From 9b36a3d2055d3bfa4844ca43acc232f064856871 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Fri, 31 Mar 2017 12:10:59 +0200
Subject: Further improvement to checkcontrols()
Static documentation rebuilt by pkgdown::build_site()
---
docs/reference/IM1xIPC81.html | 196 ++++++++++++++++++++++++++++++
docs/reference/IM1xVibrio.html | 233 ++++++++++++++++++++++++++++++++++++
docs/reference/XY.html | 121 +++++++++++++++++++
docs/reference/antifoul.html | 4 +-
docs/reference/checkcontrols.html | 25 ++--
docs/reference/checkexperiment.html | 4 +-
docs/reference/checksubstance.html | 8 +-
docs/reference/drcfit.html | 12 +-
docs/reference/drdata.html | 8 +-
docs/reference/drfit.html | 13 +-
docs/reference/drplot.html | 14 +--
docs/reference/linlogitf.html | 149 +++++++++++++++++++++++
docs/reference/pyrithione.html | 125 +++++++++++++++++++
13 files changed, 873 insertions(+), 39 deletions(-)
create mode 100644 docs/reference/IM1xIPC81.html
create mode 100644 docs/reference/IM1xVibrio.html
create mode 100644 docs/reference/XY.html
create mode 100644 docs/reference/linlogitf.html
create mode 100644 docs/reference/pyrithione.html
(limited to 'docs/reference')
diff --git a/docs/reference/IM1xIPC81.html b/docs/reference/IM1xIPC81.html
new file mode 100644
index 0000000..6ab98e7
--- /dev/null
+++ b/docs/reference/IM1xIPC81.html
@@ -0,0 +1,196 @@
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+ <div class="page-header">
+ <h1>Dose-Response data for 1-methyl-3-alkylimidazolium tetrafluoroborates in IPC-81 cells</h1>
+ </div>
+
+
+ <p>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
+ 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.
+ This is a subset (only the BF4 anion) of the data
+ shown in Figure 3 in Ranke et al. (2004).</p>
+
+
+ <pre><span class='fu'>data</span>(<span class='no'>IM1xIPC81</span>)</pre>
+
+ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>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
+ the tested organism (name of the cell line).</p>
+
+ <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>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>
+
+
+ <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'>print</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'>print</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>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
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diff --git a/docs/reference/IM1xVibrio.html b/docs/reference/IM1xVibrio.html
new file mode 100644
index 0000000..79c3d95
--- /dev/null
+++ b/docs/reference/IM1xVibrio.html
@@ -0,0 +1,233 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
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+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
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+
+<!-- Font Awesome icons -->
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+
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+
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+
+ <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>
+ </div>
+
+
+ <p>This is the raw data documenting the influence of the alkyl chain length in 3
+ position on the toxicity to the marine luminescent bacteria <em>V.
+ fischeri</em>. 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.</p>
+
+
+ <pre><span class='fu'>data</span>(<span class='no'>IM1xVibrio</span>)</pre>
+
+ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>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>
+
+ <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>
+
+
+ <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'>c</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'>print</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'>c</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'>print</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>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/XY.html b/docs/reference/XY.html
new file mode 100644
index 0000000..a585270
--- /dev/null
+++ b/docs/reference/XY.html
@@ -0,0 +1,121 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Dose-Response data for two substances X and Y — XY • drfit</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
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+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
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+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+<!-- mathjax -->
+<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
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+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
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+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">drfit</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+ </ul>
+
+ <ul class="nav navbar-nav navbar-right">
+
+ </ul>
+ </div><!--/.nav-collapse -->
+ </div><!--/.container -->
+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Dose-Response data for two substances X and Y</h1>
+ </div>
+
+
+ <p>This is just a sample Lemna growth rate data set for two substances
+ arbitrarily named X and Y.</p>
+
+
+ <pre><span class='fu'>data</span>(<span class='no'>XY</span>)</pre>
+
+ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
+
+ <p>A dataframe containing dose (concentration) and response data, as well as
+ control values where the dose is zero.</p>
+
+ <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
+
+ <p><a href = 'http://www.uft.uni-bremen.de/chemie'>http://www.uft.uni-bremen.de/chemie</a></p>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'> <span class='co'>## Not run: demo(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="#source">Source</a></li>
+
+ <li><a href="#examples">Examples</a></li>
+ </ul>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
+ </div>
+
+ </body>
+</html>
diff --git a/docs/reference/antifoul.html b/docs/reference/antifoul.html
index f5bc9fd..92fd8e8 100644
--- a/docs/reference/antifoul.html
+++ b/docs/reference/antifoul.html
@@ -72,9 +72,9 @@
</div>
- <p>This data set shows the response of the rat leukaemic cell line IPC-81 to
+ <p>This data set shows the response of the rat leukaemic cell line IPC-81 to
dilution series of tributyltin chloride (TBT) and Zink Pyrithione as retrieved
- from the "cytotox" database of the UFT Department of Bioorganic Chemistry on
+ from the "cytotox" database of the UFT Department of Bioorganic Chemistry on
February 25, 2004</p>
diff --git a/docs/reference/checkcontrols.html b/docs/reference/checkcontrols.html
index 2b2eb8b..0e89c93 100644
--- a/docs/reference/checkcontrols.html
+++ b/docs/reference/checkcontrols.html
@@ -76,7 +76,9 @@
experiments from a specified database.</p>
- <pre><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='st'>"cytotox"</span>, <span class='kw'>organism</span> <span class='kw'>=</span> <span class='st'>"Vibrio fischeri"</span>,
+ <pre><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='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'>"%"</span>, <span class='kw'>qcc</span> <span class='kw'>=</span> <span class='fu'>c</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>
@@ -98,10 +100,19 @@
"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>The organism that was exposed to the chemical. Only important if the database
- "ecotox" is used. Defaults to "Vibrio fischeri".</p></td>
+ <td><p>Only important if database "ecotox" is used.</p></td>
</tr>
<tr>
<th>endpoint</th>
@@ -110,8 +121,8 @@
</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
+ <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>
@@ -136,8 +147,8 @@
<h2>Author</h2>
- Johannes Ranke
- <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a>
+ Johannes Ranke
+ <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a>
<a href = 'http://www.uft.uni-bremen.de/chemie/ranke'>http://www.uft.uni-bremen.de/chemie/ranke</a>
</div>
diff --git a/docs/reference/checkexperiment.html b/docs/reference/checkexperiment.html
index e22705d..277bfd5 100644
--- a/docs/reference/checkexperiment.html
+++ b/docs/reference/checkexperiment.html
@@ -120,8 +120,8 @@
<h2>Author</h2>
- Johannes Ranke
- <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a>
+ Johannes Ranke
+ <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a>
<a href = 'http://www.uft.uni-bremen.de/chemie/ranke'>http://www.uft.uni-bremen.de/chemie/ranke</a>
</div>
diff --git a/docs/reference/checksubstance.html b/docs/reference/checksubstance.html
index 0fbca62..60ae6e3 100644
--- a/docs/reference/checksubstance.html
+++ b/docs/reference/checksubstance.html
@@ -122,12 +122,12 @@
</tr>
<tr>
<th>whereClause</th>
- <td><p>With this argument, additional conditions for the SQL query can be set,
+ <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
+ <td><p>With the default value "%", all data in the database is retrieved for the
specified substance.</p></td>
</tr>
</table>
@@ -153,8 +153,8 @@
<h2>Author</h2>
- Johannes Ranke
- <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a>
+ Johannes Ranke
+ <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a>
<a href = 'http://www.uft.uni-bremen.de/chemie/ranke'>http://www.uft.uni-bremen.de/chemie/ranke</a>
</div>
diff --git a/docs/reference/drcfit.html b/docs/reference/drcfit.html
index 75a168a..e7de303 100644
--- a/docs/reference/drcfit.html
+++ b/docs/reference/drcfit.html
@@ -165,10 +165,10 @@
<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
+ 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.
+ <dt>low %</dt><dd><p>The lower bound of the confidence interval of log ED50.
The name of the column depends on the requested confidence <code>level</code>.</p></dd>
<dt>high %</dt><dd><p>The higher bound of the confidence interval of log ED50.
The name of the column depends on the requested confidence <code>level</code>.</p></dd>
@@ -176,11 +176,11 @@
<dt>sigma</dt><dd><p>The square root of the estimated variance of the random error as returned
by <code>summary.drc</code>.</p></dd>
<dt>a</dt><dd><p>For the linlogit model, this is the parameter e from <code>BC.4</code>.
- For the probit and the logit model, this is the ED50. For the weibull
- model, this is parameter e from <code>W1.2</code>. Note that the Weibull
+ For the probit and the logit model, this is the ED50. For the weibull
+ model, this is parameter e from <code>W1.2</code>. Note that the Weibull
model is fitted to the untransformed data.</p></dd>
<dt>b</dt><dd><p>For the linlogit, probit, logit and weibull models, these are the
- parameters b from <code>BC.4</code>, <code>LN.2</code>,
+ parameters b from <code>BC.4</code>, <code>LN.2</code>,
<code>LL.2</code> and <code>W1.2</code>, respectively.
Note that the parameter definitions (and in the case of Weibull, the model
used) are different to the ones used in <code>drfit</code>.</p></dd>
@@ -236,7 +236,7 @@
<h2>Author</h2>
- Johannes Ranke <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a>
+ Johannes Ranke <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a>
<a href = 'http://www.uft.uni-bremen.de/chemie/ranke'>http://www.uft.uni-bremen.de/chemie/ranke</a>
The functionality of the drc package used under the hood in this function
was written by Christian Ritz.
diff --git a/docs/reference/drdata.html b/docs/reference/drdata.html
index e369c5c..dd5be7b 100644
--- a/docs/reference/drdata.html
+++ b/docs/reference/drdata.html
@@ -95,7 +95,7 @@
<tr>
<th>db</th>
<td><p>The database to be used. Currently, the databases "cytotox", "enzymes"
- and "ecotox" of the UFT Department of Bioorganic Chemistry are
+ and "ecotox" of the UFT Department of Bioorganic Chemistry are
supported (default is "cytotox").</p></td>
</tr>
<tr>
@@ -119,7 +119,7 @@
</tr>
<tr>
<th>whereClause</th>
- <td><p>With this argument, additional conditions for the SQL query can be set,
+ <td><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>
@@ -222,8 +222,8 @@
<h2>Author</h2>
- Johannes Ranke
- <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a>
+ Johannes Ranke
+ <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a>
<a href = 'http://www.uft.uni-bremen.de/chemie/ranke'>http://www.uft.uni-bremen.de/chemie/ranke</a>
</div>
diff --git a/docs/reference/drfit.html b/docs/reference/drfit.html
index 7acce23..2de949f 100644
--- a/docs/reference/drfit.html
+++ b/docs/reference/drfit.html
@@ -196,9 +196,8 @@
parameter <code>a</code> that is reported coincides with the logED50, i.e the
logED50 is one of the model parameters that is being fitted. Therefore,
a confidence interval for the confidence level <code>level</code> is calculated
- using the <code>confint.nls</code> function and listed.
-
- The following variables are in the dataframe:</p>
+ 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>
@@ -207,10 +206,10 @@
<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
+ 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.
+ <dt>low %</dt><dd><p>The lower bound of the confidence interval of log ED50.
The name of the column depends on the requested confidence <code>level</code>.</p></dd>
<dt>high %</dt><dd><p>The higher bound of the confidence interval of log ED50.
The name of the column depends on the requested confidence <code>level</code>.</p></dd>
@@ -277,8 +276,8 @@
<h2>Author</h2>
- Johannes Ranke
- <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a>
+ Johannes Ranke
+ <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a>
<a href = 'http://www.uft.uni-bremen.de/chemie/ranke'>http://www.uft.uni-bremen.de/chemie/ranke</a>
</div>
diff --git a/docs/reference/drplot.html b/docs/reference/drplot.html
index eff1338..9a678e1 100644
--- a/docs/reference/drplot.html
+++ b/docs/reference/drplot.html
@@ -72,7 +72,7 @@
</div>
- <p>Produce graphics of dose-response data and dose-response relationships
+ <p>Produce graphics of dose-response data and dose-response relationships
either combined or separately, for one or more substances.</p>
@@ -110,7 +110,7 @@
</tr>
<tr>
<th>ctype</th>
- <td><p>This argument decides if horizontal lines are drawn to show the scatter of
+ <td><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
@@ -159,13 +159,13 @@
</tr>
<tr>
<th>postscript</th>
- <td><p>If TRUE, (a) postscript graph(s) will be created. Otherwise, and if
+ <td><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
+ <td><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>
@@ -177,7 +177,7 @@
</tr>
<tr>
<th>bw</th>
- <td><p>A boolean deciding if the plots will be black and white or not. Default
+ <td><p>A boolean deciding if the plots will be black and white or not. Default
is TRUE.</p></td>
</tr>
<tr>
@@ -245,8 +245,8 @@
<h2>Author</h2>
- Johannes Ranke
- <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a>
+ Johannes Ranke
+ <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a>
<a href = 'http://www.uft.uni-bremen.de/chemie/ranke'>http://www.uft.uni-bremen.de/chemie/ranke</a>
</div>
diff --git a/docs/reference/linlogitf.html b/docs/reference/linlogitf.html
new file mode 100644
index 0000000..8b9ba0d
--- /dev/null
+++ b/docs/reference/linlogitf.html
@@ -0,0 +1,149 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+
+<title>Linear-logistic function — linlogitf • drfit</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
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+
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+
+
+<!-- pkgdown -->
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+<script src="../pkgdown.js"></script>
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+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+ </head>
+
+ <body>
+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
+ <div class="container">
+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">drfit</a>
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+
+ </ul>
+ </div><!--/.nav-collapse -->
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+
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+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Linear-logistic function</h1>
+ </div>
+
+
+ <p>Helper function describing a special type of dose-response curves, showing a stimulus
+ at subtoxic doses.</p>
+
+
+ <pre><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>
+
+ <p>van Ewijk, P. H. and Hoekstra, J. A. (1993) <em>Ecotox Environ Safety</em>
+ <b>25</b> 25-32</p>
+
+
+ </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>
+
+ <h2>Author</h2>
+
+ Johannes Ranke
+ <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a>
+ <a href = 'http://www.uft.uni-bremen.de/chemie/ranke'>http://www.uft.uni-bremen.de/chemie/ranke</a>
+
+ </div>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
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+
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+</html>
diff --git a/docs/reference/pyrithione.html b/docs/reference/pyrithione.html
new file mode 100644
index 0000000..7496be2
--- /dev/null
+++ b/docs/reference/pyrithione.html
@@ -0,0 +1,125 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+ <head>
+ <meta charset="utf-8">
+<meta http-equiv="X-UA-Compatible" content="IE=edge">
+<meta name="viewport" content="width=device-width, initial-scale=1.0">
+
+<title>Cytotoxicity data for different pyrithionates and related species — pyrithione • drfit</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
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+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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+
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+
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+
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+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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+ </head>
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+ <div class="container template-reference-topic">
+ <header>
+ <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+ <div class="navbar-header">
+ <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ <span class="icon-bar"></span>
+ </button>
+ <a class="navbar-brand" href="../index.html">drfit</a>
+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
+ </ul>
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+
+ </ul>
+ </div><!--/.nav-collapse -->
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+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <div class="page-header">
+ <h1>Cytotoxicity data for different pyrithionates and related species</h1>
+ </div>
+
+
+ <p>This data shows the cytotoxicity of pyrithione salts as well as the free
+ pyrithione, its oxidation product and some other related compounds to the
+ IPC-81 cell line.</p>
+
+
+ <pre><span class='fu'>data</span>(<span class='no'>pyrithione</span>)</pre>
+
+ <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>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>
+
+ <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>
+
+
+ <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+ <pre class="examples"><div class='input'> <span class='co'>## Not run: demo(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>
+</div>
+
+ <footer>
+ <div class="copyright">
+ <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+ <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+ </footer>
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+
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+</html>
--
cgit v1.2.1