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| -rw-r--r-- | docs/reference/drplot.html | 369 | ||||
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| -rw-r--r-- | docs/reference/linlogitf.html | 177 | ||||
| -rw-r--r-- | docs/reference/pyrithione.html | 134 |
18 files changed, 1361 insertions, 2300 deletions
diff --git a/docs/reference/IM1xIPC81.html b/docs/reference/IM1xIPC81.html index bd9211c..2ae6a33 100644 --- a/docs/reference/IM1xIPC81.html +++ b/docs/reference/IM1xIPC81.html @@ -1,42 +1,5 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - <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>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells — IM1xIPC81 • drfit</title> - - -<!-- jquery --> -<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 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 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/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" 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"> -<script src="../pkgdown.js"></script> - - - - -<meta property="og:title" content="Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells — IM1xIPC81" /> -<meta property="og:description" content="This is the raw data documenting the influence of the alkyl +<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><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>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells — IM1xIPC81 • drfit</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells — IM1xIPC81"><meta property="og:description" content="This is the raw data documenting the influence of the alkyl chain length in 3 position on the toxicity to the promyelocytic leukemia rat cell line IPC-81. The substances are named according to the UFT naming scheme of these @@ -45,29 +8,14 @@ 1-methyl-3-butylimidazolium tetrafluoroborate and IM1-10 BF4 means 1-methyl-3-decylimidazolium tetrafluoroborate. This is a subset (only the BF4 anion) of the data - shown in Figure 3 in Ranke et al. (2004)." /> -<meta name="twitter:card" content="summary" /> - - - - -<!-- mathjax --> -<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]> + shown in Figure 3 in Ranke et al. (2004)."><!-- mathjax --><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> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </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"> @@ -78,35 +26,21 @@ </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>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells</h1> @@ -127,115 +61,142 @@ shown in Figure 3 in Ranke et al. (2004).</p> </div> - <pre class="usage"><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span>(<span class='no'>IM1xIPC81</span>)</pre> - - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><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">IM1xIPC81</span><span class="op">)</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> <p>A dataframe containing the data as required for the - <code><a href='drfit.html'>drfit</a></code> function. An additional column contains + <code><a href="drfit.html">drfit</a></code> function. An additional column contains the tested organism (name of the cell line).</p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - + </div> + <div id="source"> + <h2>Source</h2> <p>Ranke J, Mölter K, Stock F, Bottin-Weber U, Poczobutt J, Hoffmann J, Ondruschka B, Filser J, Jastorff B (2004) Biological effects of imidazolium ionic liquids with varying chain lenghts in acute Vibrio fischeri and WST-1 cell viability assays. Ecotoxicology and Environmental Safety 58(3) 396-404</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='no'>rIM1xIPC81</span> <span class='kw'><-</span> <span class='fu'><a href='drfit.html'>drfit</a></span>(<span class='no'>IM1xIPC81</span>, <span class='kw'>linlogit</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='fl'>10</span>)</div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM13 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM14 BF4: Fitting data...</span></div><div class='output co'>#> <span class='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM15 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM16 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM17 BF4: 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='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM18 BF4: 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='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM19 BF4: 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='warning'>Warning: NaNs wurden erzeugt</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM1-10 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'>Waiting for profiling to be done...</span></div><div class='input'> - <span class='no'>rIM1xIPC81.drc</span> <span class='kw'><-</span> <span class='fu'><a href='drcfit.html'>drcfit</a></span>(<span class='no'>IM1xIPC81</span>, <span class='kw'>linlogit</span> <span class='kw'>=</span> <span class='fl'>TRUE</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='fl'>10</span>)</div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM13 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM14 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM15 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM16 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM17 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM18 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM19 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM1-10 BF4: Fitting data...</span></div><div class='input'> - <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>rIM1xIPC81</span>,<span class='kw'>digits</span><span class='kw'>=</span><span class='fl'>4</span>)</div><div class='output co'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma -#> 1 IM13 BF4 9 81 0.5918 3.000 inactive NA NA NA microM NA -#> 2 IM14 BF4 20 216 -0.0103 3.176 no fit NA NA NA microM NA -#> 3 IM15 BF4 9 135 0.5918 3.000 inactive NA NA NA microM NA -#> 4 IM16 BF4 9 108 0.5918 3.000 inactive NA NA NA microM NA -#> 5 IM17 BF4 9 81 0.5918 3.000 linlogit 2.5786 2.506 2.6617 microM 0.2376 -#> 6 IM18 BF4 9 135 0.5918 3.000 linlogit 1.6806 1.623 1.7419 microM 0.2325 -#> 7 IM19 BF4 9 81 0.5918 3.000 linlogit 1.6496 1.598 1.7031 microM 0.1453 -#> 8 IM1-10 BF4 11 162 -0.0103 3.000 linlogit 0.7697 0.687 0.8544 microM 0.2988 -#> a b c ED50 ED50 2.5% ED50 97.5% EDx10 -#> 1 NA NA NA NA NA NA NA -#> 2 NA NA NA NA NA NA NA -#> 3 NA NA NA NA NA NA NA -#> 4 NA NA NA NA NA NA NA -#> 5 2.5786 2.300 0.01468 378.941 320.424 458.918 230.782 -#> 6 1.6806 2.237 0.05719 47.930 41.973 55.194 27.367 -#> 7 1.6496 1.977 0.10956 44.628 39.671 50.483 23.031 -#> 8 0.7697 1.936 0.45809 5.884 4.864 7.152 2.835</div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>rIM1xIPC81.drc</span>,<span class='kw'>digits</span><span class='kw'>=</span><span class='fl'>4</span>)</div><div class='output co'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma -#> 1 IM13 BF4 9 81 0.5918 3.000 inactive NA NA NA microM NA -#> 2 IM14 BF4 20 216 -0.0103 3.176 linlogit NA NA NA microM 0.1529 -#> 3 IM15 BF4 9 135 0.5918 3.000 inactive NA NA NA microM NA -#> 4 IM16 BF4 9 108 0.5918 3.000 inactive NA NA NA microM NA -#> 5 IM17 BF4 9 81 0.5918 3.000 linlogit 2.5786 2.4935 2.6497 microM 0.2376 -#> 6 IM18 BF4 9 135 0.5918 3.000 linlogit 1.6806 1.6168 1.7362 microM 0.2325 -#> 7 IM19 BF4 9 81 0.5918 3.000 linlogit 1.6496 1.5940 1.6990 microM 0.1453 -#> 8 IM1-10 BF4 11 162 -0.0103 3.000 linlogit 0.7697 0.6774 0.8458 microM 0.2988 -#> a b c ED50 ED50 2.5% ED50 97.5% EDx10 EDx10 2.5% -#> 1 NA NA NA NA NA NA NA NA -#> 2 5.390e+15 0.3148 -0.0001736 NA NA NA NA NA -#> 3 NA NA NA NA NA NA NA NA -#> 4 NA NA NA NA NA NA NA NA -#> 5 1.281e+02 2.3001 0.0146821 378.964 311.555 446.372 230.790 202.915 -#> 6 2.079e+01 2.2373 0.0571925 47.930 41.382 54.478 27.367 23.809 -#> 7 1.342e+01 1.9773 0.1094542 44.630 39.260 50.000 23.036 20.614 -#> 8 2.258e+00 1.9362 0.4580784 5.884 4.758 7.011 2.835 2.181 -#> EDx10 97.5% -#> 1 NA -#> 2 NA -#> 3 NA -#> 4 NA -#> 5 258.665 -#> 6 30.925 -#> 7 25.459 -#> 8 3.489</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="#format">Format</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="va">rIM1xIPC81</span> <span class="op"><-</span> <span class="fu"><a href="drfit.html">drfit</a></span><span class="op">(</span><span class="va">IM1xIPC81</span>, linlogit <span class="op">=</span> <span class="cn">TRUE</span>, showED50 <span class="op">=</span> <span class="cn">TRUE</span>, EDx <span class="op">=</span> <span class="fl">10</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> IM13 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> IM14 BF4: Fitting data...</span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NaNs produced</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> IM15 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> IM16 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> IM17 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NaNs produced</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> IM18 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NaNs produced</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> IM19 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</span> +<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>NaNs produced</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> IM1-10 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="va">rIM1xIPC81.drc</span> <span class="op"><-</span> <span class="fu"><a href="drcfit.html">drcfit</a></span><span class="op">(</span><span class="va">IM1xIPC81</span>, linlogit <span class="op">=</span> <span class="cn">TRUE</span>, showED50 <span class="op">=</span> <span class="cn">TRUE</span>, EDx <span class="op">=</span> <span class="fl">10</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> IM13 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> IM14 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> IM15 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> IM16 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> IM17 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> IM18 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> IM19 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> IM1-10 BF4: Fitting data...</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">rIM1xIPC81</span>,digits<span class="op">=</span><span class="fl">4</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</span> +<span class="r-out co"><span class="r-pr">#></span> 1 IM13 BF4 9 81 0.5918 3.000 inactive NA NA NA microM NA</span> +<span class="r-out co"><span class="r-pr">#></span> 2 IM14 BF4 20 216 -0.0103 3.176 no fit NA NA NA microM NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 IM15 BF4 9 135 0.5918 3.000 inactive NA NA NA microM NA</span> +<span class="r-out co"><span class="r-pr">#></span> 4 IM16 BF4 9 108 0.5918 3.000 inactive NA NA NA microM NA</span> +<span class="r-out co"><span class="r-pr">#></span> 5 IM17 BF4 9 81 0.5918 3.000 linlogit 2.5786 2.506 2.6617 microM 0.2376</span> +<span class="r-out co"><span class="r-pr">#></span> 6 IM18 BF4 9 135 0.5918 3.000 linlogit 1.6806 1.623 1.7419 microM 0.2325</span> +<span class="r-out co"><span class="r-pr">#></span> 7 IM19 BF4 9 81 0.5918 3.000 linlogit 1.6496 1.598 1.7031 microM 0.1453</span> +<span class="r-out co"><span class="r-pr">#></span> 8 IM1-10 BF4 11 162 -0.0103 3.000 linlogit 0.7697 0.687 0.8544 microM 0.2988</span> +<span class="r-out co"><span class="r-pr">#></span> a b c ED50 ED50 2.5% ED50 97.5% EDx10</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA NA NA NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 2 NA NA NA NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 NA NA NA NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 4 NA NA NA NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 5 2.5786 2.300 0.01468 378.941 320.424 458.918 230.782</span> +<span class="r-out co"><span class="r-pr">#></span> 6 1.6806 2.237 0.05719 47.930 41.973 55.194 27.367</span> +<span class="r-out co"><span class="r-pr">#></span> 7 1.6496 1.977 0.10956 44.628 39.671 50.483 23.031</span> +<span class="r-out co"><span class="r-pr">#></span> 8 0.7697 1.936 0.45809 5.884 4.864 7.152 2.835</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">rIM1xIPC81.drc</span>,digits<span class="op">=</span><span class="fl">4</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</span> +<span class="r-out co"><span class="r-pr">#></span> 1 IM13 BF4 9 81 0.5918 3.000 inactive NA NA NA microM NA</span> +<span class="r-out co"><span class="r-pr">#></span> 2 IM14 BF4 20 216 -0.0103 3.176 linlogit NA NA NA microM 0.1529</span> +<span class="r-out co"><span class="r-pr">#></span> 3 IM15 BF4 9 135 0.5918 3.000 inactive NA NA NA microM NA</span> +<span class="r-out co"><span class="r-pr">#></span> 4 IM16 BF4 9 108 0.5918 3.000 inactive NA NA NA microM NA</span> +<span class="r-out co"><span class="r-pr">#></span> 5 IM17 BF4 9 81 0.5918 3.000 linlogit 2.5786 2.4935 2.6497 microM 0.2376</span> +<span class="r-out co"><span class="r-pr">#></span> 6 IM18 BF4 9 135 0.5918 3.000 linlogit 1.6806 1.6168 1.7362 microM 0.2325</span> +<span class="r-out co"><span class="r-pr">#></span> 7 IM19 BF4 9 81 0.5918 3.000 linlogit 1.6496 1.5940 1.6990 microM 0.1453</span> +<span class="r-out co"><span class="r-pr">#></span> 8 IM1-10 BF4 11 162 -0.0103 3.000 linlogit 0.7697 0.6774 0.8458 microM 0.2988</span> +<span class="r-out co"><span class="r-pr">#></span> a b c ED50 ED50 2.5% ED50 97.5% EDx10 EDx10 2.5%</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA NA NA NA NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 2 5.390e+15 0.3148 -0.0001736 NA NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 NA NA NA NA NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 4 NA NA NA NA NA NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 5 1.281e+02 2.3001 0.0146821 378.964 311.555 446.372 230.790 202.915</span> +<span class="r-out co"><span class="r-pr">#></span> 6 2.079e+01 2.2373 0.0571925 47.930 41.382 54.478 27.367 23.809</span> +<span class="r-out co"><span class="r-pr">#></span> 7 1.342e+01 1.9773 0.1094542 44.630 39.260 50.000 23.036 20.614</span> +<span class="r-out co"><span class="r-pr">#></span> 8 2.258e+00 1.9362 0.4580784 5.884 4.758 7.011 2.835 2.181</span> +<span class="r-out co"><span class="r-pr">#></span> EDx10 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 2 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 3 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 4 NA</span> +<span class="r-out co"><span class="r-pr">#></span> 5 258.665</span> +<span class="r-out co"><span class="r-pr">#></span> 6 30.925</span> +<span class="r-out co"><span class="r-pr">#></span> 7 25.459</span> +<span class="r-out co"><span class="r-pr">#></span> 8 3.489</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> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + 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1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri — IM1xVibrio • drfit</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" 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property="og:title" content="Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri — IM1xVibrio"><meta property="og:description" content="This is the raw data documenting the influence of the alkyl chain length in 3 position on the toxicity to the marine luminescent bacteria V. fischeri. The substances are named according to the UFT naming scheme of these substances. IM13 BF4 means 1-methyl-3-propylimidazolium tetrafluoroborate, IM14 BF4 means 1-methyl-3-butylimidazolium tetrafluoroborate and - IM1-10 BF4 means 1-methyl-3-decylimidazolium tetrafluoroborate." /> -<meta name="twitter:card" content="summary" /> - - - - -<!-- mathjax --> -<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]> + IM1-10 BF4 means 1-methyl-3-decylimidazolium tetrafluoroborate."><!-- mathjax --><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> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </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"> @@ -75,35 +23,21 @@ </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>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri</h1> @@ -121,155 +55,190 @@ IM1-10 BF4 means 1-methyl-3-decylimidazolium tetrafluoroborate.</p> </div> - <pre class="usage"><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span>(<span class='no'>IM1xVibrio</span>)</pre> - - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><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">IM1xVibrio</span><span class="op">)</span></span></code></pre></div> + </div> - <p>A dataframe containing the data as required for the <code><a href='drfit.html'>drfit</a></code> + <div id="format"> + <h2>Format</h2> + <p>A dataframe containing the data as required for the <code><a href="drfit.html">drfit</a></code> function. Additional columns contain the species tested (luminescent bacteria Vibrio fischeri, <code>organism</code>), and a field specifying if the data is regarded valid (<code>ok</code>).</p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - + </div> + <div id="source"> + <h2>Source</h2> <p>Ranke J, Mölter K, Stock F, Bottin-Weber U, Poczobutt J, Hoffmann J, Ondruschka B, Filser J, Jastorff B (2004) Biological effects of imidazolium ionic liquids with varying chain lenghts in acute Vibrio fischeri and WST-1 cell viability assays. Ecotoxicology and Environmental Safety 58(3) 396-404</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='no'>rIM1xVibrio</span> <span class='kw'><-</span> <span class='fu'><a href='drfit.html'>drfit</a></span>(<span class='no'>IM1xVibrio</span>, <span class='kw'>logit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>chooseone</span> <span class='kw'>=</span> <span class='fl'>FALSE</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'>10</span>, <span class='fl'>20</span>))</div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM13 BF4: 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'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM14 BF4: 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'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM15 BF4: 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'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM16 BF4: 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'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM17 BF4: 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'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM18 BF4: 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'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM19 BF4: 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'>Waiting for profiling to be done...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM1-10 BF4: 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'>Waiting for profiling to be done...</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>rIM1xVibrio</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>4</span>)</div><div class='output co'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma -#> 1 IM13 BF4 13 22 -5.301 4.699 probit 3.9399 3.8636 4.0160 microM 0.06303 -#> 2 IM13 BF4 13 22 -5.301 4.699 logit 3.9461 3.8708 4.0211 microM 0.06188 -#> 3 IM14 BF4 12 57 -4.301 4.699 probit 3.5442 3.5030 3.5855 microM 0.05905 -#> 4 IM14 BF4 12 57 -4.301 4.699 logit 3.5465 3.5044 3.5885 microM 0.06030 -#> 5 IM15 BF4 7 20 -0.301 4.699 probit 3.1398 3.1136 3.1662 microM 0.02695 -#> 6 IM15 BF4 7 20 -0.301 4.699 logit 3.1387 3.1118 3.1659 microM 0.02723 -#> 7 IM16 BF4 13 30 -4.301 4.699 probit 3.1804 3.1436 3.2176 microM 0.04514 -#> 8 IM16 BF4 13 30 -4.301 4.699 logit 3.1814 3.1440 3.2190 microM 0.04553 -#> 9 IM17 BF4 10 20 -1.301 4.699 probit 2.4317 2.3681 2.4951 microM 0.04773 -#> 10 IM17 BF4 10 20 -1.301 4.699 logit 2.4353 2.3672 2.5026 microM 0.05050 -#> 11 IM18 BF4 10 17 -2.301 2.699 probit 1.4015 1.3147 1.4881 microM 0.05611 -#> 12 IM18 BF4 10 17 -2.301 2.699 logit 1.4051 1.3129 1.4966 microM 0.05898 -#> 13 IM19 BF4 13 22 -5.301 2.699 probit 0.7158 0.6704 0.7592 microM 0.02956 -#> 14 IM19 BF4 13 22 -5.301 2.699 logit 0.7172 0.6689 0.7635 microM 0.03210 -#> 15 IM1-10 BF4 11 20 -6.301 2.699 probit -0.1790 -0.2569 -0.1037 microM 0.04099 -#> 16 IM1-10 BF4 11 20 -6.301 2.699 logit -0.1831 -0.2620 -0.1055 microM 0.04192 -#> a b ED50 ED50 2.5% ED50 97.5% EDx10 EDx20 -#> 1 3.9399 0.5763 8707.8956 7305.0279 1.038e+04 1.590e+03 2850.222 -#> 2 3.9461 0.3426 8832.9407 7426.2282 1.050e+04 1.561e+03 2959.147 -#> 3 3.5442 0.6561 3501.1558 3184.3196 3.851e+03 5.051e+02 981.759 -#> 4 3.5465 0.3911 3519.5779 3194.6808 3.877e+03 4.867e+02 1010.014 -#> 5 3.1398 0.5527 1379.9037 1298.9533 1.466e+03 2.701e+02 472.823 -#> 6 3.1387 0.3347 1376.4086 1293.7152 1.465e+03 2.532e+02 472.911 -#> 7 3.1804 0.4882 1515.0421 1391.8150 1.650e+03 3.588e+02 588.292 -#> 8 3.1814 0.2957 1518.4650 1393.2665 1.656e+03 3.401e+02 590.840 -#> 9 2.4317 0.6387 270.2279 233.3814 3.127e+02 4.105e+01 78.382 -#> 10 2.4353 0.3810 272.4409 232.9287 3.182e+02 3.965e+01 80.754 -#> 11 1.4015 0.8009 25.2069 20.6383 3.077e+01 2.372e+00 5.340 -#> 12 1.4051 0.4816 25.4135 20.5545 3.138e+01 2.222e+00 5.463 -#> 13 0.7158 0.6969 5.1975 4.6814 5.744e+00 6.647e-01 1.347 -#> 14 0.7172 0.4132 5.2141 4.6652 5.801e+00 6.446e-01 1.394 -#> 15 -0.1790 0.8019 0.6622 0.5534 7.876e-01 6.212e-02 0.140 -#> 16 -0.1831 0.4816 0.6560 0.5470 7.843e-01 5.738e-02 0.141</div><div class='input'> - <span class='no'>rIM1xVibrio.drc</span> <span class='kw'><-</span> <span class='fu'><a href='drcfit.html'>drcfit</a></span>(<span class='no'>IM1xVibrio</span>, <span class='kw'>logit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>chooseone</span> <span class='kw'>=</span> <span class='fl'>FALSE</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'>10</span>, <span class='fl'>20</span>))</div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM13 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM14 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM15 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM16 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM17 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM18 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM19 BF4: Fitting data...</span></div><div class='output co'>#> <span class='message'></span> -#> <span class='message'>IM1-10 BF4: Fitting data...</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/base/print.html'>print</a></span>(<span class='no'>rIM1xVibrio.drc</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>4</span>)</div><div class='output co'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% unit sigma -#> 1 IM13 BF4 13 22 -5.301 4.699 probit 3.9399 3.8563 4.0100 microM 0.06303 -#> 2 IM13 BF4 13 22 -5.301 4.699 logit 3.9461 3.8637 4.0153 microM 0.06188 -#> 3 IM14 BF4 12 57 -4.301 4.699 probit 3.5442 3.5009 3.5836 microM 0.05905 -#> 4 IM14 BF4 12 57 -4.301 4.699 logit 3.5465 3.5023 3.5866 microM 0.06030 -#> 5 IM15 BF4 7 20 -0.301 4.699 probit 3.1398 3.1127 3.1654 microM 0.02695 -#> 6 IM15 BF4 7 20 -0.301 4.699 logit 3.1387 3.1109 3.1649 microM 0.02723 -#> 7 IM16 BF4 13 30 -4.301 4.699 probit 3.1804 3.1419 3.2158 microM 0.04514 -#> 8 IM16 BF4 13 30 -4.301 4.699 logit 3.1814 3.1424 3.2172 microM 0.04553 -#> 9 IM17 BF4 10 20 -1.301 4.699 probit 2.4317 2.3632 2.4909 microM 0.04773 -#> 10 IM17 BF4 10 20 -1.301 4.699 logit 2.4353 2.3618 2.4981 microM 0.05050 -#> 11 IM18 BF4 10 17 -2.301 2.699 probit 1.4015 1.3052 1.4803 microM 0.05611 -#> 12 IM18 BF4 10 17 -2.301 2.699 logit 1.4051 1.3023 1.4881 microM 0.05898 -#> 13 IM19 BF4 13 22 -5.301 2.699 probit 0.7158 0.6690 0.7580 microM 0.02956 -#> 14 IM19 BF4 13 22 -5.301 2.699 logit 0.7172 0.6672 0.7620 microM 0.03210 -#> 15 IM1-10 BF4 11 20 -6.301 2.699 probit -0.1790 -0.2628 -0.1088 microM 0.04099 -#> 16 IM1-10 BF4 11 20 -6.301 2.699 logit -0.1831 -0.2690 -0.1114 microM 0.04192 -#> a b ED50 ED50 2.5% ED50 97.5% EDx10 EDx10 2.5% -#> 1 8707.5571 -0.7536 8707.5571 7183.0127 1.023e+04 1.590e+03 968.72501 -#> 2 8832.8773 1.2676 8832.8773 7306.8669 1.036e+04 1.561e+03 925.39582 -#> 3 3501.1967 -0.6619 3501.1967 3168.9639 3.833e+03 5.051e+02 395.26341 -#> 4 3519.5773 1.1105 3519.5773 3179.2923 3.860e+03 4.866e+02 371.84710 -#> 5 1379.9019 -0.7858 1379.9019 1296.3162 1.463e+03 2.701e+02 233.25320 -#> 6 1376.4086 1.2976 1376.4086 1290.8397 1.462e+03 2.531e+02 215.79719 -#> 7 1515.0427 -0.8896 1515.0427 1386.3308 1.644e+03 3.588e+02 283.79434 -#> 8 1518.4644 1.4686 1518.4644 1387.9173 1.649e+03 3.401e+02 262.20564 -#> 9 270.2279 -0.6800 270.2279 230.7905 3.097e+02 4.105e+01 27.78507 -#> 10 272.4526 1.1401 272.4526 230.0588 3.148e+02 3.966e+01 25.34948 -#> 11 25.2059 -0.5423 25.2059 20.1927 3.022e+01 2.372e+00 1.29116 -#> 12 25.4145 0.9017 25.4145 20.0576 3.077e+01 2.223e+00 1.09707 -#> 13 5.1971 -0.6231 5.1971 4.6665 5.728e+00 6.646e-01 0.49235 -#> 14 5.2141 1.0511 5.2141 4.6477 5.781e+00 6.446e-01 0.46046 -#> 15 0.6622 -0.5416 0.6622 0.5460 7.783e-01 6.213e-02 0.03513 -#> 16 0.6560 0.9018 0.6560 0.5383 7.737e-01 5.738e-02 0.03163 -#> EDx10 97.5% EDx20 EDx20 2.5% EDx20 97.5% -#> 1 2.211e+03 2850.328 2.019e+03 3681.2703 -#> 2 2.196e+03 2958.988 2.092e+03 3826.1457 -#> 3 6.149e+02 981.743 8.254e+02 1138.0862 -#> 4 6.014e+02 1010.061 8.414e+02 1178.7611 -#> 5 3.070e+02 472.838 4.257e+02 520.0197 -#> 6 2.905e+02 472.906 4.239e+02 521.8955 -#> 7 4.337e+02 588.259 4.999e+02 676.6627 -#> 8 4.181e+02 590.824 4.972e+02 684.4677 -#> 9 5.431e+01 78.383 5.955e+01 97.2142 -#> 10 5.396e+01 80.763 5.975e+01 101.7713 -#> 11 3.454e+00 5.339 3.544e+00 7.1350 -#> 12 3.348e+00 5.463 3.489e+00 7.4370 -#> 13 8.369e-01 1.346 1.084e+00 1.6086 -#> 14 8.288e-01 1.394 1.106e+00 1.6832 -#> 15 8.912e-02 0.140 9.501e-02 0.1850 -#> 16 8.314e-02 0.141 9.588e-02 0.1862</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="#format">Format</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="va">rIM1xVibrio</span> <span class="op"><-</span> <span class="fu"><a href="drfit.html">drfit</a></span><span class="op">(</span><span class="va">IM1xVibrio</span>, logit <span class="op">=</span> <span class="cn">TRUE</span>, chooseone <span class="op">=</span> <span class="cn">FALSE</span>,</span></span> +<span class="r-in"><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">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> IM13 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</span> +<span class="r-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> IM14 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</span> +<span class="r-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> IM15 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</span> +<span class="r-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> IM16 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</span> +<span class="r-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> IM17 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</span> +<span class="r-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> IM18 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</span> +<span class="r-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> IM19 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</span> +<span class="r-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> IM1-10 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</span> +<span class="r-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">rIM1xVibrio</span>, digits <span class="op">=</span> <span class="fl">4</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</span> +<span class="r-out co"><span class="r-pr">#></span> 1 IM13 BF4 13 22 -5.301 4.699 probit 3.9399 3.8636 4.0160 microM 0.06303</span> +<span class="r-out co"><span class="r-pr">#></span> 2 IM13 BF4 13 22 -5.301 4.699 logit 3.9461 3.8708 4.0211 microM 0.06188</span> +<span class="r-out co"><span class="r-pr">#></span> 3 IM14 BF4 12 57 -4.301 4.699 probit 3.5442 3.5030 3.5855 microM 0.05905</span> +<span class="r-out co"><span class="r-pr">#></span> 4 IM14 BF4 12 57 -4.301 4.699 logit 3.5465 3.5044 3.5885 microM 0.06030</span> +<span class="r-out co"><span class="r-pr">#></span> 5 IM15 BF4 7 20 -0.301 4.699 probit 3.1398 3.1136 3.1662 microM 0.02695</span> +<span class="r-out co"><span class="r-pr">#></span> 6 IM15 BF4 7 20 -0.301 4.699 logit 3.1387 3.1118 3.1659 microM 0.02723</span> +<span class="r-out co"><span class="r-pr">#></span> 7 IM16 BF4 13 30 -4.301 4.699 probit 3.1804 3.1436 3.2176 microM 0.04514</span> +<span class="r-out co"><span class="r-pr">#></span> 8 IM16 BF4 13 30 -4.301 4.699 logit 3.1814 3.1440 3.2190 microM 0.04553</span> +<span class="r-out co"><span class="r-pr">#></span> 9 IM17 BF4 10 20 -1.301 4.699 probit 2.4317 2.3681 2.4951 microM 0.04773</span> +<span class="r-out co"><span class="r-pr">#></span> 10 IM17 BF4 10 20 -1.301 4.699 logit 2.4353 2.3672 2.5026 microM 0.05050</span> +<span class="r-out co"><span class="r-pr">#></span> 11 IM18 BF4 10 17 -2.301 2.699 probit 1.4015 1.3147 1.4881 microM 0.05611</span> +<span class="r-out co"><span class="r-pr">#></span> 12 IM18 BF4 10 17 -2.301 2.699 logit 1.4051 1.3129 1.4966 microM 0.05898</span> +<span class="r-out co"><span class="r-pr">#></span> 13 IM19 BF4 13 22 -5.301 2.699 probit 0.7158 0.6704 0.7592 microM 0.02956</span> +<span class="r-out co"><span class="r-pr">#></span> 14 IM19 BF4 13 22 -5.301 2.699 logit 0.7172 0.6689 0.7635 microM 0.03210</span> +<span class="r-out co"><span class="r-pr">#></span> 15 IM1-10 BF4 11 20 -6.301 2.699 probit -0.1790 -0.2569 -0.1037 microM 0.04099</span> +<span class="r-out co"><span class="r-pr">#></span> 16 IM1-10 BF4 11 20 -6.301 2.699 logit -0.1831 -0.2620 -0.1055 microM 0.04192</span> +<span class="r-out co"><span class="r-pr">#></span> a b ED50 ED50 2.5% ED50 97.5% EDx10 EDx20</span> +<span class="r-out co"><span class="r-pr">#></span> 1 3.9399 0.5763 8707.8956 7305.0279 1.038e+04 1.590e+03 2850.222</span> +<span class="r-out co"><span class="r-pr">#></span> 2 3.9461 0.3426 8832.9407 7426.2282 1.050e+04 1.561e+03 2959.147</span> +<span class="r-out co"><span class="r-pr">#></span> 3 3.5442 0.6561 3501.1558 3184.3196 3.851e+03 5.051e+02 981.759</span> +<span class="r-out co"><span class="r-pr">#></span> 4 3.5465 0.3911 3519.5779 3194.6808 3.877e+03 4.867e+02 1010.014</span> +<span class="r-out co"><span class="r-pr">#></span> 5 3.1398 0.5527 1379.9037 1298.9533 1.466e+03 2.701e+02 472.823</span> +<span class="r-out co"><span class="r-pr">#></span> 6 3.1387 0.3347 1376.4086 1293.7152 1.465e+03 2.532e+02 472.911</span> +<span class="r-out co"><span class="r-pr">#></span> 7 3.1804 0.4882 1515.0421 1391.8150 1.650e+03 3.588e+02 588.292</span> +<span class="r-out co"><span class="r-pr">#></span> 8 3.1814 0.2957 1518.4650 1393.2665 1.656e+03 3.401e+02 590.840</span> +<span class="r-out co"><span class="r-pr">#></span> 9 2.4317 0.6387 270.2279 233.3814 3.127e+02 4.105e+01 78.382</span> +<span class="r-out co"><span class="r-pr">#></span> 10 2.4353 0.3810 272.4409 232.9287 3.182e+02 3.965e+01 80.754</span> +<span class="r-out co"><span class="r-pr">#></span> 11 1.4015 0.8009 25.2069 20.6383 3.077e+01 2.372e+00 5.340</span> +<span class="r-out co"><span class="r-pr">#></span> 12 1.4051 0.4816 25.4135 20.5545 3.138e+01 2.222e+00 5.463</span> +<span class="r-out co"><span class="r-pr">#></span> 13 0.7158 0.6969 5.1975 4.6814 5.744e+00 6.647e-01 1.347</span> +<span class="r-out co"><span class="r-pr">#></span> 14 0.7172 0.4132 5.2141 4.6652 5.801e+00 6.446e-01 1.394</span> +<span class="r-out co"><span class="r-pr">#></span> 15 -0.1790 0.8019 0.6622 0.5534 7.876e-01 6.212e-02 0.140</span> +<span class="r-out co"><span class="r-pr">#></span> 16 -0.1831 0.4816 0.6560 0.5470 7.843e-01 5.738e-02 0.141</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="va">rIM1xVibrio.drc</span> <span class="op"><-</span> <span class="fu"><a href="drcfit.html">drcfit</a></span><span class="op">(</span><span class="va">IM1xVibrio</span>, logit <span class="op">=</span> <span class="cn">TRUE</span>, chooseone <span class="op">=</span> <span class="cn">FALSE</span>,</span></span> +<span class="r-in"><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">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> IM13 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> IM14 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> IM15 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> IM16 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> IM17 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> IM18 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> IM19 BF4: Fitting data...</span> +<span class="r-msg co"><span class="r-pr">#></span> </span> +<span class="r-msg co"><span class="r-pr">#></span> IM1-10 BF4: Fitting data...</span> +<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">rIM1xVibrio.drc</span>, digits <span class="op">=</span> <span class="fl">4</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</span> +<span class="r-out co"><span class="r-pr">#></span> 1 IM13 BF4 13 22 -5.301 4.699 probit 3.9399 3.8563 4.0100 microM 0.06303</span> +<span class="r-out co"><span class="r-pr">#></span> 2 IM13 BF4 13 22 -5.301 4.699 logit 3.9461 3.8637 4.0153 microM 0.06188</span> +<span class="r-out co"><span class="r-pr">#></span> 3 IM14 BF4 12 57 -4.301 4.699 probit 3.5442 3.5009 3.5836 microM 0.05905</span> +<span class="r-out co"><span class="r-pr">#></span> 4 IM14 BF4 12 57 -4.301 4.699 logit 3.5465 3.5023 3.5866 microM 0.06030</span> +<span class="r-out co"><span class="r-pr">#></span> 5 IM15 BF4 7 20 -0.301 4.699 probit 3.1398 3.1127 3.1654 microM 0.02695</span> +<span class="r-out co"><span class="r-pr">#></span> 6 IM15 BF4 7 20 -0.301 4.699 logit 3.1387 3.1109 3.1649 microM 0.02723</span> +<span class="r-out co"><span class="r-pr">#></span> 7 IM16 BF4 13 30 -4.301 4.699 probit 3.1804 3.1419 3.2158 microM 0.04514</span> +<span class="r-out co"><span class="r-pr">#></span> 8 IM16 BF4 13 30 -4.301 4.699 logit 3.1814 3.1424 3.2172 microM 0.04553</span> +<span class="r-out co"><span class="r-pr">#></span> 9 IM17 BF4 10 20 -1.301 4.699 probit 2.4317 2.3632 2.4909 microM 0.04773</span> +<span class="r-out co"><span class="r-pr">#></span> 10 IM17 BF4 10 20 -1.301 4.699 logit 2.4353 2.3618 2.4981 microM 0.05050</span> +<span class="r-out co"><span class="r-pr">#></span> 11 IM18 BF4 10 17 -2.301 2.699 probit 1.4015 1.3052 1.4803 microM 0.05611</span> +<span class="r-out co"><span class="r-pr">#></span> 12 IM18 BF4 10 17 -2.301 2.699 logit 1.4051 1.3023 1.4881 microM 0.05898</span> +<span class="r-out co"><span class="r-pr">#></span> 13 IM19 BF4 13 22 -5.301 2.699 probit 0.7158 0.6690 0.7580 microM 0.02956</span> +<span class="r-out co"><span class="r-pr">#></span> 14 IM19 BF4 13 22 -5.301 2.699 logit 0.7172 0.6672 0.7620 microM 0.03210</span> +<span class="r-out co"><span class="r-pr">#></span> 15 IM1-10 BF4 11 20 -6.301 2.699 probit -0.1790 -0.2628 -0.1088 microM 0.04099</span> +<span class="r-out co"><span class="r-pr">#></span> 16 IM1-10 BF4 11 20 -6.301 2.699 logit -0.1831 -0.2690 -0.1114 microM 0.04192</span> +<span class="r-out co"><span class="r-pr">#></span> a b ED50 ED50 2.5% ED50 97.5% EDx10 EDx10 2.5%</span> +<span class="r-out co"><span class="r-pr">#></span> 1 8707.5571 -0.7536 8707.5571 7183.0127 1.023e+04 1.590e+03 968.72497</span> +<span class="r-out co"><span class="r-pr">#></span> 2 8832.8773 1.2676 8832.8773 7306.8669 1.036e+04 1.561e+03 925.39582</span> +<span class="r-out co"><span class="r-pr">#></span> 3 3501.1967 -0.6619 3501.1967 3168.9639 3.833e+03 5.051e+02 395.26341</span> +<span class="r-out co"><span class="r-pr">#></span> 4 3519.5773 1.1105 3519.5773 3179.2923 3.860e+03 4.866e+02 371.84710</span> +<span class="r-out co"><span class="r-pr">#></span> 5 1379.9019 -0.7858 1379.9019 1296.3162 1.463e+03 2.701e+02 233.25320</span> +<span class="r-out co"><span class="r-pr">#></span> 6 1376.4086 1.2976 1376.4086 1290.8397 1.462e+03 2.531e+02 215.79719</span> +<span class="r-out co"><span class="r-pr">#></span> 7 1515.0427 -0.8896 1515.0427 1386.3308 1.644e+03 3.588e+02 283.79434</span> +<span class="r-out co"><span class="r-pr">#></span> 8 1518.4644 1.4686 1518.4644 1387.9173 1.649e+03 3.401e+02 262.20564</span> +<span class="r-out co"><span class="r-pr">#></span> 9 270.2279 -0.6800 270.2279 230.7905 3.097e+02 4.105e+01 27.78507</span> +<span class="r-out co"><span class="r-pr">#></span> 10 272.4526 1.1401 272.4526 230.0588 3.148e+02 3.966e+01 25.34948</span> +<span class="r-out co"><span class="r-pr">#></span> 11 25.2059 -0.5423 25.2059 20.1927 3.022e+01 2.372e+00 1.29116</span> +<span class="r-out co"><span class="r-pr">#></span> 12 25.4145 0.9017 25.4145 20.0576 3.077e+01 2.223e+00 1.09707</span> +<span class="r-out co"><span class="r-pr">#></span> 13 5.1971 -0.6231 5.1971 4.6665 5.728e+00 6.646e-01 0.49235</span> +<span class="r-out co"><span class="r-pr">#></span> 14 5.2141 1.0511 5.2141 4.6477 5.781e+00 6.446e-01 0.46046</span> +<span class="r-out co"><span class="r-pr">#></span> 15 0.6622 -0.5416 0.6622 0.5460 7.783e-01 6.213e-02 0.03513</span> +<span class="r-out co"><span class="r-pr">#></span> 16 0.6560 0.9018 0.6560 0.5383 7.737e-01 5.738e-02 0.03163</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 2.211e+03 2850.328 2.019e+03 3681.2704</span> +<span class="r-out co"><span class="r-pr">#></span> 2 2.196e+03 2958.988 2.092e+03 3826.1457</span> +<span class="r-out co"><span class="r-pr">#></span> 3 6.149e+02 981.743 8.254e+02 1138.0862</span> +<span class="r-out co"><span class="r-pr">#></span> 4 6.014e+02 1010.061 8.414e+02 1178.7611</span> +<span class="r-out co"><span class="r-pr">#></span> 5 3.070e+02 472.838 4.257e+02 520.0197</span> +<span class="r-out co"><span class="r-pr">#></span> 6 2.905e+02 472.906 4.239e+02 521.8955</span> +<span class="r-out co"><span class="r-pr">#></span> 7 4.337e+02 588.259 4.999e+02 676.6627</span> +<span class="r-out co"><span class="r-pr">#></span> 8 4.181e+02 590.824 4.972e+02 684.4677</span> +<span class="r-out co"><span class="r-pr">#></span> 9 5.431e+01 78.383 5.955e+01 97.2142</span> +<span class="r-out co"><span class="r-pr">#></span> 10 5.396e+01 80.763 5.975e+01 101.7713</span> +<span class="r-out co"><span class="r-pr">#></span> 11 3.454e+00 5.339 3.544e+00 7.1350</span> +<span class="r-out co"><span class="r-pr">#></span> 12 3.348e+00 5.463 3.489e+00 7.4370</span> +<span class="r-out co"><span class="r-pr">#></span> 13 8.369e-01 1.346 1.084e+00 1.6086</span> +<span class="r-out co"><span class="r-pr">#></span> 14 8.288e-01 1.394 1.106e+00 1.6832</span> +<span class="r-out co"><span class="r-pr">#></span> 15 8.912e-02 0.140 9.501e-02 0.1850</span> +<span class="r-out co"><span class="r-pr">#></span> 16 8.314e-02 0.141 9.588e-02 0.1862</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> - <footer> - <div 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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>Dose-Response data for two substances X and Y</h1> @@ -111,44 +45,42 @@ arbitrarily named X and Y.</p> </div> - <pre class="usage"><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span>(<span class='no'>XY</span>)</pre> - - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><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">XY</span><span class="op">)</span></span></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> <p>A dataframe containing dose (concentration) and response data, as well as control values where the dose is zero.</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='kw'>if</span> (<span class='fl'>FALSE</span>) <span class='fu'><a href='https://rdrr.io/r/utils/demo.html'>demo</a></span>(<span class='no'>XY</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="#format">Format</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/utils/demo.html" class="external-link">demo</a></span><span class="op">(</span><span class="va">XY</span><span class="op">)</span></span></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> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/reference/antifoul.html b/docs/reference/antifoul.html index b3e5604..e679ce3 100644 --- a/docs/reference/antifoul.html +++ b/docs/reference/antifoul.html @@ -1,67 +1,15 @@ -<!-- 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of the UFT Department of Bioorganic Chemistry on - February 25, 2004" /> -<meta name="twitter:card" content="summary" /> - - - - -<!-- mathjax --> -<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]> + from the "cytotox" database of the UFT Department of Bioorganic Chemistry on + February 25, 2004'><!-- mathjax --><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=" 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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>Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells</h1> @@ -115,108 +49,121 @@ February 25, 2004</p> </div> - <pre class="usage"><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span>(<span class='no'>antifoul</span>)</pre> - - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><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></code></pre></div> + </div> + <div id="format"> + <h2>Format</h2> <p>A dataframe containing 135 and 81 data points for concentrations and responses for TBT and Zink Pyrithione, respectively. Some additional columns from the database are also present.</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='no'>rantifoul.ED50</span> <span class='kw'><-</span> <span class='fu'><a href='drfit.html'>drfit</a></span>(<span class='no'>antifoul</span>, - <span class='kw'>linlogit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>logit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>weibull</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>chooseone</span> <span class='kw'>=</span> <span class='fl'>FALSE</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'>10</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'>Waiting for profiling to be done...</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='output co'>#> <span class='message'>Waiting for profiling to be done...</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/print.html'>print</a></span>(<span class='no'>rantifoul.ED50</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>5</span>)</div><div class='output co'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% -#> 1 TBT 38 135 -2.7093 2.3979 linlogit -0.15809 -0.26021 -0.050475 -#> 2 TBT 38 135 -2.7093 2.3979 probit -0.16436 -0.26504 -0.056498 -#> 3 TBT 38 135 -2.7093 2.3979 logit -0.16012 -0.26116 -0.052591 -#> 4 TBT 38 135 -2.7093 2.3979 weibull -0.11507 NA NA -#> 5 Zn Pyrithion 27 81 -2.1072 2.0000 linlogit -0.41329 -0.52932 -0.299799 -#> 6 Zn Pyrithion 27 81 -2.1072 2.0000 probit -0.39792 -0.50783 -0.291563 -#> 7 Zn Pyrithion 27 81 -2.1072 2.0000 logit -0.40035 -0.51049 -0.293501 -#> 8 Zn Pyrithion 27 81 -2.1072 2.0000 weibull -0.38795 NA NA -#> unit sigma a b c ED50 ED50 2.5% ED50 97.5% -#> 1 microM 0.19264 -0.15809 1.04065 -0.024165 0.69487 0.54927 0.89028 -#> 2 microM 0.19286 -0.16436 0.67637 NA 0.68493 0.54320 0.87801 -#> 3 microM 0.19199 -0.16012 0.41358 NA 0.69164 0.54808 0.88595 -#> 4 microM 0.18810 0.63743 1.28891 NA 0.76724 NA NA -#> 5 microM 0.22878 -0.41329 1.74249 0.610900 0.38611 0.29558 0.50142 -#> 6 microM 0.22866 -0.39792 0.41696 NA 0.40002 0.31058 0.51102 -#> 7 microM 0.22802 -0.40035 0.25395 NA 0.39779 0.30868 0.50874 -#> 8 microM 0.23008 0.47647 2.51561 NA 0.40931 NA NA -#> EDx10 -#> 1 0.085214 -#> 2 0.093077 -#> 3 0.085340 -#> 4 0.053392 -#> 5 0.120233 -#> 6 0.116872 -#> 7 0.110068 -#> 8 0.121166</div><div class='input'> -<span class='no'>rantifoul.drc</span> <span class='kw'><-</span> <span class='fu'><a href='drcfit.html'>drcfit</a></span>(<span class='no'>antifoul</span>, - <span class='kw'>linlogit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>logit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>weibull</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, - <span class='kw'>chooseone</span> <span class='kw'>=</span> <span class='fl'>FALSE</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'>10</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/print.html'>print</a></span>(<span class='no'>rantifoul.drc</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>5</span>)</div><div class='output co'>#> Substance ndl n lld lhd mtype logED50 2.5% 97.5% -#> 1 TBT 38 135 -2.7093 2.3979 linlogit NA NA NA -#> 2 TBT 38 135 -2.7093 2.3979 probit -0.16436 -0.28178 -0.072022 -#> 3 TBT 38 135 -2.7093 2.3979 logit -0.16012 -0.27782 -0.067603 -#> 4 TBT 38 135 -2.7093 2.3979 weibull -0.13012 -0.23786 -0.043860 -#> 5 Zn Pyrithion 27 81 -2.1072 2.0000 linlogit -0.41330 -0.54457 -0.312631 -#> 6 Zn Pyrithion 27 81 -2.1072 2.0000 probit -0.39792 -0.52005 -0.302705 -#> 7 Zn Pyrithion 27 81 -2.1072 2.0000 logit -0.40035 -0.52324 -0.304676 -#> 8 Zn Pyrithion 27 81 -2.1072 2.0000 weibull -0.37351 -0.49792 -0.276917 -#> unit sigma a b c ED50 ED50 2.5% ED50 97.5% -#> 1 microM 0.19264 0.71806 1.04061 -0.024169 NA NA NA -#> 2 microM 0.19286 0.68492 -0.64209 NA 0.68492 0.52267 0.84718 -#> 3 microM 0.19199 0.69165 1.05007 NA 0.69165 0.52744 0.85585 -#> 4 microM 0.18900 -0.13012 0.79816 NA 0.74111 0.57828 0.90394 -#> 5 microM 0.22878 0.30926 1.74257 0.611358 0.38610 0.28538 0.48682 -#> 6 microM 0.22866 0.40002 -1.04159 NA 0.40002 0.30196 0.49808 -#> 7 microM 0.22802 0.39779 1.71015 NA 0.39779 0.29975 0.49582 -#> 8 microM 0.23077 -0.37351 1.19152 NA 0.42315 0.31775 0.52855 -#> EDx10 EDx10 2.5% EDx10 97.5% -#> 1 NA NA NA -#> 2 0.093074 0.040308 0.14584 -#> 3 0.085338 0.035963 0.13471 -#> 4 0.069958 0.026197 0.11372 -#> 5 0.120238 0.043513 0.19696 -#> 6 0.116878 0.048151 0.18561 -#> 7 0.110068 0.043085 0.17705 -#> 8 0.087066 0.017958 0.15617</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="#format">Format</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">rantifoul.ED50</span> <span class="op"><-</span> <span class="fu"><a href="drfit.html">drfit</a></span><span class="op">(</span><span class="va">antifoul</span>,</span></span> +<span class="r-in"><span> linlogit <span class="op">=</span> <span class="cn">TRUE</span>, logit <span class="op">=</span> <span class="cn">TRUE</span>, weibull <span class="op">=</span> <span class="cn">TRUE</span>,</span></span> +<span class="r-in"><span> chooseone <span class="op">=</span> <span class="cn">FALSE</span>,</span></span> +<span class="r-in"><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">10</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> Waiting for profiling to be done...</span> +<span class="r-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</span> +<span class="r-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</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-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</span> +<span class="r-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</span> +<span class="r-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</span> +<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">rantifoul.ED50</span>, digits <span class="op">=</span> <span class="fl">5</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%</span> +<span class="r-out co"><span class="r-pr">#></span> 1 TBT 38 135 -2.7093 2.3979 linlogit -0.15810 -0.26021 -0.050475</span> +<span class="r-out co"><span class="r-pr">#></span> 2 TBT 38 135 -2.7093 2.3979 probit -0.16436 -0.26504 -0.056498</span> +<span class="r-out co"><span class="r-pr">#></span> 3 TBT 38 135 -2.7093 2.3979 logit -0.16012 -0.26116 -0.052591</span> +<span class="r-out co"><span class="r-pr">#></span> 4 TBT 38 135 -2.7093 2.3979 weibull -0.11507 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 5 Zn Pyrithion 27 81 -2.1072 2.0000 linlogit -0.41329 -0.52932 -0.299799</span> +<span class="r-out co"><span class="r-pr">#></span> 6 Zn Pyrithion 27 81 -2.1072 2.0000 probit -0.39792 -0.50783 -0.291563</span> +<span class="r-out co"><span class="r-pr">#></span> 7 Zn Pyrithion 27 81 -2.1072 2.0000 logit -0.40035 -0.51049 -0.293501</span> +<span class="r-out co"><span class="r-pr">#></span> 8 Zn Pyrithion 27 81 -2.1072 2.0000 weibull -0.38795 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> unit sigma a b c ED50 ED50 2.5% ED50 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> 1 microM 0.19264 -0.15810 1.04066 -0.024161 0.69487 0.54927 0.89028</span> +<span class="r-out co"><span class="r-pr">#></span> 2 microM 0.19286 -0.16436 0.67637 NA 0.68493 0.54320 0.87801</span> +<span class="r-out co"><span class="r-pr">#></span> 3 microM 0.19199 -0.16012 0.41358 NA 0.69164 0.54808 0.88595</span> +<span class="r-out co"><span class="r-pr">#></span> 4 microM 0.18810 0.63743 1.28891 NA 0.76724 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 5 microM 0.22878 -0.41329 1.74249 0.610809 0.38611 0.29558 0.50142</span> +<span class="r-out co"><span class="r-pr">#></span> 6 microM 0.22866 -0.39792 0.41696 NA 0.40002 0.31058 0.51102</span> +<span class="r-out co"><span class="r-pr">#></span> 7 microM 0.22802 -0.40035 0.25395 NA 0.39779 0.30868 0.50874</span> +<span class="r-out co"><span class="r-pr">#></span> 8 microM 0.23008 0.47647 2.51561 NA 0.40931 NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> EDx10</span> +<span class="r-out co"><span class="r-pr">#></span> 1 0.085214</span> +<span class="r-out co"><span class="r-pr">#></span> 2 0.093077</span> +<span class="r-out co"><span class="r-pr">#></span> 3 0.085340</span> +<span class="r-out co"><span class="r-pr">#></span> 4 0.053392</span> +<span class="r-out co"><span class="r-pr">#></span> 5 0.120232</span> +<span class="r-out co"><span class="r-pr">#></span> 6 0.116872</span> +<span class="r-out co"><span class="r-pr">#></span> 7 0.110068</span> +<span class="r-out co"><span class="r-pr">#></span> 8 0.121166</span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="va">rantifoul.drc</span> <span class="op"><-</span> <span class="fu"><a href="drcfit.html">drcfit</a></span><span class="op">(</span><span class="va">antifoul</span>,</span></span> +<span class="r-in"><span> linlogit <span class="op">=</span> <span class="cn">TRUE</span>, logit <span class="op">=</span> <span class="cn">TRUE</span>, weibull <span class="op">=</span> <span class="cn">TRUE</span>,</span></span> +<span class="r-in"><span> chooseone <span class="op">=</span> <span class="cn">FALSE</span>,</span></span> +<span class="r-in"><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">10</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/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">rantifoul.drc</span>, digits <span class="op">=</span> <span class="fl">5</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%</span> +<span class="r-out co"><span class="r-pr">#></span> 1 TBT 38 135 -2.7093 2.3979 linlogit NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 2 TBT 38 135 -2.7093 2.3979 probit -0.16436 -0.28178 -0.072022</span> +<span class="r-out co"><span class="r-pr">#></span> 3 TBT 38 135 -2.7093 2.3979 logit -0.16012 -0.27782 -0.067603</span> +<span class="r-out co"><span class="r-pr">#></span> 4 TBT 38 135 -2.7093 2.3979 weibull -0.13012 -0.23786 -0.043860</span> +<span class="r-out co"><span class="r-pr">#></span> 5 Zn Pyrithion 27 81 -2.1072 2.0000 linlogit -0.41330 -0.54457 -0.312631</span> +<span class="r-out co"><span class="r-pr">#></span> 6 Zn Pyrithion 27 81 -2.1072 2.0000 probit -0.39792 -0.52005 -0.302705</span> +<span class="r-out co"><span class="r-pr">#></span> 7 Zn Pyrithion 27 81 -2.1072 2.0000 logit -0.40035 -0.52324 -0.304676</span> +<span class="r-out co"><span class="r-pr">#></span> 8 Zn Pyrithion 27 81 -2.1072 2.0000 weibull -0.37351 -0.49792 -0.276917</span> +<span class="r-out co"><span class="r-pr">#></span> unit sigma a b c ED50 ED50 2.5% ED50 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> 1 microM 0.19264 0.71806 1.04061 -0.024169 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 2 microM 0.19286 0.68492 -0.64209 NA 0.68492 0.52267 0.84718</span> +<span class="r-out co"><span class="r-pr">#></span> 3 microM 0.19199 0.69165 1.05007 NA 0.69165 0.52744 0.85585</span> +<span class="r-out co"><span class="r-pr">#></span> 4 microM 0.18900 -0.13012 0.79816 NA 0.74111 0.57828 0.90394</span> +<span class="r-out co"><span class="r-pr">#></span> 5 microM 0.22878 0.30926 1.74257 0.611358 0.38610 0.28538 0.48682</span> +<span class="r-out co"><span class="r-pr">#></span> 6 microM 0.22866 0.40002 -1.04159 NA 0.40002 0.30196 0.49808</span> +<span class="r-out co"><span class="r-pr">#></span> 7 microM 0.22802 0.39779 1.71015 NA 0.39779 0.29975 0.49582</span> +<span class="r-out co"><span class="r-pr">#></span> 8 microM 0.23077 -0.37351 1.19152 NA 0.42315 0.31775 0.52855</span> +<span class="r-out co"><span class="r-pr">#></span> EDx10 EDx10 2.5% EDx10 97.5%</span> +<span class="r-out co"><span class="r-pr">#></span> 1 NA NA NA</span> +<span class="r-out co"><span class="r-pr">#></span> 2 0.093074 0.040308 0.14584</span> +<span class="r-out co"><span class="r-pr">#></span> 3 0.085338 0.035963 0.13471</span> +<span class="r-out co"><span class="r-pr">#></span> 4 0.069958 0.026197 0.11372</span> +<span class="r-out co"><span class="r-pr">#></span> 5 0.120238 0.043513 0.19696</span> +<span class="r-out co"><span class="r-pr">#></span> 6 0.116878 0.048151 0.18561</span> +<span class="r-out co"><span class="r-pr">#></span> 7 0.110068 0.043085 0.17705</span> +<span class="r-out co"><span class="r-pr">#></span> 8 0.087066 0.017958 0.15617</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> - <footer> - <div class="copyright"> - 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experiments from a specified database."><!-- mathjax --><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> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </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>Check raw data from range of plates or experiments</h1> @@ -111,96 +45,88 @@ experiments from a specified database.</p> </div> - <pre class="usage"><span class='fu'>checkcontrols</span>(<span class='kw'>last</span> <span class='kw'>=</span> <span class='fl'>10</span>, <span class='kw'>id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, - <span class='kw'>db</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"cytotox"</span>, <span class='st'>"enzymes"</span>, <span class='st'>"ecotox"</span>), - <span class='kw'>celltype</span> <span class='kw'>=</span> <span class='st'>"IPC-81"</span>, <span class='kw'>enzymetype</span> <span class='kw'>=</span> <span class='st'>"AChE"</span>, - <span class='kw'>organism</span> <span class='kw'>=</span> <span class='st'>"Vibrio fischeri"</span>, - <span class='kw'>endpoint</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>qcc</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"R"</span>, <span class='st'>"xbar"</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>last</th> - <td><p>If <code>id</code> is not specified, this argument specifies the number of + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">checkcontrols</span><span class="op">(</span>last <span class="op">=</span> <span class="fl">10</span>, id <span class="op">=</span> <span class="cn">NULL</span>, </span> +<span> db <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="st">"cytotox"</span>, <span class="st">"enzymes"</span>, <span class="st">"ecotox"</span><span class="op">)</span>,</span> +<span> celltype <span class="op">=</span> <span class="st">"IPC-81"</span>, enzymetype <span class="op">=</span> <span class="st">"AChE"</span>, </span> +<span> organism <span class="op">=</span> <span class="st">"Vibrio fischeri"</span>,</span> +<span> endpoint <span class="op">=</span> <span class="st">"%"</span>, qcc <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="st">"R"</span>, <span class="st">"xbar"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>last</dt> +<dd><p>If <code>id</code> is not specified, this argument specifies the number of plates/experiments that should be evaluated. The plates/experiments with - the hightest numbers are selected.</p></td> - </tr> - <tr> - <th>id</th> - <td><p>A numeric vector of integers, specifying the plates or experiments explicitly.</p></td> - </tr> - <tr> - <th>db</th> - <td><p>The database to be used. Currently, the microtiter plate databases + the hightest numbers are selected.</p></dd> + + <dt>id</dt> +<dd><p>A numeric vector of integers, specifying the plates or experiments explicitly.</p></dd> + + <dt>db</dt> +<dd><p>The database to be used. Currently, the microtiter plate databases "cytotox", "enzymes" of the UFT Department of Bioorganic Chemistry are - supported, as well as the database of ecotoxicity experiments "ecotox".</p></td> - </tr> - <tr> - <th>celltype</th> - <td><p>Only important if database "cytotox" is used. Data for - "IPC-81", "C6", "NB4", "HeLa", "Jurkat" and "U937" are available.</p></td> - </tr> - <tr> - <th>enzymetype</th> - <td><p>Only important if database "enzymes" is used. - Data for "AChE", "GR" and "GST" are available.</p></td> - </tr> - <tr> - <th>organism</th> - <td><p>Only important if database "ecotox" is used.</p></td> - </tr> - <tr> - <th>endpoint</th> - <td><p>The endpoint that should be used for selecting the data. Only important if - the database "ecotox" is used. Defaults to "%".</p></td> - </tr> - <tr> - <th>qcc</th> - <td><p>The type of quality control charts to be plotted. By default, an R chart - (showing ranges of control values within plates/experiments), and an - xbar chart (showing means) are generated.</p></td> - </tr> - </table> + supported, as well as the database of ecotoxicity experiments "ecotox".</p></dd> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + <dt>celltype</dt> +<dd><p>Only important if database "cytotox" is used. Data for + "IPC-81", "C6", "NB4", "HeLa", "Jurkat" and "U937" are available.</p></dd> - <p>The function lists a report and shows two graphs.</p> + <dt>enzymetype</dt> +<dd><p>Only important if database "enzymes" is used. + Data for "AChE", "GR" and "GST" are available.</p></dd> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='kw'>if</span> (<span class='fl'>FALSE</span>) <span class='fu'>checkcontrols</span>(<span class='fl'>15</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="#examples">Examples</a></li> - </ul> + <dt>organism</dt> +<dd><p>Only important if database "ecotox" is used.</p></dd> + <dt>endpoint</dt> +<dd><p>The endpoint that should be used for selecting the data. Only important if + the database "ecotox" is used. Defaults to "%".</p></dd> + + <dt>qcc</dt> +<dd><p>The type of quality control charts to be plotted. By default, an R chart + (showing ranges of control values within plates/experiments), and an + xbar chart (showing means) are generated.</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>The function lists a report and shows two graphs.</p> + </div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke - <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a></p> + <a href="mailto:jranke@uni-bremen.de">jranke@uni-bremen.de</a></p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="fu">checkcontrols</span><span class="op">(</span><span class="fl">15</span><span class="op">)</span></span></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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- - - </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>Check raw data from a specified experiment or microtiter plate</h1> @@ -111,78 +45,74 @@ specified database, box plot controls, and plot the dose-response data.</p> </div> - <pre class="usage"><span class='fu'>checkplate</span>(<span class='no'>id</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"cytotox"</span>, <span class='st'>"enzymes"</span>)) - <span class='fu'>checkexperiment</span>(<span class='no'>id</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"ecotox"</span>, <span class='st'>"cytotox"</span>, <span class='st'>"enzymes"</span>), <span class='kw'>endpoint</span> <span class='kw'>=</span> <span class='st'>"%"</span>, - <span class='kw'>whereClause</span> <span class='kw'>=</span> <span class='st'>"1"</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>id</th> - <td><p>The id of the experiment or the plate identifying it within the database.</p></td> - </tr> - <tr> - <th>db</th> - <td><p>The database to be used. Currently, the microtiter plate databases - "cytotox", "enzymes" of the UFT Department of Bioorganic Chemistry are - supported, as well as the database of ecotoxicity experiments "ecotox".</p></td> - </tr> - <tr> - <th>endpoint</th> - <td><p>The endpoint that should be used for selecting the data. Only important if - the database "ecotox" is used. Defaults to "%".</p></td> - </tr> - <tr> - <th>whereClause</th> - <td><p>With this argument, additional conditions for the SQL query can be set, - e.g. "duration = 48" (i.e. "Only retrieve data with duration 48"). The - default is 1 (in SQL syntax this means TRUE).</p></td> - </tr> - </table> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">checkplate</span><span class="op">(</span><span class="va">id</span>, db <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="st">"cytotox"</span>, <span class="st">"enzymes"</span><span class="op">)</span><span class="op">)</span></span> +<span> <span class="fu">checkexperiment</span><span class="op">(</span><span class="va">id</span>, db <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="st">"ecotox"</span>, <span class="st">"cytotox"</span>, <span class="st">"enzymes"</span><span class="op">)</span>, endpoint <span class="op">=</span> <span class="st">"%"</span>, </span> +<span> whereClause <span class="op">=</span> <span class="st">"1"</span><span class="op">)</span></span></code></pre></div> + </div> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>id</dt> +<dd><p>The id of the experiment or the plate identifying it within the database.</p></dd> - <p>The function lists a report and shows two graphs.</p> + <dt>db</dt> +<dd><p>The database to be used. Currently, the microtiter plate databases + "cytotox", "enzymes" of the UFT Department of Bioorganic Chemistry are + supported, as well as the database of ecotoxicity experiments "ecotox".</p></dd> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># Check plate number 3 in the cytotox database</span> -<span class='kw'>if</span> (<span class='fl'>FALSE</span>) <span class='fu'>checkplate</span>(<span class='fl'>3</span>) + <dt>endpoint</dt> +<dd><p>The endpoint that should be used for selecting the data. Only important if + the database "ecotox" is used. Defaults to "%".</p></dd> -<span class='co'># Check data from experiment 1517 with duration 48 hours</span> -<span class='kw'>if</span> (<span class='fl'>FALSE</span>) <span class='fu'>checkexperiment</span>(<span class='fl'>1517</span>, <span class='kw'>whereClause</span> <span class='kw'>=</span> <span class='st'>"duration = 48"</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="#examples">Examples</a></li> - </ul> + <dt>whereClause</dt> +<dd><p>With this argument, additional conditions for the SQL query can be set, + e.g. "duration = 48" (i.e. "Only retrieve data with duration 48"). The + default is 1 (in SQL syntax this means TRUE).</p></dd> +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>The function lists a report and shows two graphs.</p> + </div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke - <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a></p> + <a href="mailto:jranke@uni-bremen.de">jranke@uni-bremen.de</a></p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Check plate number 3 in the cytotox database</span></span></span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="fu">checkplate</span><span class="op">(</span><span class="fl">3</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span><span class="co"># Check data from experiment 1517 with duration 48 hours</span></span></span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="fu">checkexperiment</span><span class="op">(</span><span class="fl">1517</span>, whereClause <span class="op">=</span> <span class="st">"duration = 48"</span><span class="op">)</span></span></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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- - - </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>Check raw data for a specified substance</h1> @@ -111,104 +45,95 @@ the data.</p> </div> - <pre class="usage"><span class='fu'>checksubstance</span>(<span class='no'>substance</span>, - <span class='kw'>db</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"cytotox"</span>, <span class='st'>"enzymes"</span>, <span class='st'>"ecotox"</span>), - <span class='kw'>experimentator</span> <span class='kw'>=</span> <span class='st'>"%"</span>, - <span class='kw'>celltype</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>enzymetype</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>organism</span> <span class='kw'>=</span> <span class='st'>"%"</span>, - <span class='kw'>endpoint</span> <span class='kw'>=</span> <span class='st'>"%"</span>, - <span class='kw'>whereClause</span> <span class='kw'>=</span> <span class='st'>"1"</span>, <span class='kw'>ok</span> <span class='kw'>=</span> <span class='st'>"%"</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>substance</th> - <td><p>The name of the substance identifying it within the database. Matching is not - case-sensitive.</p></td> - </tr> - <tr> - <th>db</th> - <td><p>The database to be used. Currently, the databases "cytotox" and "enzymes" + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">checksubstance</span><span class="op">(</span><span class="va">substance</span>, </span> +<span> db <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="st">"cytotox"</span>, <span class="st">"enzymes"</span>, <span class="st">"ecotox"</span><span class="op">)</span>, </span> +<span> experimentator <span class="op">=</span> <span class="st">"%"</span>,</span> +<span> celltype <span class="op">=</span> <span class="st">"%"</span>, enzymetype <span class="op">=</span> <span class="st">"%"</span>, organism <span class="op">=</span> <span class="st">"%"</span>,</span> +<span> endpoint <span class="op">=</span> <span class="st">"%"</span>,</span> +<span> whereClause <span class="op">=</span> <span class="st">"1"</span>, ok <span class="op">=</span> <span class="st">"%"</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>substance</dt> +<dd><p>The name of the substance identifying it within the database. Matching is not + case-sensitive.</p></dd> + + <dt>db</dt> +<dd><p>The database to be used. Currently, the databases "cytotox" and "enzymes" of the UFT Department of Bioorganic Chemistry are supported (default is - "cytotox").</p></td> - </tr> - <tr> - <th>experimentator</th> - <td><p>The name of the experimentator whose data is to be used. Default is "%", - which means that data from all experimentators are shown.</p></td> - </tr> - <tr> - <th>celltype</th> - <td><p>Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are + "cytotox").</p></dd> + + <dt>experimentator</dt> +<dd><p>The name of the experimentator whose data is to be used. Default is "%", + which means that data from all experimentators are shown.</p></dd> + + <dt>celltype</dt> +<dd><p>Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are supported. Default is "%", i.e. data for any cell type will be - displayed.</p></td> - </tr> - <tr> - <th>enzymetype</th> - <td><p>Currently, only data for AChE, GR and GST are supported. The default value - is "%", i.e. data for any enzyme type will be displayed.</p></td> - </tr> - <tr> - <th>organism</th> - <td><p>The latin name of the tested organism, if the ecotox db was selected. The - default value is "%", i.e. data for any organism will be displayed.</p></td> - </tr> - <tr> - <th>endpoint</th> - <td><p>The endpoint that should be used for selecting the data. Only important if - the database "ecotox" is used. Defaults to "%".</p></td> - </tr> - <tr> - <th>whereClause</th> - <td><p>With this argument, additional conditions for the SQL query can be set, - e.g. "plate != 710". The default is 1 (in SQL syntax this means TRUE).</p></td> - </tr> - <tr> - <th>ok</th> - <td><p>With the default value "%", all data in the database is retrieved for the - specified substance.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>The function lists a report and shows one graph.</p> - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'><span class='co'># Check substance IM14 BF4 in the cytotox database</span> -<span class='kw'>if</span> (<span class='fl'>FALSE</span>) <span class='fu'>checksubstance</span>(<span class='st'>"IM14 BF4"</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="#examples">Examples</a></li> - </ul> + displayed.</p></dd> + + <dt>enzymetype</dt> +<dd><p>Currently, only data for AChE, GR and GST are supported. The default value + is "%", i.e. data for any enzyme type will be displayed.</p></dd> + + <dt>organism</dt> +<dd><p>The latin name of the tested organism, if the ecotox db was selected. The + default value is "%", i.e. data for any organism will be displayed.</p></dd> + <dt>endpoint</dt> +<dd><p>The endpoint that should be used for selecting the data. Only important if + the database "ecotox" is used. Defaults to "%".</p></dd> + + <dt>whereClause</dt> +<dd><p>With this argument, additional conditions for the SQL query can be set, + e.g. "plate != 710". The default is 1 (in SQL syntax this means TRUE).</p></dd> + + <dt>ok</dt> +<dd><p>With the default value "%", all data in the database is retrieved for the + specified substance.</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>The function lists a report and shows one graph.</p> + </div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke - <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a></p> + <a href="mailto:jranke@uni-bremen.de">jranke@uni-bremen.de</a></p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># Check substance IM14 BF4 in the cytotox database</span></span></span> +<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="fu">checksubstance</span><span class="op">(</span><span class="st">"IM14 BF4"</span><span class="op">)</span></span></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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- </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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- - - </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"> @@ -69,35 +17,21 @@ </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>Get dose-response data via RODBC</h1> @@ -109,75 +43,67 @@ <p>Get dose-response data from an adequate ODBC data source</p> </div> - <pre class="usage"><span class='fu'>drdata</span>(<span class='no'>substances</span>, <span class='kw'>experimentator</span> <span class='kw'>=</span> <span class='st'>"%"</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"cytotox"</span>, - <span class='kw'>celltype</span> <span class='kw'>=</span> <span class='st'>"IPC-81"</span>, <span class='kw'>enzymetype</span> <span class='kw'>=</span> <span class='st'>"AChE"</span>, <span class='kw'>organism</span> <span class='kw'>=</span> <span class='st'>"Vibrio fischeri"</span>, - <span class='kw'>endpoint</span> <span class='kw'>=</span> <span class='st'>"Luminescence"</span>, - <span class='kw'>whereClause</span> <span class='kw'>=</span> <span class='st'>"1"</span>, <span class='kw'>ok</span> <span class='kw'>=</span> <span class='st'>"'ok','no fit'"</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>substances</th> - <td><p>A string or an array of strings with the substance names for - which dose-response data is to be retrieved. Matching is case-sensitive.</p></td> - </tr> - <tr> - <th>experimentator</th> - <td><p>The name of the experimentator whose data is to be used. Default is "<!-- %", --> - which means that data from all experimentators are retrieved.</p></td> - </tr> - <tr> - <th>db</th> - <td><p>The database to be used. Currently, the databases "cytotox", "enzymes" + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">drdata</span><span class="op">(</span><span class="va">substances</span>, experimentator <span class="op">=</span> <span class="st">"%"</span>, db <span class="op">=</span> <span class="st">"cytotox"</span>, </span> +<span> celltype <span class="op">=</span> <span class="st">"IPC-81"</span>, enzymetype <span class="op">=</span> <span class="st">"AChE"</span>, organism <span class="op">=</span> <span class="st">"Vibrio fischeri"</span>,</span> +<span> endpoint <span class="op">=</span> <span class="st">"Luminescence"</span>,</span> +<span> whereClause <span class="op">=</span> <span class="st">"1"</span>, ok <span class="op">=</span> <span class="st">"'ok','no fit'"</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>substances</dt> +<dd><p>A string or an array of strings with the substance names for + which dose-response data is to be retrieved. Matching is case-sensitive.</p></dd> + + <dt>experimentator</dt> +<dd><p>The name of the experimentator whose data is to be used. Default is "<!-- %", --> + which means that data from all experimentators are retrieved.</p></dd> + + <dt>db</dt> +<dd><p>The database to be used. Currently, the databases "cytotox", "enzymes" and "ecotox" of the UFT Department of Bioorganic Chemistry are - supported (default is "cytotox").</p></td> - </tr> - <tr> - <th>celltype</th> - <td><p>Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are - supported.</p></td> - </tr> - <tr> - <th>enzymetype</th> - <td><p>Currently, only data for AChE, GR and GST are supported.</p></td> - </tr> - <tr> - <th>organism</th> - <td><p>The organism that was exposed to the chemical. Only important if the database - "ecotox" is used. Defaults to "Vibrio fischeri".</p></td> - </tr> - <tr> - <th>endpoint</th> - <td><p>The endpoint that should be used for selecting the data. Only important if - the database "ecotox" is used. Defaults to "Luminescence".</p></td> - </tr> - <tr> - <th>whereClause</th> - <td><p>With this argument, additional conditions for the SQL query can be set, + supported (default is "cytotox").</p></dd> + + <dt>celltype</dt> +<dd><p>Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are + supported.</p></dd> + + <dt>enzymetype</dt> +<dd><p>Currently, only data for AChE, GR and GST are supported.</p></dd> + + <dt>organism</dt> +<dd><p>The organism that was exposed to the chemical. Only important if the database + "ecotox" is used. Defaults to "Vibrio fischeri".</p></dd> + + <dt>endpoint</dt> +<dd><p>The endpoint that should be used for selecting the data. Only important if + the database "ecotox" is used. Defaults to "Luminescence".</p></dd> + + <dt>whereClause</dt> +<dd><p>With this argument, additional conditions for the SQL query can be set, e.g. "plate != 710" (i.e. "Do not retrieve data for plate 710"). The - default is 1 (in SQL syntax this means TRUE).</p></td> - </tr> - <tr> - <th>ok</th> - <td><p>With the default value "'ok','no fit'", only data that has been checked and + default is 1 (in SQL syntax this means TRUE).</p></dd> + + <dt>ok</dt> +<dd><p>With the default value "'ok','no fit'", only data that has been checked and set to "ok" or "no fit" in the database is retrieved. The argument "no fit" will result in not using the data for fitting, but it will be plotted. Another sensible argument would be "'ok','no fit','?'", in order to - additionally retrieve data which has not yet been checked.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + additionally retrieve data which has not yet been checked.</p></dd> - <p></p> -<dt>data</dt><dd><p>A data frame with a factor describing the dose levels, the numeric dose +</dl></div> + <div id="value"> + <h2>Value</h2> + <dl><dt>data</dt> +<dd><p>A data frame with a factor describing the dose levels, the numeric dose levels and a numeric column describing the response, as well as the entries for plate, experimentator, performed (date of test performance), celltype, unit (of the dose/concentration), and for the ok field in the database.</p></dd> - <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> - +</dl></div> + <div id="details"> + <h2>Details</h2> <p>The function is currently only used for retrieving data from the mysql database "cytotox" of the UFT Department of Bioorganic Chemistry. Access to this database is limited to UFT staff. Additionally to the @@ -186,66 +112,45 @@ myODBC. Then, under Unix, you can use iodbc or unixodbc for setting up the respective data source with data source name (DSN) "cytotox". For my setting using unixodbc, I am using the file <code class="file">/etc/odbcinst.ini</code> - containing:</p><table class='table'> -<tr><td>[MySQL]</td><td></td><td></td></tr> -<tr><td>Description</td><td>=</td><td>MySQL driver for ODBC</td></tr> -<tr><td>Driver</td><td>=</td><td>/usr/local/lib/libmyodbc.so</td></tr> -<tr><td>Setup</td><td>=</td><td>/usr/lib/odbc/libodbcmyS.so</td></tr> -</table> -<p>and the file <code class="file">/etc/odbc.ini</code> containing:</p><table class='table'> -<tr><td>[cytotox]</td><td></td><td></td></tr> -<tr><td>Description</td><td>=</td><td>Cytotoxicity database of the department of bioorganic chemistry, UFT Bremen</td></tr> -<tr><td>Driver</td><td>=</td><td>MySQL</td></tr> -<tr><td>Trace</td><td>=</td><td>Yes</td></tr> -<tr><td>TraceFile</td><td>=</td><td>/tmp/odbc.log</td></tr> -<tr><td>Database</td><td>=</td><td>cytotox</td></tr> -<tr><td>Server</td><td>=</td><td>eckehaat</td></tr> -<tr><td>Port</td><td>=</td><td>3306</td></tr> -</table> - - - - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='kw'>if</span> (<span class='fl'>FALSE</span>) { - - <span class='co'># Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81</span> - <span class='co'># cells</span> - <span class='fu'>drdata</span>(<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"TBT"</span>, <span class='st'>"ZnPT2"</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="#details">Details</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - + containing:</p><table class="table table"><tr><td>[MySQL]</td><td></td><td></td></tr><tr><td>Description</td><td>=</td><td>MySQL driver for ODBC</td></tr><tr><td>Driver</td><td>=</td><td>/usr/local/lib/libmyodbc.so</td></tr><tr><td>Setup</td><td>=</td><td>/usr/lib/odbc/libodbcmyS.so</td></tr></table><p>and the file <code class="file">/etc/odbc.ini</code> containing:</p><table class="table table"><tr><td>[cytotox]</td><td></td><td></td></tr><tr><td>Description</td><td>=</td><td>Cytotoxicity database of the department of bioorganic chemistry, UFT Bremen</td></tr><tr><td>Driver</td><td>=</td><td>MySQL</td></tr><tr><td>Trace</td><td>=</td><td>Yes</td></tr><tr><td>TraceFile</td><td>=</td><td>/tmp/odbc.log</td></tr><tr><td>Database</td><td>=</td><td>cytotox</td></tr><tr><td>Server</td><td>=</td><td>eckehaat</td></tr><tr><td>Port</td><td>=</td><td>3306</td></tr></table></div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke - <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a></p> + <a href="mailto:jranke@uni-bremen.de">jranke@uni-bremen.de</a></p> + </div> + + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="co"># Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81</span></span></span> +<span class="r-in"><span> <span class="co"># cells</span></span></span> +<span class="r-in"><span> <span class="fu">drdata</span><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="st">"TBT"</span>, <span class="st">"ZnPT2"</span><span class="op">)</span><span class="op">)</span></span></span> +<span class="r-in"><span></span></span> +<span class="r-in"><span> <span class="op">}</span></span></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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- - - </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</h1> @@ -111,220 +45,241 @@ 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>, - <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 + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">drfit</span><span class="op">(</span><span class="va">data</span>, startlogED50 <span class="op">=</span> <span class="cn">NA</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>, linlogitWrong <span class="op">=</span> <span class="cn">NA</span>,</span> +<span> allWrong <span class="op">=</span> <span class="cn">NA</span>, ps0 <span class="op">=</span> <span class="fl">1</span>, ls0 <span class="op">=</span> <span class="fl">0.5</span>, ws0 <span class="op">=</span> <span class="fl">0.5</span>, b0 <span class="op">=</span> <span class="fl">2</span>, f0 <span class="op">=</span> <span class="fl">0</span>,</span> +<span> showED50 <span class="op">=</span> <span class="cn">FALSE</span>,</span> +<span> EDx <span class="op">=</span> <span class="cn">NULL</span>, EDx.tolerance <span class="op">=</span> <span class="fl">1e-4</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>startlogED50</th> - <td><p>Especially for the linlogit model, a suitable log10 of the ED50 has to be + the fitting procedure, although it will be plotted.</p></dd> + + <dt>startlogED50</dt> +<dd><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><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><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><a href='https://rdrr.io/r/stats/Weibull.html'>pweibull</a></code> with additionall location parameter and scale=1) + hormesis with the default estimation method.</p></dd> + + <dt>probit</dt> +<dd><p>A boolean defining if cumulative density curves of normal distributions + <code><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">pnorm</a></code> are fitted against the decadic logarithm of the dose. + Default ist TRUE.</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.</p></dd> + + <dt>weibull</dt> +<dd><p>A boolean defining if the cumulative density curves of weibull distributions + (<code><a href="https://rdrr.io/r/stats/Weibull.html" class="external-link">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> - </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, + which appears to be an uncommon approach.</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.</p></dd> + + <dt>level</dt> +<dd><p>The level for the confidence interval listed for the log ED50.</p></dd> + + <dt>linlogitWrong</dt> +<dd><p>An optional vector containing the names of the substances for which the + linlogit function produces a wrong fit.</p></dd> + + <dt>allWrong</dt> +<dd><p>An optional vector containing the names of the substances for which all + functions produce a wrong fit.</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>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><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><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><a href='https://rdrr.io/r/stats/Weibull.html'>pweibull</a></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><a href='https://rdrr.io/r/stats/nls.html'>nls</a></code>. The dataframe has at least + reported.</p></dd> + + <dt>ps0</dt> +<dd><p>If the probit model is fitted, <code>ps0</code> gives the possibility to adjust + the starting value for the scale parameter of <code><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">pnorm</a></code>.</p></dd> + + <dt>ls0</dt> +<dd><p>If the logit model is fitted, <code>ls0</code> gives the possibility to adjust + the starting value for the scale parameter of <code><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">plogis</a></code>.</p></dd> + + <dt>ws0</dt> +<dd><p>If the weibull model is fitted, <code>ws0</code> gives the possibility to adjust + the starting value for the shape parameter of <code><a href="https://rdrr.io/r/stats/Weibull.html" class="external-link">pweibull</a></code>.</p></dd> + + <dt>b0,f0</dt> +<dd><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></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> + + <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>EDx.tolerance</dt> +<dd><p>Tolerance of the effect level, expressed on the response scale from 0 to 1.</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>For the “linlogit”, “logit” and “probit” models, the + + +<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.</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 - 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 + + <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><a href="https://rdrr.io/r/stats/summary.nls.html" class="external-link">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> - <dt>b</dt><dd><p>Parameter <code>b</code> in the case of the “linlogit” fit is the variable - b from the <code><a href='linlogitf.html'>linlogitf</a></code> function. In the case of “probit” + “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><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><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 - confidence intervals are also included on the original dose scale. + case of the “logit” fit it is the <code>scale</code> parameter in the + <code><a href="https://rdrr.io/r/stats/Logistic.html" class="external-link">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" class="external-link">pweibull</a></code> function.</p></dd> - If one or more response leves were specified in the argument EDx, - the corresponding dose levels are given in addition. + <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> - <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> +</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> - <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>If one or more response leves were specified in the argument <code>EDx</code>, + the corresponding dose levels are given in addition.</p> + </div> + <div id="note"> + <h2>Note</h2> + <p>There is a demo for each dataset that can be accessed by + <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>. 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 + <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'><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'><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 -#> 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> - + </div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke - <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a></p> + <a href="mailto:jranke@uni-bremen.de">jranke@uni-bremen.de</a></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">drfit</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> Waiting for profiling to be done...</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-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</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 -0.27 -0.056 microM 0.19 -0.16</span> +<span class="r-out co"><span class="r-pr">#></span> 2 Zn Pyrithion 27 81 -2.1 2.0 probit -0.40 -0.51 -0.292 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 EDx10 EDx20</span> +<span class="r-out co"><span class="r-pr">#></span> 1 0.68 0.68 0.54 0.88 0.053 0.093 0.18</span> +<span class="r-out co"><span class="r-pr">#></span> 2 0.42 0.40 0.31 0.51 0.082 0.117 0.18</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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- - - </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>Plot dose-response models</h1> @@ -111,191 +45,172 @@ either combined or separately, for one or more substances.</p> </div> - <pre class="usage"><span class='fu'>drplot</span>(<span class='no'>drresults</span>, <span class='no'>data</span>, <span class='no'>dtype</span>, <span class='no'>alpha</span>, <span class='no'>ctype</span>, <span class='no'>path</span>, - <span class='no'>fileprefix</span>, <span class='no'>overlay</span>, <span class='no'>xlim</span>, <span class='no'>ylim</span>, <span class='no'>xlab</span>, <span class='no'>ylab</span>, <span class='no'>axes</span>, <span class='no'>frame.plot</span>, <span class='no'>postscript</span>, - <span class='no'>pdf</span>, <span class='no'>png</span>, <span class='no'>bw</span>, <span class='no'>pointsize</span>, <span class='no'>colors</span>, <span class='no'>ltys</span>, <span class='no'>pchs</span>, <span class='no'>devoff</span>, <span class='no'>lpos</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>drresults</th> - <td><p>A data frame as returned from <code><a href='drfit.html'>drfit</a></code>.</p></td> - </tr> - <tr> - <th>data</th> - <td><p>A data frame as returned from <code><a href='drdata.html'>drdata</a></code>. The data frame has to + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">drplot</span><span class="op">(</span><span class="va">drresults</span>, <span class="va">data</span>, <span class="va">dtype</span>, <span class="va">alpha</span>, <span class="va">ctype</span>, <span class="va">path</span>,</span> +<span> <span class="va">fileprefix</span>, <span class="va">overlay</span>, <span class="va">xlim</span>, <span class="va">ylim</span>, <span class="va">xlab</span>, <span class="va">ylab</span>, <span class="va">axes</span>, <span class="va">frame.plot</span>, <span class="va">postscript</span>,</span> +<span> <span class="va">pdf</span>, <span class="va">png</span>, <span class="va">bw</span>, <span class="va">pointsize</span>, <span class="va">colors</span>, <span class="va">ltys</span>, <span class="va">pchs</span>, <span class="va">devoff</span>, <span class="va">lpos</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>drresults</dt> +<dd><p>A data frame as returned from <code><a href="drfit.html">drfit</a></code>.</p></dd> + + <dt>data</dt> +<dd><p>A data frame as returned from <code><a href="drdata.html">drdata</a></code>. The data frame has to contain at least a factor called "substance", a vector called "unit" containing the unit used for the dose, a column "response" with the response values of the test system normalized between 0 and 1, a column "dose" with the numeric dose values and a factor called "dosefactor" - containing the dose as a factor.</p></td> - </tr> - <tr> - <th>dtype</th> - <td><p>A string describing if the raw data should be plotted ("raw"), or an error + containing the dose as a factor.</p></dd> + + <dt>dtype</dt> +<dd><p>A string describing if the raw data should be plotted ("raw"), or an error bar should be constructed from the standard deviations of the responses at each dose level ("std", default value) or from the confidence intervals - ("conf"). If you don't want to see the data, set it to "none".</p></td> - </tr> - <tr> - <th>alpha</th> - <td><p>The confidence level, defaulting to 0.95, only used if dtype "conf" has been - chosen.</p></td> - </tr> - <tr> - <th>ctype</th> - <td><p>This argument decides if horizontal lines are drawn to show the scatter of + ("conf"). If you don't want to see the data, set it to "none".</p></dd> + + <dt>alpha</dt> +<dd><p>The confidence level, defaulting to 0.95, only used if dtype "conf" has been + chosen.</p></dd> + + <dt>ctype</dt> +<dd><p>This argument decides if horizontal lines are drawn to show the scatter of the control values (dose = 0), if there are more than three of them. Defaults to "none", further allowed values are "std" and "conf" for displaying the standard deviation of the controls or the confidence - interval for the mean of the controls.</p></td> - </tr> - <tr> - <th>path</th> - <td><p>The path where graphic files should be put if any are produced. Defaults - to "./" i.e. the current working directory of R.</p></td> - </tr> - <tr> - <th>fileprefix</th> - <td><p>A string which will form the beginning of each filename, if graphic files - are created. Defaults to "drplot".</p></td> - </tr> - <tr> - <th>overlay</th> - <td><p>If TRUE, all output will be put into one graph, otherwise a separate graph - will be created for each substance.</p></td> - </tr> - <tr> - <th>xlim</th> - <td><p>The plot limits (min,max) on the dose axis.</p></td> - </tr> - <tr> - <th>ylim</th> - <td><p>The plot limits (min,max) on the response axis.</p></td> - </tr> - <tr> - <th>xlab</th> - <td><p>The axis title for the x axis. Defaults to "Concentration in" <code>unit</code>.</p></td> - </tr> - <tr> - <th>ylab</th> - <td><p>The axis title for the y axis. Defaults to "Normalized response".</p></td> - </tr> - <tr> - <th>axes</th> - <td><p>Specifies if axes should be drawn. Default is TRUE, as in - <code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot.default</a></code></p></td> - </tr> - <tr> - <th>frame.plot</th> - <td><p>Specifies if the plot should be framed. Default is TRUE, as in - <code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot.default</a></code></p></td> - </tr> - <tr> - <th>postscript</th> - <td><p>If TRUE, (a) postscript graph(s) will be created. Otherwise, and if + interval for the mean of the controls.</p></dd> + + <dt>path</dt> +<dd><p>The path where graphic files should be put if any are produced. Defaults + to "./" i.e. the current working directory of R.</p></dd> + + <dt>fileprefix</dt> +<dd><p>A string which will form the beginning of each filename, if graphic files + are created. Defaults to "drplot".</p></dd> + + <dt>overlay</dt> +<dd><p>If TRUE, all output will be put into one graph, otherwise a separate graph + will be created for each substance.</p></dd> + + <dt>xlim</dt> +<dd><p>The plot limits (min,max) on the dose axis.</p></dd> + + <dt>ylim</dt> +<dd><p>The plot limits (min,max) on the response axis.</p></dd> + + <dt>xlab</dt> +<dd><p>The axis title for the x axis. Defaults to "Concentration in" <code>unit</code>.</p></dd> + + <dt>ylab</dt> +<dd><p>The axis title for the y axis. Defaults to "Normalized response".</p></dd> + + <dt>axes</dt> +<dd><p>Specifies if axes should be drawn. Default is TRUE, as in + <code><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot.default</a></code></p></dd> + + <dt>frame.plot</dt> +<dd><p>Specifies if the plot should be framed. Default is TRUE, as in + <code><a href="https://rdrr.io/r/graphics/plot.default.html" class="external-link">plot.default</a></code></p></dd> + + <dt>postscript</dt> +<dd><p>If TRUE, (a) postscript graph(s) will be created. Otherwise, and if the pdf and png arguments are also FALSE, graphics will be - displayed with a screen graphics device.</p></td> - </tr> - <tr> - <th>pdf</th> - <td><p>If TRUE, (a) pdf graph(s) will be created. Otherwise, and if + displayed with a screen graphics device.</p></dd> + + <dt>pdf</dt> +<dd><p>If TRUE, (a) pdf graph(s) will be created. Otherwise, and if the postscript, and png arguments are also FALSE, graphics will be - displayed with a screen graphics device.</p></td> - </tr> - <tr> - <th>png</th> - <td><p>If TRUE, (a) png graph(s) will be created. Otherwise, and if the + displayed with a screen graphics device.</p></dd> + + <dt>png</dt> +<dd><p>If TRUE, (a) png graph(s) will be created. Otherwise, and if the postscript and pdf arguments are also FALSE, graphics will be displayed - with a screen graphics device.</p></td> - </tr> - <tr> - <th>bw</th> - <td><p>A boolean deciding if the plots will be black and white or not. Default - is TRUE.</p></td> - </tr> - <tr> - <th>pointsize</th> - <td><p>The pointsize used for pdf, png and postscript graphics.</p></td> - </tr> - <tr> - <th>colors</th> - <td><p>This is a vector of colors, defaulting to 1:8, used for plotting the data.</p></td> - </tr> - <tr> - <th>ltys</th> - <td><p>This is a vector of line types for the dose-response models, defaulting to 1:8.</p></td> - </tr> - <tr> - <th>pchs</th> - <td><p>This is a vector of character types for the data. The default uses built-in + with a screen graphics device.</p></dd> + + <dt>bw</dt> +<dd><p>A boolean deciding if the plots will be black and white or not. Default + is TRUE.</p></dd> + + <dt>pointsize</dt> +<dd><p>The pointsize used for pdf, png and postscript graphics.</p></dd> + + <dt>colors</dt> +<dd><p>This is a vector of colors, defaulting to 1:8, used for plotting the data.</p></dd> + + <dt>ltys</dt> +<dd><p>This is a vector of line types for the dose-response models, defaulting to 1:8.</p></dd> + + <dt>pchs</dt> +<dd><p>This is a vector of character types for the data. The default uses built-in characters 1:n with n being the number of substances for which data are plotted - for overlays, or always 1 when no overlay plot is generated.</p></td> - </tr> - <tr> - <th>lpos</th> - <td><p>An optional argument defaulting to "topright" specifying the position + for overlays, or always 1 when no overlay plot is generated.</p></dd> + + <dt>lpos</dt> +<dd><p>An optional argument defaulting to "topright" specifying the position of the legend by being passed to the legend function. See the help for the - legend function for all possiblities.</p></td> - </tr> - <tr> - <th>devoff</th> - <td><p>If set to FALSE, the device will not be closed after creation of an overlay - pdf, png or postscript graph, so texts and other elements can - be added.</p></td> - </tr> - </table> + legend function for all possiblities.</p></dd> - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + <dt>devoff</dt> +<dd><p>If set to FALSE, the device will not be closed after creation of an overlay + pdf, png or postscript graph, so texts and other elements can + be added.</p></dd> - <p></p> -<dt>results</dt><dd><p>You will get plots of data and/or the fitted dose-response curves, on the +</dl></div> + <div id="value"> + <h2>Value</h2> + <dl><dt>results</dt> +<dd><p>You will get plots of data and/or the fitted dose-response curves, on the screen and/or as postscript/pdf/png files, depending on the parameters.</p></dd> - <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> - +</dl></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="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'><a href='drfit.html'>drfit</a></span>(<span class='no'>antifoul</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'>drplot</span>(<span class='no'>r</span>,<span class='no'>antifoul</span>)</div><div class='img'><img src='drplot-1.png' alt='' width='700' height='433' /></div><div class='img'><img src='drplot-2.png' alt='' width='700' height='433' /></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="#examples">Examples</a></li> - </ul> - + <code>demo(dataset)</code></p> + </div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke - <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a></p> + <a href="mailto:jranke@uni-bremen.de">jranke@uni-bremen.de</a></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"><a href="drfit.html">drfit</a></span><span class="op">(</span><span class="va">antifoul</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> Waiting for profiling to be done...</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-msg co"><span class="r-pr">#></span> Waiting for profiling to be done...</span> +<span class="r-in"><span><span class="fu">drplot</span><span class="op">(</span><span class="va">r</span>,<span class="va">antifoul</span><span class="op">)</span></span></span> +<span class="r-plt img"><img src="drplot-1.png" alt="" width="700" height="433"></span> +<span class="r-plt img"><img src="drplot-2.png" alt="" width="700" height="433"></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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- </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="contents col-md-9"> <div class="page-header"> <h1>Reference</h1> </div> - <table class="ref-index"> - - <colgroup> - - <col class="alias" /> - <col class="title" /> - </colgroup> - - <tbody> - <tr> - <th colspan="2"> - <h2 id="section-main-functions" class="hasAnchor"><a href="#section-main-functions" class="anchor"></a>Main functions</h2> + <table class="ref-index"><colgroup><col class="alias"><col class="title"></colgroup><tbody><tr><th colspan="2"> + <h2 id="main-functions">Main functions <a href="#main-functions" class="anchor" aria-hidden="true"></a></h2> <p class="section-desc"></p> </th> - </tr> - <tr> - - <td> + </tr></tbody><tbody><tr><td> <p><code><a href="drfit.html">drfit()</a></code> </p> </td> <td><p>Fit dose-response models</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="drcfit.html">drcfit()</a></code> </p> </td> <td><p>Fit dose-response models using the drc package</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="drplot.html">drplot()</a></code> </p> </td> <td><p>Plot dose-response models</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-get-and-check-data-from-a-drfit-database" class="hasAnchor"><a href="#section-get-and-check-data-from-a-drfit-database" class="anchor"></a>Get and check data from a drfit database</h2> - <p class="section-desc"><p>These functions only work if you have such a database</p></p> + </tr></tbody><tbody><tr><th colspan="2"> + <h2 id="get-and-check-data-from-a-drfit-database">Get and check data from a drfit database <a href="#get-and-check-data-from-a-drfit-database" class="anchor" aria-hidden="true"></a></h2> + <p class="section-desc"></p><p>These functions only work if you have such a database</p> </th> - </tr> - <tr> - - <td> + </tr></tbody><tbody><tr><td> <p><code><a href="checkcontrols.html">checkcontrols()</a></code> </p> </td> <td><p>Check raw data from range of plates or experiments</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="checkexperiment.html">checkplate()</a></code> <code><a href="checkexperiment.html">checkexperiment()</a></code> </p> </td> <td><p>Check raw data from a specified experiment or microtiter plate</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="drdata.html">drdata()</a></code> </p> </td> <td><p>Get dose-response data via RODBC</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-datasets-and-example-evaluations" class="hasAnchor"><a href="#section-datasets-and-example-evaluations" class="anchor"></a>Datasets and example evaluations</h2> + </tr></tbody><tbody><tr><th colspan="2"> + <h2 id="datasets-and-example-evaluations">Datasets and example evaluations <a href="#datasets-and-example-evaluations" class="anchor" aria-hidden="true"></a></h2> <p class="section-desc"></p> </th> - </tr> - <tr> - - <td> + </tr></tbody><tbody><tr><td> <p><code><a href="antifoul.html">antifoul</a></code> </p> </td> <td><p>Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="IM1xIPC81.html">IM1xIPC81</a></code> </p> </td> <td><p>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="IM1xVibrio.html">IM1xVibrio</a></code> </p> </td> <td><p>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in V. fischeri</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="pyrithione.html">pyrithione</a></code> </p> </td> <td><p>Cytotoxicity data for different pyrithionates and related species</p></td> - </tr><tr> - - <td> + </tr><tr><td> <p><code><a href="XY.html">XY</a></code> </p> </td> <td><p>Dose-Response data for two substances X and Y</p></td> - </tr> - </tbody><tbody> - <tr> - <th colspan="2"> - <h2 id="section-helper-functions" class="hasAnchor"><a href="#section-helper-functions" class="anchor"></a>Helper functions</h2> + </tr></tbody><tbody><tr><th colspan="2"> + <h2 id="helper-functions">Helper functions <a href="#helper-functions" class="anchor" aria-hidden="true"></a></h2> <p class="section-desc"></p> </th> - </tr> - <tr> - - <td> + </tr></tbody><tbody><tr><td> <p><code><a href="linlogitf.html">linlogitf()</a></code> </p> </td> <td><p>Linear-logistic function</p></td> - </tr> - </tbody> - </table> - </div> + </tr></tbody></table></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="#section-main-functions">Main functions</a></li> - <li><a href="#section-get-and-check-data-from-a-drfit-database">Get and check data from a drfit database</a></li> - <li><a href="#section-datasets-and-example-evaluations">Datasets and example evaluations</a></li> - <li><a href="#section-helper-functions">Helper functions</a></li> - </ul> - </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> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - 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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>Linear-logistic function</h1> @@ -111,73 +45,66 @@ at subtoxic doses.</p> </div> - <pre class="usage"><span class='fu'>linlogitf</span>(<span class='no'>x</span>,<span class='no'>k</span>,<span class='no'>f</span>,<span class='no'>mu</span>,<span class='no'>b</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>x</th> - <td><p>In this context, the x variable is the dose.</p></td> - </tr> - <tr> - <th>k</th> - <td><p>In the drfit functions, k is set to 1.</p></td> - </tr> - <tr> - <th>f</th> - <td><p>One of the parameters describing the curve shape.</p></td> - </tr> - <tr> - <th>mu</th> - <td><p>The parameter describing the location of the curve (log ED50).</p></td> - </tr> - <tr> - <th>b</th> - <td><p>One of the parameters describing the curve shape.</p></td> - </tr> - </table> - - <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - - <p>The response at dose x.</p> - <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">linlogitf</span><span class="op">(</span><span class="va">x</span>,<span class="va">k</span>,<span class="va">f</span>,<span class="va">mu</span>,<span class="va">b</span><span class="op">)</span></span></code></pre></div> + </div> + + <div id="arguments"> + <h2>Arguments</h2> + <dl><dt>x</dt> +<dd><p>In this context, the x variable is the dose.</p></dd> - <p>van Ewijk, P. H. and Hoekstra, J. A. (1993) <em>Ecotox Environ Safety</em> - <b>25</b> 25-32</p> + <dt>k</dt> +<dd><p>In the drfit functions, k is set to 1.</p></dd> - </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="#references">References</a></li> - </ul> + <dt>f</dt> +<dd><p>One of the parameters describing the curve shape.</p></dd> + + <dt>mu</dt> +<dd><p>The parameter describing the location of the curve (log ED50).</p></dd> + <dt>b</dt> +<dd><p>One of the parameters describing the curve shape.</p></dd> + +</dl></div> + <div id="value"> + <h2>Value</h2> + + +<p>The response at dose x.</p> + </div> + <div id="references"> + <h2>References</h2> + <p>van Ewijk, P. H. and Hoekstra, J. A. (1993) <em>Ecotox Environ Safety</em> + <b>25</b> 25-32</p> + </div> + <div id="author"> <h2>Author</h2> <p>Johannes Ranke - <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a></p> + <a href="mailto:jranke@uni-bremen.de">jranke@uni-bremen.de</a></p> + </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> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> diff --git a/docs/reference/pyrithione.html b/docs/reference/pyrithione.html index 0175c25..cc8668e 100644 --- a/docs/reference/pyrithione.html +++ b/docs/reference/pyrithione.html @@ -1,66 +1,14 @@ -<!-- Generated by pkgdown: do not edit by hand --> <!DOCTYPE html> -<html lang="en"> - 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IPC-81 cell line." /> -<meta name="twitter:card" content="summary" /> - - - - -<!-- mathjax --> -<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]> + IPC-81 cell line."><!-- mathjax --><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> <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script> -<![endif]--> - - - - </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"> @@ -71,35 +19,21 @@ </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>Cytotoxicity data for different pyrithionates and related species</h1> @@ -113,51 +47,49 @@ IPC-81 cell line.</p> </div> - <pre class="usage"><span class='fu'><a href='https://rdrr.io/r/utils/data.html'>data</a></span>(<span class='no'>pyrithione</span>)</pre> - - - <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2> + <div id="ref-usage"> + <div class="sourceCode"><pre class="sourceCode r"><code><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">pyrithione</span><span class="op">)</span></span></code></pre></div> + </div> - <p>A dataframe containing the data as required for the <code><a href='drfit.html'>drfit</a></code> + <div id="format"> + <h2>Format</h2> + <p>A dataframe containing the data as required for the <code><a href="drfit.html">drfit</a></code> function.</p> - <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> - + </div> + <div id="source"> + <h2>Source</h2> <p>Doose C, Ranke J, Stock F, Bottin-Weber U, Jastorff B (2004) Structure-activity relationships of pyrithiones - IPC-81 toxicity tests with antifouling biocide zinc pyrithione and structural analogues. Green Chemistry 6(5) 259-266</p> + </div> - <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"><div class='input'> <span class='kw'>if</span> (<span class='fl'>FALSE</span>) <span class='fu'><a href='https://rdrr.io/r/utils/demo.html'>demo</a></span>(<span class='no'>pyrithione</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="#format">Format</a></li> - <li><a href="#source">Source</a></li> - <li><a href="#examples">Examples</a></li> - </ul> - + <div id="ref-examples"> + <h2>Examples</h2> + <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span> <span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/utils/demo.html" class="external-link">demo</a></span><span class="op">(</span><span class="va">pyrithione</span><span class="op">)</span></span></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> - <footer> - <div class="copyright"> - <p>Developed by Johannes Ranke.</p> + <footer><div class="copyright"> + <p></p><p>Developed by Johannes Ranke.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p> + <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p> </div> - </footer> - </div> + </footer></div> - </body> -</html> + + </body></html> |
