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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 using the drc package</h1>
+ </div>
+
+
+ <p>Fit dose-response relationships to dose-response data and calculate
+ biometric results for (eco)toxicity evaluation using the drc package</p>
+
+
+ <pre><span class='fu'>drcfit</span>(<span class='no'>data</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'>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>)</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>probit</th>
+ <td><p>A boolean defining if cumulative density curves of normal distributions
+ are fitted against the decadic logarithm of the dose. Default ist TRUE.
+ Note that the parameter definitions used in the model are different to the
+ ones used in <code><a href='drfit.html'>drfit</a></code>. Parameter e from <code>LN.2</code> is listed
+ as a here, and parameter b from there is listed as b.</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.
+ Again the parameter definitions used in the model are different to the
+ ones used in <code><a href='drfit.html'>drfit</a></code>. Parameter e from <code>LL.2</code> is listed
+ as a here, and parameter b from LL.2 is listed as b.</p></td>
+ </tr>
+ <tr>
+ <th>weibull</th>
+ <td><p>A boolean defining if Weibull dose-response models
+ (<code>W1.2</code> are fitted to the untransformed dose. Default is FALSE.
+ Note that the results differ from the ones obtained with
+ <code><a href='drfit.html'>drfit</a></code>, due to a different model specification.</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. Obtaining the ED50 (and EDx values
+ in general) uses <code>ED</code> internally and does not always give a
+ result.</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>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>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>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>
+ </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>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.drc</code>.</p></dd>
+ <dt>a</dt><dd><p>For the linlogit model, this is the parameter e from <code>BC.4</code>.
+ For the probit and the logit model, this is the ED50. For the weibull
+ model, this is parameter e from <code>W1.2</code>. Note that the Weibull
+ model is fitted to the untransformed data.</p></dd>
+ <dt>b</dt><dd><p>For the linlogit, probit, logit and weibull models, these are the
+ parameters b from <code>BC.4</code>, <code>LN.2</code>,
+ <code>LL.2</code> and <code>W1.2</code>, respectively.
+ Note that the parameter definitions (and in the case of Weibull, the model
+ used) are different to the ones used in <code>drfit</code>.</p></dd>
+ <dt>c</dt><dd><p>Only the &#8220;linlogit&#8221; fit produces a third parameter <code>c</code>, which is
+ the parameter f from the <code>BC.4</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, together with their
+ confidence intervals as calculated by ED from the drc package.
+
+
+ <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>.</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'>drcfit</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='error'>Error in ED50["1:50", "Lower"]: Indizierung außerhalb der Grenzen</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; <span class='error'>Error in format(r, digits = 2): Objekt 'r' nicht gefunden</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="#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>
+ The functionality of the drc package used under the hood in this function
+ was written by Christian Ritz.
+
+ </div>
+</div>
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+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
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