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| author | Johannes Ranke <jranke@uni-bremen.de> | 2017-03-24 15:22:07 +0100 |
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| committer | Johannes Ranke <jranke@uni-bremen.de> | 2017-03-24 15:22:07 +0100 |
| commit | ae13a2e7f373f697cdfb6acb7ae042d6e27d8967 (patch) | |
| tree | 61bc66f752a81e9d50becf173d138ca9dfa80778 /docs/reference/drfit.html | |
| parent | cd9d3e214233b0a6862200f60bf70a4214bc2115 (diff) | |
Add pkgdown docu, change package build directory
Diffstat (limited to 'docs/reference/drfit.html')
| -rw-r--r-- | docs/reference/drfit.html | 300 |
1 files changed, 300 insertions, 0 deletions
diff --git a/docs/reference/drfit.html b/docs/reference/drfit.html new file mode 100644 index 0000000..7acce23 --- /dev/null +++ b/docs/reference/drfit.html @@ -0,0 +1,300 @@ +<!-- 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>Fit dose-response models — drfit • 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>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 “substance”, a numeric vector “dose” + with the dose values, a vector called “unit” containing the unit + used for the dose and a numeric vector “response” 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 “ok” and it is set to “no fit” 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 “linlogit”, “logit” and “probit” 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 < 0.5 at the highest dose level, + the modeltype is set to “inactive”. If the mean response at the + lowest dose is smaller than 0.5, the modeltype is set to “active”. + In both cases, no fitting procedure is carried out. If the fitted ED50 + is higher than the highest dose, “no fit” 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 “linlogit”, “logit” and “probit” models, the + parameter <code>a</code> coincides with the logED50. In the case of the + “weibull” model, <code>a</code> is a location parameter.</p></dd> + <dt>b</dt><dd><p>Parameter <code>b</code> in the case of the “linlogit” fit is the variable + b from the <code>linlogitf</code> function. In the case of “probit” + fit it is the standard deviation of the fitted normal distribution, in the + case of the “logit” fit it is the <code>scale</code> parameter in the + <code>plogis</code> function, and in the “weibull” fit it is the + <code>shape</code> parameter of the fitted <code>pweibull</code> function.</p></dd> + <dt>c</dt><dd><p>Only the “linlogit” 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'><-</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'>#> <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'>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'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma a +#> 1 TBT 38 135 -2.7 2.4 probit -0.16 -0.27 -0.056 microM 0.19 -0.16 +#> 2 Zn Pyrithion 27 81 -2.1 2.0 probit -0.40 -0.51 -0.292 microM 0.23 -0.40 +#> b ED50 ED50 2.5% ED50 97.5% EDx5 EDx10 EDx20 +#> 1 0.68 0.68 0.54 0.88 0.053 0.093 0.18 +#> 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> + + </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> |