><p>The total number of data points in the raw data used for the fit</p></dd>
+ <dt>lld</dt><dd><p>The decadic logarithm of the lowest dose</p></dd>
+ <dt>lhd</dt><dd><p>The total number of data points in the raw data used for the fit</p></dd>
+ <dt>mtype</dt><dd><p>If the data did not show a mean response &lt; 0.5 at the highest dose level,
+ the modeltype is set to &#8220;inactive&#8221;. If the mean response at the
+ lowest dose is smaller than 0.5, the modeltype is set to &#8220;active&#8221;.
+ In both cases, no fitting procedure is carried out. If the fitted ED50
+ is higher than the highest dose, &#8220;no fit&#8221; is given here.</p></dd>
+ <dt>logED50</dt><dd><p>The decadic logarithm of the ED50</p></dd>
+ <dt>low %</dt><dd><p>The lower bound of the confidence interval of log ED50.
+ The name of the column depends on the requested confidence <code>level</code>.</p></dd>
+ <dt>high %</dt><dd><p>The higher bound of the confidence interval of log ED50.
+ The name of the column depends on the requested confidence <code>level</code>.</p></dd>
+ <dt>unit</dt><dd><p>The unit used for the dose levels in the dose-response data</p></dd>
+ <dt>sigma</dt><dd><p>The square root of the estimated variance of the random error as returned
+ by <code>summary.nls</code>.</p></dd>
+ <dt>a</dt><dd><p>For the &#8220;linlogit&#8221;, &#8220;logit&#8221; and &#8220;probit&#8221; models, the
+ parameter <code>a</code> coincides with the logED50. In the case of the
+ &#8220;weibull&#8221; model, <code>a</code> is a location parameter.</p></dd>
+ <dt>b</dt><dd><p>Parameter <code>b</code> in the case of the &#8220;linlogit&#8221; fit is the variable
+ b from the <code>linlogitf</code> function. In the case of &#8220;probit&#8221;
+ fit it is the standard deviation of the fitted normal distribution, in the
+ case of the &#8220;logit&#8221; fit it is the <code>scale</code> parameter in the
+ <code>plogis</code> function, and in the &#8220;weibull&#8221; fit it is the
+ <code>shape</code> parameter of the fitted <code>pweibull</code> function.</p></dd>
+ <dt>c</dt><dd><p>Only the &#8220;linlogit&#8221; fit produces a third parameter <code>c</code> which is
+ the variable f from the <code>linlogitf</code> function.</p></dd>
+ If the parameter showED50 was set to TRUE, the ED50 values and their
+ confidence intervals are also included on the original dose scale.
+
+ If one or more response leves were specified in the argument EDx,
+ the corresponding dose levels are given in addition.
+
+
+ <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="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+ <p>Further examples are given in help pages to the datasets
+ <code><a href='antifoul.html'>antifoul</a></code>, <code><a href='IM1xIPC81.html'>IM1xIPC81</a></code> and
+ <code><a href='IM1xVibrio.html'>IM1xVibrio</a></code>.
+ Since version 0.6.1 of this package, there is a drop-in replacement function
+ <code><a href='drcfit.html'>drcfit</a></code> which internally uses the drc package and also gives
+ confidence intervals for EDx values via this package.</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'>drfit</span>(<span class='no'>antifoul</span>, <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>5</span>, <span class='fl'>10</span>, <span class='fl'>20</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='fu'>format</span>(<span class='no'>r</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>2</span>)</div><div class='output co'>#&gt; Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma a
+#&gt; 1 TBT 38 135 -2.7 2.4 probit -0.16 -0.27 -0.056 microM 0.19 -0.16
+#&gt; 2 Zn Pyrithion 27 81 -2.1 2.0 probit -0.40 -0.51 -0.292 microM 0.23 -0.40
+#&gt; b ED50 ED50 2.5% ED50 97.5% EDx5 EDx10 EDx20
+#&gt; 1 0.68 0.68 0.54 0.88 0.053 0.093 0.18
+#&gt; 2 0.42 0.40 0.31 0.51 0.082 0.117 0.18</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="#see-also">See also</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>
+
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