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Diffstat (limited to 'docs/reference/drfit.html')
| -rw-r--r-- | docs/reference/drfit.html | 88 |
1 files changed, 44 insertions, 44 deletions
diff --git a/docs/reference/drfit.html b/docs/reference/drfit.html index 93c2dae..d707a5f 100644 --- a/docs/reference/drfit.html +++ b/docs/reference/drfit.html @@ -1,6 +1,6 @@ <!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html> +<html lang="en"> <head> <meta charset="utf-8"> <meta http-equiv="X-UA-Compatible" content="IE=edge"> @@ -8,21 +8,25 @@ <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> +<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" 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> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" /> + +<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" 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"> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" /> +<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" /> <!-- clipboard.js --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/1.7.1/clipboard.min.js" integrity="sha384-cV+rhyOuRHc9Ub/91rihWcGmMmCXDeksTtCihMupQHSsi8GIIRDG0ThDc3HGQFJ3" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script> -<!-- sticky kit --> -<script src="https://cdnjs.cloudflare.com/ajax/libs/sticky-kit/1.1.3/sticky-kit.min.js" integrity="sha256-c4Rlo1ZozqTPE2RLuvbusY3+SU1pQaJC0TjuhygMipw=" crossorigin="anonymous"></script> +<!-- headroom.js --> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script> <!-- pkgdown --> <link href="../pkgdown.css" rel="stylesheet"> @@ -30,16 +34,18 @@ -<meta property="og:title" content="Fit dose-response models — drfit" /> +<meta property="og:title" content="Fit dose-response models — drfit" /> <meta property="og:description" content="Fit dose-response relationships to dose-response data and calculate biometric results for (eco)toxicity evaluation" /> <meta name="twitter:card" content="summary" /> + <!-- mathjax --> -<script src='https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script> +<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script> <!--[if lt IE 9]> <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script> @@ -47,6 +53,7 @@ <![endif]--> + </head> <body> @@ -55,14 +62,15 @@ <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"> + <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false"> + <span class="sr-only">Toggle navigation</span> <span class="icon-bar"></span> <span class="icon-bar"></span> <span class="icon-bar"></span> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">drfit</a> - <span class="label label-default" data-toggle="tooltip" data-placement="bottom" title="Released package">0.7.2</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.3</span> </span> </div> @@ -70,7 +78,7 @@ <ul class="nav navbar-nav"> <li> <a href="../index.html"> - <span class="fa fa-home fa-lg"></span> + <span class="fas fa fas fa-home fa-lg"></span> </a> </li> @@ -78,7 +86,6 @@ <a href="../reference/index.html">Reference</a> </li> </ul> - <ul class="nav navbar-nav navbar-right"> </ul> @@ -88,6 +95,7 @@ </div><!--/.navbar --> + </header> <div class="row"> @@ -99,10 +107,8 @@ </div> <div class="ref-description"> - <p>Fit dose-response relationships to dose-response data and calculate biometric results for (eco)toxicity evaluation</p> - </div> <pre class="usage"><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>, @@ -110,7 +116,7 @@ <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> @@ -136,19 +142,19 @@ <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. + <code><a href='https://rdrr.io/r/stats/Normal.html'>pnorm</a></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. + <code><a href='https://rdrr.io/r/stats/Logistic.html'>plogis</a></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) + (<code><a href='https://rdrr.io/r/stats/Weibull.html'>pweibull</a></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> @@ -183,17 +189,17 @@ <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> + the starting value for the scale parameter of <code><a href='https://rdrr.io/r/stats/Normal.html'>pnorm</a></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> + the starting value for the scale parameter of <code><a href='https://rdrr.io/r/stats/Logistic.html'>plogis</a></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> + the starting value for the shape parameter of <code><a href='https://rdrr.io/r/stats/Weibull.html'>pweibull</a></code>.</p></td> </tr> <tr> <th>b0,f0</th> @@ -215,11 +221,11 @@ <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 + dose-response models of class <code><a href='https://rdrr.io/r/stats/nls.html'>nls</a></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 @@ -244,7 +250,7 @@ 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> + by <code><a href='https://rdrr.io/r/stats/summary.nls.html'>summary.nls</a></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> @@ -252,8 +258,8 @@ b from the <code><a href='linlogitf.html'>linlogitf</a></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> + <code><a href='https://rdrr.io/r/stats/Logistic.html'>plogis</a></code> function, and in the “weibull” fit it is the + <code>shape</code> parameter of the fitted <code><a href='https://rdrr.io/r/stats/Weibull.html'>pweibull</a></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><a href='linlogitf.html'>linlogitf</a></code> function.</p></dd> If the parameter showED50 was set to TRUE, the ED50 values and their @@ -262,12 +268,10 @@ 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> - + <code><a href='https://rdrr.io/r/utils/demo.html'>demo(dataset)</a></code></p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> <div class='dont-index'><p>Further examples are given in help pages to the datasets @@ -276,13 +280,12 @@ 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></div> - <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> + <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'>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'><a href='https://rdrr.io/r/base/c.html'>c</a></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 +#> <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'><a href='https://rdrr.io/r/base/format.html'>format</a></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 @@ -293,31 +296,26 @@ <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> - + <p>Johannes Ranke + <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a></p> </div> </div> + <footer> <div class="copyright"> <p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="http://pkgdown.r-lib.org/">pkgdown</a>.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> </div> </footer> @@ -325,6 +323,8 @@ + </body> </html> + |