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| author | Johannes Ranke <jranke@uni-bremen.de> | 2023-07-21 08:24:12 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2023-07-21 08:32:32 +0200 |
| commit | d04bac001217855b4e9a1490a35bef3325441b55 (patch) | |
| tree | 26bf1a06d038c796c2dbce21e5867088c555ee06 /docs/reference/drcfit.html | |
| parent | 0bc79f02e99d719be5dbb96ed1591d46c8373c9f (diff) | |
Maintenance prompted by email from CRAN
- Fix an improper use of 'packageVersion'
- Update .Rbuildignore
- Fix a link in the README
- Static documentation rebuilt by pkgdown::build_site()
Diffstat (limited to 'docs/reference/drcfit.html')
| -rw-r--r-- | docs/reference/drcfit.html | 369 |
1 files changed, 164 insertions, 205 deletions
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- - - </head> +<![endif]--></head><body data-spy="scroll" data-target="#toc"> + - <body> <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"> @@ -70,35 +18,21 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">drfit</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.7.3</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.7.4</span> </span> </div> <div id="navbar" class="navbar-collapse collapse"> - <ul class="nav navbar-nav"> - <li> - <a href="../index.html"> - <span class="fas fa fas fa-home fa-lg"></span> - - </a> -</li> -<li> + <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 --> + </ul><ul class="nav navbar-nav navbar-right"></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>Fit dose-response models using the drc package</h1> @@ -111,181 +45,206 @@ biometric results for (eco)toxicity evaluation using the drc package</p> </div> - <pre class="usage"><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 “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 + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">drcfit</span><span class="op">(</span><span class="va">data</span>, chooseone <span class="op">=</span> <span class="cn">TRUE</span>, probit <span class="op">=</span> <span class="cn">TRUE</span>, logit <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> weibull <span class="op">=</span> <span class="cn">FALSE</span>, linlogit <span class="op">=</span> <span class="cn">FALSE</span>, level <span class="op">=</span> <span class="fl">0.95</span>,</span> +<span> showED50 <span class="op">=</span> <span class="cn">FALSE</span>, EDx <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>data</dt> +<dd><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 + 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>probit</th> - <td><p>A boolean defining if cumulative density curves of normal distributions + the fitting procedure, although it will be plotted.</p></dd> + + <dt>probit</dt> +<dd><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><a href='https://rdrr.io/r/stats/Logistic.html'>plogis</a></code> are fitted to the decadic logarithm of the dose. + 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></dd> + + <dt>logit</dt> +<dd><p>A boolean defining if cumulative density curves of logistic distributions + <code><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">plogis</a></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 + 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></dd> + + <dt>weibull</dt> +<dd><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 + <code><a href="drfit.html">drfit</a></code>, due to a different model specification.</p></dd> + + <dt>linlogit</dt> +<dd><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, + result.</p></dd> + + <dt>level</dt> +<dd><p>The level for the confidence interval listed for the log ED50.</p></dd> + + <dt>chooseone</dt> +<dd><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><a href='https://rdrr.io/r/stats/nls.html'>nls</a></code>. The dataframe has at least + reported.</p></dd> + + <dt>EDx</dt> +<dd><p>A vector of inhibition values x in percent for which the corresponding doses + EDx should be reported.</p></dd> + + <dt>showED50</dt> +<dd><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></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>A dataframe with the attribute <code>models</code> holding a list of the fitted + dose-response models of class <code><a href="https://rdrr.io/r/stats/nls.html" class="external-link">nls</a></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 < 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”. +<dl><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. + 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. + + <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 + + <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>. + + <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 + + <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><a href='drfit.html'>drfit</a></code>.</p></dd> - <dt>c</dt><dd><p>Only the “linlogit” fit produces a third parameter <code>c</code>, which is + used) are different to the ones used in <code><a href="drfit.html">drfit</a></code>.</p></dd> + + <dt>c</dt> +<dd><p>Only the “linlogit” 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. +</dl><p>If the parameter <code>showED50</code> was set to TRUE, the ED50 values and their + confidence intervals are also included on the original dose scale.</p> - <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> +<p>If one or more response leves were specified in the argument <code>EDx</code>, + the corresponding dose levels are given in addition, together with their + confidence intervals as calculated by <code>ED</code> from the drc package.</p> + </div> + <div id="note"> + <h2>Note</h2> <p>There is a demo for each dataset that can be accessed by - <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 - <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></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='no'>antifoul</span>) -<span class='no'>r</span> <span class='kw'><-</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'><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'></span> -#> <span class='message'>Zn Pyrithion: Fitting data...</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 -0.28 -0.072 microM 0.19 0.68 -#> 2 Zn Pyrithion 27 81 -2.1 2.0 probit -0.40 -0.52 -0.303 microM 0.23 0.40 -#> b ED50 ED50 2.5% ED50 97.5% EDx5 EDx5 2.5% EDx5 97.5% EDx10 EDx10 2.5% -#> 1 -0.64 0.68 0.52 0.85 0.053 0.015 0.091 0.093 0.040 -#> 2 -1.04 0.40 0.30 0.50 0.082 0.023 0.142 0.117 0.048 -#> EDx10 97.5% EDx20 EDx20 2.5% EDx20 97.5% -#> 1 0.15 0.18 0.11 0.26 -#> 2 0.19 0.18 0.10 0.26</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> - + <code>demo(dataset)</code></p> + </div> + <div id="see-also"> + <h2>See also</h2> + <div class="dont-index"><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></div> + </div> + <div id="author"> <h2>Author</h2> - <p>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> The functionality of the drc package used under the hood in this function was written by Christian Ritz.</p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><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">antifoul</span><span class="op">)</span></span></span> +<span class="r-in"><span><span class="va">r</span> <span class="op"><-</span> <span class="fu">drcfit</span><span class="op">(</span><span class="va">antifoul</span>, showED50 <span class="op">=</span> <span class="cn">TRUE</span>, EDx <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="fl">5</span>, <span class="fl">10</span>, <span class="fl">20</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> TBT: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> Zn Pyrithion: Fitting data...</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/format.html" class="external-link">format</a></span><span class="op">(</span><span class="va">r</span>, digits <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span></span> +<span class="r-out co"><span class="r-pr">#></span> Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma a</span> +<span class="r-out co"><span class="r-pr">#></span> 1 TBT 38 135 -2.7 2.4 probit -0.16 -0.28 -0.072 microM 0.19 0.68</span> +<span class="r-out co"><span class="r-pr">#></span> 2 Zn Pyrithion 27 81 -2.1 2.0 probit -0.40 -0.52 -0.303 microM 0.23 0.40</span> +<span class="r-out co"><span class="r-pr">#></span> b ED50 ED50 2.5% ED50 97.5% EDx5 EDx5 2.5% EDx5 97.5% EDx10 EDx10 2.5%</span> +<span class="r-out co"><span class="r-pr">#></span> 1 -0.64 0.68 0.52 0.85 0.053 0.015 0.091 0.093 0.040</span> +<span class="r-out co"><span class="r-pr">#></span> 2 -1.04 0.40 0.30 0.50 0.082 0.023 0.142 0.117 0.048</span> +<span class="r-out co"><span class="r-pr">#></span> EDx10 97.5% EDx20 EDx20 2.5% EDx20 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> 1 0.15 0.18 0.11 0.26</span> +<span class="r-out co"><span class="r-pr">#></span> 2 0.19 0.18 0.10 0.26</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> </div> - 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