Add pkgdown docu, change package build directory

author: Johannes Ranke <jranke@uni-bremen.de> 2017-03-24 15:22:07 +0100
committer: Johannes Ranke <jranke@uni-bremen.de> 2017-03-24 15:22:07 +0100
commit: ae13a2e7f373f697cdfb6acb7ae042d6e27d8967 (patch)
tree: 61bc66f752a81e9d50becf173d138ca9dfa80778
parent: cd9d3e214233b0a6862200f60bf70a4214bc2115 (diff)
18 files changed, 2400 insertions, 7 deletions
diff --git a/GNUmakefile b/GNUmakefile
index 64aa9d4..6b5e68c 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -1,7 +1,7 @@
 PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
 PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
 PKGSRC  := $(shell basename $(PWD))
-TGZ     := ../$(PKGNAME)_$(PKGVERS).tar.gz
+TGZ     := $(PKGNAME)_$(PKGVERS).tar.gz
 
 # Specify the directory holding R binaries. To use an alternate R build (say a
 # pre-prelease version) use `make RBIN=/path/to/other/R/` or `export RBIN=...`
@@ -10,16 +10,18 @@ TGZ     := ../$(PKGNAME)_$(PKGVERS).tar.gz
 RBIN ?= $(shell dirname "`which R`")
 
 build:
-	cd ..;\
-		"$(RBIN)/R" CMD build $(PKGSRC)
+	"$(RBIN)/R" CMD build .
 
 install: build
-	cd ..;\
-		"$(RBIN)/R" CMD INSTALL $(PKGNAME)_$(PKGVERS).tar.gz
+	"$(RBIN)/R" CMD INSTALL $(TGZ)
 
 check: build
-	cd ..;\
-		"$(RBIN)/R" CMD check --as-cran $(PKGNAME)_$(PKGVERS).tar.gz
+	"$(RBIN)/R" CMD check --as-cran $(TGZ)
+
+pd:
+	"$(RBIN)/Rscript" -e "pkgdown::build_site()"
+	git add -A
+	git commit -m 'Static documentation rebuilt by pkgdown::build_site()' -e
 
 winbuilder: build
 	@echo "Uploading to R-release on win-builder"
diff --git a/docs/authors.html b/docs/authors.html
new file mode 100644
index 0000000..3db937a
--- /dev/null
+++ b/docs/authors.html
@@ -0,0 +1,99 @@
+<!-- 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>Authors • drfit</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script>
+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="pkgdown.css" rel="stylesheet">
+<script src="jquery.sticky-kit.min.js"></script>
+<script src="pkgdown.js"></script>
+
+<!-- mathjax -->
+<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
+  </head>
+
+  <body>
+    <div class="container template-authors">
+      <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="contents col-md-12">
+    <div class="page-header">
+      <h1>Authors</h1>
+    </div>
+
+    <ul class="list-unstyled">
+      <li>
+        <p><strong>Johannes Ranke</strong>. Author, maintainer.
+        </p>
+      </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/index.html b/docs/index.html
new file mode 100644
index 0000000..3ad6d4a
--- /dev/null
+++ b/docs/index.html
@@ -0,0 +1,88 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html>
+<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 Evaluation • drfit</title>
+<!-- jquery --><script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
+<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha384-Tc5IQib027qvyjSMfHjOMaLkfuWVxZxUPnCJA7l2mCWNIpG9mGCD8wGNIcPD7Txa" crossorigin="anonymous"></script><!-- Font Awesome icons --><link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+<!-- pkgdown --><link href="pkgdown.css" rel="stylesheet">
+<script src="jquery.sticky-kit.min.js"></script><script src="pkgdown.js"></script><!-- mathjax --><script src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script><!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+</head>
+<body>
+    <div class="container template-home">
+      <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="contents col-md-9">
+    A somewhat outdated package of basic and easy-to-use functions for
+  fitting dose-response curves to continuous dose-response data, calculating some
+  (eco)toxicological parameters and plotting the results. Please consider using
+  the more powerful and actively developed 'drc' package.  Functions that are
+  fitted are the cumulative density function of the lognormal distribution
+  (probit fit), of the logistic distribution (logit fit), of the weibull
+  distribution (weibull fit) and a linear-logistic model ("linlogit" fit),
+  derived from the latter, which is used to describe data showing stimulation at
+  low doses (hormesis). In addition, functions checking, plotting and retrieving
+  dose-response data retrieved from a database accessed via RODBC are included.
+  As an alternative to the original fitting methods, the algorithms from the drc
+  package can be used.
+  </div>
+
+  <div class="col-md-3" id="sidebar">
+    <h2>Links</h2>
+<ul class="list-unstyled">
+<li>Download from CRAN at <br><a href="https://cran.r-project.org/package=drfit">https://cran.r-project.org/package=drfit</a>
+</li>
+</ul>
+<h2>License</h2>
+<p>GPL (&gt;= 2)</p>
+<h2>Developers</h2>
+<ul class="list-unstyled">
+<li>Johannes Ranke <br><small class="roles"> Author, maintainer </small> </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/jquery.sticky-kit.min.js b/docs/jquery.sticky-kit.min.js
new file mode 100644
index 0000000..e2a3c6d
--- /dev/null
+++ b/docs/jquery.sticky-kit.min.js
@@ -0,0 +1,9 @@
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+ Sticky-kit v1.1.2 | WTFPL | Leaf Corcoran 2015 | http://leafo.net
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diff --git a/docs/link.svg b/docs/link.svg
new file mode 100644
index 0000000..88ad827
--- /dev/null
+++ b/docs/link.svg
@@ -0,0 +1,12 @@
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diff --git a/docs/pkgdown.css b/docs/pkgdown.css
new file mode 100644
index 0000000..e704e06
--- /dev/null
+++ b/docs/pkgdown.css
@@ -0,0 +1,137 @@
+/* Sticker footer */
+body > .container {
+  display: flex;
+  padding-top: 60px;
+  min-height: calc(100vh);
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+}
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+}
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+}
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+}
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+}
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+}
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+.contents h1, .contents h2, .contents h3, .contents h4 {
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+  margin-top: -60px;
+}
+
+/* Sidebar --------------------------*/
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+  margin-top: 30px;
+}
+#sidebar h2 {
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+  margin-top: 1em;
+}
+
+#sidebar h2:first-child {
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+}
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+#sidebar .list-unstyled li {
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+}
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+/* Reference index & topics ----------------------------------------------- */
+
+.ref-index th {font-weight: normal;}
+.ref-index h2 {font-size: 20px;}
+
+.ref-index td {vertical-align: top;}
+.ref-index .alias {width: 40%;}
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diff --git a/docs/pkgdown.js b/docs/pkgdown.js
new file mode 100644
index 0000000..c8b38c4
--- /dev/null
+++ b/docs/pkgdown.js
@@ -0,0 +1,8 @@
+$(function() {
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diff --git a/docs/reference/antifoul.html b/docs/reference/antifoul.html
new file mode 100644
index 0000000..5a2b886
--- /dev/null
+++ b/docs/reference/antifoul.html
@@ -0,0 +1,160 @@
+<!-- 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 TBT and Zink Pyrithione in IPC-81 cells — antifoul • drfit</title>
+
+<!-- jquery -->
+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></script>
+<!-- Bootstrap -->
+
+<link href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous">
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+
+<!-- Font Awesome icons -->
+<link href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css" rel="stylesheet" integrity="sha384-T8Gy5hrqNKT+hzMclPo118YTQO6cYprQmhrYwIiQ/3axmI1hQomh7Ud2hPOy8SP1" crossorigin="anonymous">
+
+
+<!-- pkgdown -->
+<link href="../pkgdown.css" rel="stylesheet">
+<script src="../jquery.sticky-kit.min.js"></script>
+<script src="../pkgdown.js"></script>
+
+<!-- mathjax -->
+<script src='https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'></script>
+
+<!--[if lt IE 9]>
+<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
+<![endif]-->
+
+
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+
+  <body>
+    <div class="container template-reference-topic">
+      <header>
+      <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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+        <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 TBT and Zink Pyrithione in IPC-81 cells</h1>
+    </div>
+
+    
+    <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 
+  February 25, 2004</p>
+    
+
+    <pre><span class='fu'>data</span>(<span class='no'>antifoul</span>)</pre>
+        
+    <h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>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>
+    
+    <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='no'>rantifoul.ED50</span> <span class='kw'>&lt;-</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'>c</span>(<span class='fl'>10</span>))</div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>TBT: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>Zn Pyrithion: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='input'><span class='fu'>print</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'>#&gt;      Substance ndl   n     lld    lhd    mtype  logED50     2.5%     97.5%
+#&gt; 1          TBT  38 135 -2.7093 2.3979 linlogit -0.15809 -0.26021 -0.050475
+#&gt; 2          TBT  38 135 -2.7093 2.3979   probit -0.16436 -0.26504 -0.056498
+#&gt; 3          TBT  38 135 -2.7093 2.3979    logit -0.16012 -0.26116 -0.052591
+#&gt; 4          TBT  38 135 -2.7093 2.3979  weibull -0.11507       NA        NA
+#&gt; 5 Zn Pyrithion  27  81 -2.1072 2.0000 linlogit -0.41329 -0.52932 -0.299799
+#&gt; 6 Zn Pyrithion  27  81 -2.1072 2.0000   probit -0.39792 -0.50783 -0.291563
+#&gt; 7 Zn Pyrithion  27  81 -2.1072 2.0000    logit -0.40035 -0.51049 -0.293501
+#&gt; 8 Zn Pyrithion  27  81 -2.1072 2.0000  weibull -0.38795       NA        NA
+#&gt;     unit   sigma        a       b         c    ED50 ED50 2.5% ED50 97.5%
+#&gt; 1 microM 0.19264 -0.15809 1.04065 -0.024165 0.69487   0.54927    0.89028
+#&gt; 2 microM 0.19286 -0.16436 0.67637        NA 0.68493   0.54320    0.87801
+#&gt; 3 microM 0.19199 -0.16012 0.41358        NA 0.69164   0.54808    0.88595
+#&gt; 4 microM 0.18810  0.63743 1.28891        NA 0.76724        NA         NA
+#&gt; 5 microM 0.22878 -0.41329 1.74249  0.610810 0.38611   0.29558    0.50142
+#&gt; 6 microM 0.22866 -0.39792 0.41696        NA 0.40002   0.31058    0.51102
+#&gt; 7 microM 0.22802 -0.40035 0.25395        NA 0.39779   0.30868    0.50874
+#&gt; 8 microM 0.23008  0.47647 2.51561        NA 0.40931        NA         NA
+#&gt;      EDx10
+#&gt; 1 0.085214
+#&gt; 2 0.093077
+#&gt; 3 0.085340
+#&gt; 4 0.053392
+#&gt; 5 0.120232
+#&gt; 6 0.116872
+#&gt; 7 0.110068
+#&gt; 8 0.121166</div><div class='input'>
+<span class='no'>rantifoul.drc</span> <span class='kw'>&lt;-</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'>c</span>(<span class='fl'>10</span>))</div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>TBT: Fitting data...</span></div><div class='output co'>#&gt; <span class='error'>Error in ED50["1:50", "Lower"]: Indizierung außerhalb der Grenzen</span></div><div class='input'><span class='fu'>print</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'>#&gt; <span class='error'>Error in print(rantifoul.drc, digits = 5): Objekt 'rantifoul.drc' nicht gefunden</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/checkcontrols.html b/docs/reference/checkcontrols.html
new file mode 100644
index 0000000..2b2eb8b
--- /dev/null
+++ b/docs/reference/checkcontrols.html
@@ -0,0 +1,159 @@
+<!-- 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>Check raw data from range of plates or experiments — checkcontrols • 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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+
+<!-- Font Awesome icons -->
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+
+
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+  <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>Check raw data from range of plates or experiments</h1>
+    </div>
+
+    
+    <p>Report control data from a specified range of microtiter plates or
+  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>,
+                <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>
+    <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
+    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
+    "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>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 "%".</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>
+    
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p>The function lists a report and shows two graphs.</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: checkcontrols(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>
+
+    <h2>Author</h2>
+    
+  Johannes Ranke 
+  <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> 
+  <a href = 'http://www.uft.uni-bremen.de/chemie/ranke'>http://www.uft.uni-bremen.de/chemie/ranke</a>
+
+  </div>
+</div>
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+      </footer>
+   </div>
+
+  </body>
+</html>
diff --git a/docs/reference/checkexperiment.html b/docs/reference/checkexperiment.html
new file mode 100644
index 0000000..e22705d
--- /dev/null
+++ b/docs/reference/checkexperiment.html
@@ -0,0 +1,143 @@
+<!-- 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>Check raw data from a specified experiment or microtiter plate — checkexperiment • 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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+
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+<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
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+
+
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+
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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>Check raw data from a specified experiment or microtiter plate</h1>
+    </div>
+
+    
+    <p>Report metadata from a specified experiment or microtiter plate from a
+  specified database, box plot controls, and plot the dose-response data.</p>
+    
+
+    <pre><span class='fu'>checkplate</span>(<span class='no'>id</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"cytotox"</span>)
+  <span class='fu'>checkexperiment</span>(<span class='no'>id</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"ecotox"</span>, <span class='kw'>endpoint</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>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>
+    </table>
+    
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p>The function lists a report and shows two graphs.</p>
+    
+
+    <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='co'>## Not run: checkplate(3)</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>
+
+    <h2>Author</h2>
+    
+  Johannes Ranke 
+  <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> 
+  <a href = 'http://www.uft.uni-bremen.de/chemie/ranke'>http://www.uft.uni-bremen.de/chemie/ranke</a>
+
+  </div>
+</div>
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+      </footer>
+   </div>
+
+  </body>
+</html>
diff --git a/docs/reference/checksubstance.html b/docs/reference/checksubstance.html
new file mode 100644
index 0000000..0fbca62
--- /dev/null
+++ b/docs/reference/checksubstance.html
@@ -0,0 +1,176 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
+<html>
+  <head>
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+<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+
+<title>Check raw data for a specified substance — checksubstance • drfit</title>
+
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+      <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 -->
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+</div><!--/.navbar -->
+
+      
+      </header>
+
+      <div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Check raw data for a specified substance</h1>
+    </div>
+
+    
+    <p>Report metadata for a specified substance from a specified database, and plot
+  the data.</p>
+    
+
+    <pre><span class='fu'>checksubstance</span>(<span class='no'>substance</span>, <span class='kw'>db</span> <span class='kw'>=</span> <span class='st'>"cytotox"</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.</p></td>
+    </tr>
+    <tr>
+      <th>db</th>
+      <td><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
+    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='co'>## Not run: checksubstance("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>
+
+    <h2>Author</h2>
+    
+  Johannes Ranke 
+  <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> 
+  <a href = 'http://www.uft.uni-bremen.de/chemie/ranke'>http://www.uft.uni-bremen.de/chemie/ranke</a>
+
+  </div>
+</div>
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+      </footer>
+   </div>
+
+  </body>
+</html>
diff --git a/docs/reference/drcfit.html b/docs/reference/drcfit.html
new file mode 100644
index 0000000..ccf4641
--- /dev/null
+++ b/docs/reference/drcfit.html
@@ -0,0 +1,251 @@
+<!-- Generated by pkgdown: do not edit by hand -->
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+  <a href="../reference/index.html">Reference</a>
+</li>
+      </ul>
+      
+      <ul class="nav navbar-nav navbar-right">
+        
+      </ul>
+    </div><!--/.nav-collapse -->
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+</div><!--/.navbar -->
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+      </header>
+
+      <div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Fit dose-response models using the drc package</h1>
+    </div>
+
+    
+    <p>Fit dose-response relationships to dose-response data and calculate
+  biometric results for (eco)toxicity evaluation using the drc package</p>
+    
+
+    <pre><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 &#8220;substance&#8221;, a numeric vector &#8220;dose&#8221;
+    with the dose values, a vector called &#8220;unit&#8221; containing the unit
+    used for the dose and a numeric vector &#8220;response&#8221; 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 &#8220;ok&#8221; and it is set to &#8220;no fit&#8221; 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
+    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>plogis</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
+    (<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
+    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,
+    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>nls</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 &lt; 0.5 at the highest dose level,
+    the modeltype is set to &#8220;inactive&#8221;. If the mean response at the
+    lowest dose is smaller than 0.5, the modeltype is set to &#8220;active&#8221;.
+    In both cases, no fitting procedure is carried out. If the fitted ED50 
+    is higher than the highest dose, &#8220;no fit&#8221; is given here.</p></dd>
+  <dt>logED50</dt><dd><p>The decadic logarithm of the ED50</p></dd>
+  <dt>low %</dt><dd><p>The lower bound of the confidence interval of log ED50. 
+    The name of the column depends on the requested confidence <code>level</code>.</p></dd>
+  <dt>high %</dt><dd><p>The higher bound of the confidence interval of log ED50.
+    The name of the column depends on the requested confidence <code>level</code>.</p></dd>
+  <dt>unit</dt><dd><p>The unit used for the dose levels in the dose-response data</p></dd>
+  <dt>sigma</dt><dd><p>The square root of the estimated variance of the random error as returned
+    by <code>summary.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 
+    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>, 
+    <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>
+  <dt>c</dt><dd><p>Only the &#8220;linlogit&#8221; 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.
+
+    
+    <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
+
+    <p>There is a demo for each dataset that can be accessed by
+  <code>demo(dataset)</code></p>
+    
+    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+    <p>Further examples are given in help pages to the datasets
+  <code><a href='antifoul.html'>antifoul</a></code>, <code><a href='IM1xIPC81.html'>IM1xIPC81</a></code> and
+  <code><a href='IM1xVibrio.html'>IM1xVibrio</a></code>.</p>
+    
+
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>antifoul</span>)
+<span class='no'>r</span> <span class='kw'>&lt;-</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'>c</span>(<span class='fl'>5</span>, <span class='fl'>10</span>, <span class='fl'>20</span>))</div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>TBT: Fitting data...</span></div><div class='output co'>#&gt; <span class='error'>Error in ED50["1:50", "Lower"]: Indizierung außerhalb der Grenzen</span></div><div class='input'><span class='fu'>format</span>(<span class='no'>r</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>2</span>)</div><div class='output co'>#&gt; <span class='error'>Error in format(r, digits = 2): Objekt 'r' nicht gefunden</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="#note">Note</a></li>
+
+      <li><a href="#see-also">See also</a></li>
+      
+      <li><a href="#examples">Examples</a></li>
+    </ul>
+
+    <h2>Author</h2>
+    
+  Johannes Ranke <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> 
+  <a href = 'http://www.uft.uni-bremen.de/chemie/ranke'>http://www.uft.uni-bremen.de/chemie/ranke</a>
+  The functionality of the drc package used under the hood in this function
+  was written by Christian Ritz.
+
+  </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/drdata.html b/docs/reference/drdata.html
new file mode 100644
index 0000000..e369c5c
--- /dev/null
+++ b/docs/reference/drdata.html
@@ -0,0 +1,245 @@
+<!-- Generated by pkgdown: do not edit by hand -->
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+      <a class="navbar-brand" href="../index.html">drfit</a>
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+    <div id="navbar" class="navbar-collapse collapse">
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+        <li>
+  <a href="../reference/index.html">Reference</a>
+</li>
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+      
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+        
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+
+      
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+
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+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Get dose-response data via RODBC</h1>
+    </div>
+
+    
+    <p>Get dose-response data from an adequate ODBC data source</p>
+    
+
+    <pre><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.</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"
+    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, 
+    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
+    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>
+
+    <p></p>
+<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>
+
+    <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
+  installation of the RODBC package, it is required to set up a ODBC data
+  source with the name "cytotox", using an ODBC driver for mysql, probably
+  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><tr><td>
+    [MySQL] </td>
+<td> </td>
+</tr><tr><td> </td>
+<td>
+    Description </td>
+</tr><tr><td> = </td>
+<td> MySQL driver for ODBC </td>
+</tr><tr><td>
+    Driver </td>
+<td> = </td>
+</tr><tr><td> /usr/local/lib/libmyodbc.so </td>
+<td>
+    Setup </td>
+</tr><tr><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><tr><td>
+    [cytotox] </td>
+<td> </td>
+</tr><tr><td> </td>
+<td>
+    Description </td>
+</tr><tr><td> = </td>
+<td> Cytotoxicity database of the department of bioorganic chemistry, UFT Bremen </td>
+</tr><tr><td>
+    Driver </td>
+<td> = </td>
+</tr><tr><td> MySQL </td>
+<td>
+    Trace </td>
+</tr><tr><td> = </td>
+<td> Yes  </td>
+</tr><tr><td>
+    TraceFile </td>
+<td> = </td>
+</tr><tr><td> /tmp/odbc.log  </td>
+<td>
+    Database </td>
+</tr><tr><td> = </td>
+<td> cytotox  </td>
+</tr><tr><td>
+    Server </td>
+<td> = </td>
+</tr><tr><td> eckehaat  </td>
+<td>
+    Port </td>
+</tr><tr><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='co'># Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81</span>
+<span class='co'># cells</span>
+<span class='co'>## Not run: drdata(c("TBT","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>
+
+    <h2>Author</h2>
+    
+  Johannes Ranke 
+  <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> 
+  <a href = 'http://www.uft.uni-bremen.de/chemie/ranke'>http://www.uft.uni-bremen.de/chemie/ranke</a>
+
+  </div>
+</div>
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+      </footer>
+   </div>
+
+  </body>
+</html>
diff --git a/docs/reference/drfit-package-9.png b/docs/reference/drfit-package-9.png
new file mode 100644
index 0000000..1095620
--- /dev/null
+++ b/docs/reference/drfit-package-9.png
diff --git a/docs/reference/drfit-package.html b/docs/reference/drfit-package.html
new file mode 100644
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--- /dev/null
+++ b/docs/reference/drfit-package.html
@@ -0,0 +1,141 @@
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+    <div class="page-header">
+    <h1>Dose-response data evaluation</h1>
+    </div>
+
+    
+    <p>See <a href = '../DESCRIPTION'>../DESCRIPTION</a></p>
+    
+
+        
+    <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
+
+    <p>There is an introductory article located in <a href = '../doc/drfit-Rnews.pdf'>../doc/drfit-Rnews.pdf</a>,
+which will be published in the R News special edition on the use
+of R for chemists.</p>
+    
+    <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
+
+    <p>There is a demo for each dataset that can be accessed by
+  <code>demo(dataset)</code></p>
+    
+    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+    <p>On CRAN, there is another, more statistically sophisticated package with
+similar functionality called <code>drc</code>. I think the advantage of my package
+is its user-friendliness.</p>
+    
+
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>antifoul</span>)
+<span class='no'>r</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='drfit.html'>drfit</a></span>(<span class='no'>antifoul</span>)</div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>TBT: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>Zn Pyrithion: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='input'><span class='fu'>format</span>(<span class='no'>r</span>,<span class='kw'>digits</span><span class='kw'>=</span><span class='fl'>2</span>)</div><div class='output co'>#&gt;      Substance ndl   n  lld lhd  mtype logED50  2.5%  97.5%   unit sigma     a
+#&gt; 1          TBT  38 135 -2.7 2.4 probit   -0.16 -0.27 -0.056 microM  0.19 -0.16
+#&gt; 2 Zn Pyrithion  27  81 -2.1 2.0 probit   -0.40 -0.51 -0.292 microM  0.23 -0.40
+#&gt;      b
+#&gt; 1 0.68
+#&gt; 2 0.42</div><div class='input'><span class='fu'><a href='drplot.html'>drplot</a></span>(<span class='no'>r</span>,<span class='no'>antifoul</span>,<span class='kw'>overlay</span><span class='kw'>=</span><span class='fl'>TRUE</span>,<span class='kw'>bw</span><span class='kw'>=</span><span class='fl'>FALSE</span>)</div><img src='drfit-package-9.png' alt='' width='540' height='400' /></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="#details">Details</a></li>
+
+      <li><a href="#note">Note</a></li>
+
+      <li><a href="#see-also">See also</a></li>
+      
+      <li><a href="#examples">Examples</a></li>
+    </ul>
+
+    <h2>Author</h2>
+    
+Author and Maintainer: Johannes Ranke &lt;jranke@uni-bremen.de&gt;
+
+  </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/drfit.html b/docs/reference/drfit.html
new file mode 100644
index 0000000..7acce23
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@@ -0,0 +1,300 @@
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+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Fit dose-response models</h1>
+    </div>
+
+    
+    <p>Fit dose-response relationships to dose-response data and calculate
+  biometric results for (eco)toxicity evaluation</p>
+    
+
+    <pre><span class='fu'>drfit</span>(<span class='no'>data</span>, <span class='kw'>startlogED50</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>chooseone</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>probit</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>logit</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+  <span class='kw'>weibull</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>linlogit</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>level</span> <span class='kw'>=</span> <span class='fl'>0.95</span>, <span class='kw'>linlogitWrong</span> <span class='kw'>=</span> <span class='fl'>NA</span>,
+  <span class='kw'>allWrong</span> <span class='kw'>=</span> <span class='fl'>NA</span>, <span class='kw'>ps0</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>ls0</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>ws0</span> <span class='kw'>=</span> <span class='fl'>0.5</span>, <span class='kw'>b0</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>f0</span> <span class='kw'>=</span> <span class='fl'>0</span>,
+  <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
+  <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>EDx.tolerance</span> <span class='kw'>=</span> <span class='fl'>1e-4</span>)</pre>
+    
+    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a> Arguments</h2>
+    <table class="ref-arguments">
+    <colgroup><col class="name" /><col class="desc" /></colgroup>
+    <tr>
+      <th>data</th>
+      <td><p>A data frame containing dose-response data. The data frame has to contain
+    at least a factor called &#8220;substance&#8221;, a numeric vector &#8220;dose&#8221;
+    with the dose values, a vector called &#8220;unit&#8221; containing the unit
+    used for the dose and a numeric vector &#8220;response&#8221; 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 &#8220;ok&#8221; and it is set to &#8220;no fit&#8221; in
+    a specific line, then the corresponding data point will be excluded from
+    the fitting procedure, although it will be plotted.</p></td>
+    </tr>
+    <tr>
+      <th>startlogED50</th>
+      <td><p>Especially for the linlogit model, a suitable log10 of the ED50 has to be
+    given by the user, since it is not correctly estimated for data showing
+    hormesis with the default estimation method.</p></td>
+    </tr>
+    <tr>
+      <th>probit</th>
+      <td><p>A boolean defining if cumulative density curves of normal distributions
+    <code>pnorm</code> are fitted against the decadic logarithm of the dose.
+    Default ist TRUE.</p></td>
+    </tr>
+    <tr>
+      <th>logit</th>
+      <td><p>A boolean defining if cumulative density curves of logistic distributions
+    <code>plogis</code> are fitted to the decadic logarithm of the dose.
+    Default is FALSE.</p></td>
+    </tr>
+    <tr>
+      <th>weibull</th>
+      <td><p>A boolean defining if the cumulative density curves of weibull distributions
+    (<code>pweibull</code> with additionall location parameter and scale=1)
+    are fitted to the decadic logarithm of the dose. Default is FALSE.
+    Note that the weibull distribution is fitted here to the log transformed doses
+    which appears to be an uncommon approach.</p></td>
+    </tr>
+    <tr>
+      <th>linlogit</th>
+      <td><p>A boolean defining if the linear-logistic function
+    <code><a href='linlogitf.html'>linlogitf</a></code> as defined by van Ewijk and Hoekstra 1993 is
+    fitted to the data. Default is FALSE.</p></td>
+    </tr>
+    <tr>
+      <th>level</th>
+      <td><p>The level for the confidence interval listed for the log ED50.</p></td>
+    </tr>
+    <tr>
+      <th>linlogitWrong</th>
+      <td><p>An optional vector containing the names of the substances for which the
+    linlogit function produces a wrong fit.</p></td>
+    </tr>
+    <tr>
+      <th>allWrong</th>
+      <td><p>An optional vector containing the names of the substances for which all
+    functions produce a wrong fit.</p></td>
+    </tr>
+    <tr>
+      <th>chooseone</th>
+      <td><p>If TRUE (default), the models are tried in the order linlogit, probit,
+    logit, weibull, and the first model that produces a valid fit is used.
+    If FALSE, all models that are set to TRUE and that can be fitted will be
+    reported.</p></td>
+    </tr>
+    <tr>
+      <th>ps0</th>
+      <td><p>If the probit model is fitted, <code>ps0</code> gives the possibility to adjust
+    the starting value for the scale parameter of <code>pnorm</code>.</p></td>
+    </tr>
+    <tr>
+      <th>ls0</th>
+      <td><p>If the logit model is fitted, <code>ls0</code> gives the possibility to adjust
+    the starting value for the scale parameter of <code>plogis</code>.</p></td>
+    </tr>
+    <tr>
+      <th>ws0</th>
+      <td><p>If the weibull model is fitted, <code>ws0</code> gives the possibility to adjust
+    the starting value for the shape parameter of <code>pweibull</code>.</p></td>
+    </tr>
+    <tr>
+      <th>b0,f0</th>
+      <td><p>If the linearlogistic model is fitted, <code>b0</code> and <code>f0</code> give the
+    possibility to adjust the starting values for the parameters b and f.</p></td>
+    </tr>
+    <tr>
+      <th>showED50</th>
+      <td><p>If set to TRUE, the ED50 and its confidence interval on the original dose
+    scale (not log scale) is included in the output.</p></td>
+    </tr>
+    <tr>
+      <th>EDx</th>
+      <td><p>A vector of inhibition values x in percent for which the corresponding doses
+    EDx should be reported.</p></td>
+    </tr>
+    <tr>
+      <th>EDx.tolerance</th>
+      <td><p>Tolerance of the effect level, expressed on the response scale from 0 to 1.</p></td>
+    </tr>
+    </table>
+    
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p>A dataframe with the attribute <code>models</code> holding a list of the fitted
+  dose-response models of class <code>nls</code>. The dataframe has at least
+  one line for each substance.</p>
+<p>For the &#8220;linlogit&#8221;, &#8220;logit&#8221; and &#8220;probit&#8221; models, the
+  parameter <code>a</code> that is reported coincides with the logED50, i.e the
+  logED50 is one of the model parameters that is being fitted. Therefore,
+  a confidence interval for the confidence level <code>level</code> is calculated
+  using the <code>confint.nls</code> function and listed.
+  
+  The following variables are in the dataframe:</p>
+<dt>Substance</dt><dd><p>The name of the substance</p></dd>
+  <dt>ndl</dt><dd><p>The number of dose levels in the raw data</p></dd>
+  <dt>n</dt><dd><p>The total number of data points in the raw data used for the fit</p></dd>
+  <dt>lld</dt><dd><p>The decadic logarithm of the lowest dose</p></dd>
+  <dt>lhd</dt><dd><p>The total number of data points in the raw data used for the fit</p></dd>
+  <dt>mtype</dt><dd><p>If the data did not show a mean response &lt; 0.5 at the highest dose level,
+    the modeltype is set to &#8220;inactive&#8221;. If the mean response at the
+    lowest dose is smaller than 0.5, the modeltype is set to &#8220;active&#8221;.
+    In both cases, no fitting procedure is carried out. If the fitted ED50 
+    is higher than the highest dose, &#8220;no fit&#8221; is given here.</p></dd>
+  <dt>logED50</dt><dd><p>The decadic logarithm of the ED50</p></dd>
+  <dt>low %</dt><dd><p>The lower bound of the confidence interval of log ED50. 
+    The name of the column depends on the requested confidence <code>level</code>.</p></dd>
+  <dt>high %</dt><dd><p>The higher bound of the confidence interval of log ED50.
+    The name of the column depends on the requested confidence <code>level</code>.</p></dd>
+  <dt>unit</dt><dd><p>The unit used for the dose levels in the dose-response data</p></dd>
+  <dt>sigma</dt><dd><p>The square root of the estimated variance of the random error as returned
+    by <code>summary.nls</code>.</p></dd>
+  <dt>a</dt><dd><p>For the &#8220;linlogit&#8221;, &#8220;logit&#8221; and &#8220;probit&#8221; models, the
+    parameter <code>a</code> coincides with the logED50.  In the case of the
+    &#8220;weibull&#8221; model, <code>a</code> is a location parameter.</p></dd>
+  <dt>b</dt><dd><p>Parameter <code>b</code> in the case of the &#8220;linlogit&#8221; fit is the variable
+    b from the <code>linlogitf</code> function. In the case of &#8220;probit&#8221;
+    fit it is the standard deviation of the fitted normal distribution, in the
+    case of the &#8220;logit&#8221; fit it is the <code>scale</code> parameter in the
+    <code>plogis</code> function, and in the &#8220;weibull&#8221; fit it is the
+    <code>shape</code> parameter of the fitted <code>pweibull</code> function.</p></dd>
+  <dt>c</dt><dd><p>Only the &#8220;linlogit&#8221; fit produces a third parameter <code>c</code> which is
+    the variable f from the <code>linlogitf</code> function.</p></dd>
+  If the parameter showED50 was set to TRUE, the ED50 values and their
+  confidence intervals are also included on the original dose scale.
+
+  If one or more response leves were specified in the argument EDx,
+  the corresponding dose levels are given in addition.
+
+    
+    <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2>
+
+    <p>There is a demo for each dataset that can be accessed by
+  <code>demo(dataset)</code></p>
+    
+    <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
+
+    <p>Further examples are given in help pages to the datasets
+  <code><a href='antifoul.html'>antifoul</a></code>, <code><a href='IM1xIPC81.html'>IM1xIPC81</a></code> and
+  <code><a href='IM1xVibrio.html'>IM1xVibrio</a></code>.
+  Since version 0.6.1 of this package, there is a drop-in replacement function
+  <code><a href='drcfit.html'>drcfit</a></code> which internally uses the drc package and also gives
+  confidence intervals for EDx values via this package.</p>
+    
+
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>antifoul</span>)
+<span class='no'>r</span> <span class='kw'>&lt;-</span> <span class='fu'>drfit</span>(<span class='no'>antifoul</span>, <span class='kw'>showED50</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>EDx</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>5</span>, <span class='fl'>10</span>, <span class='fl'>20</span>))</div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>TBT: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>Zn Pyrithion: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='input'><span class='fu'>format</span>(<span class='no'>r</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>2</span>)</div><div class='output co'>#&gt;      Substance ndl   n  lld lhd  mtype logED50  2.5%  97.5%   unit sigma     a
+#&gt; 1          TBT  38 135 -2.7 2.4 probit   -0.16 -0.27 -0.056 microM  0.19 -0.16
+#&gt; 2 Zn Pyrithion  27  81 -2.1 2.0 probit   -0.40 -0.51 -0.292 microM  0.23 -0.40
+#&gt;      b ED50 ED50 2.5% ED50 97.5%  EDx5 EDx10 EDx20
+#&gt; 1 0.68 0.68      0.54       0.88 0.053 0.093  0.18
+#&gt; 2 0.42 0.40      0.31       0.51 0.082 0.117  0.18</div></pre>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
+    <h2>Contents</h2>
+    <ul class="nav nav-pills nav-stacked">
+      <li><a href="#arguments">Arguments</a></li>
+      
+      <li><a href="#value">Value</a></li>
+
+      <li><a href="#note">Note</a></li>
+
+      <li><a href="#see-also">See also</a></li>
+      
+      <li><a href="#examples">Examples</a></li>
+    </ul>
+
+    <h2>Author</h2>
+    
+  Johannes Ranke 
+  <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> 
+  <a href = 'http://www.uft.uni-bremen.de/chemie/ranke'>http://www.uft.uni-bremen.de/chemie/ranke</a>
+
+  </div>
+</div>
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+      </footer>
+   </div>
+
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+</html>
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+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Plot dose-response models</h1>
+    </div>
+
+    
+    <p>Produce graphics of dose-response data and dose-response relationships 
+  either combined or separately, for one or more substances.</p>
+    
+
+    <pre><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
+    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
+    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 
+    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>plot.default</code></p></td>
+    </tr>
+    <tr>
+      <th>frame.plot</th>
+      <td><p>Specifies if the plot should be framed. Default is TRUE, as in
+    <code>plot.default</code></p></td>
+    </tr>
+    <tr>
+      <th>postscript</th>
+      <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 
+    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
+    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
+    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
+    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>
+    
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p></p>
+<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>
+
+    <p>There is a demo for each dataset that can be accessed by
+  <code>demo(dataset)</code></p>
+    
+
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><div class='input'><span class='fu'>data</span>(<span class='no'>antifoul</span>)
+<span class='no'>r</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='drfit.html'>drfit</a></span>(<span class='no'>antifoul</span>)</div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>TBT: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='output co'>#&gt; <span class='message'></span>
+#&gt; <span class='message'>Zn Pyrithion: Fitting data...</span></div><div class='output co'>#&gt; <span class='message'>Waiting for profiling to be done...</span></div><div class='input'><span class='co'>## Not run: drplot(r,antifoul)</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="#note">Note</a></li>
+      
+      <li><a href="#examples">Examples</a></li>
+    </ul>
+
+    <h2>Author</h2>
+    
+  Johannes Ranke 
+  <a href='mailto:jranke@uni-bremen.de'>jranke@uni-bremen.de</a> 
+  <a href = 'http://www.uft.uni-bremen.de/chemie/ranke'>http://www.uft.uni-bremen.de/chemie/ranke</a>
+
+  </div>
+</div>
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
+</div>
+
+      </footer>
+   </div>
+
+  </body>
+</html>
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+++ b/docs/reference/index.html
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+        
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+
+      
+      </header>
+
+      <div class="row">
+  <div class="col-md-9">
+    <div class="page-header">
+      <h1>Function reference</h1>
+      <h4>version&nbsp;0.7.1</h4>
+    </div>
+
+    <div class="contents">
+      <table class="ref-index">
+
+      <colgroup>
+        <col class="alias" />
+        <col class="title" />
+      </colgroup>
+
+      <tbody>
+        <tr>
+          <th colspan="2">
+            <h2 id="section-all-functions" class="hasAnchor"><a href="#section-all-functions" class="anchor"></a>All functions</h2>
+            <p class="section-desc"></p>
+          </th>
+        </tr>
+        <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>
+            <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>
+            <p><code><a href="checkexperiment.html">checkexperiment</a></code> <code><a href="checkexperiment.html">checkplate</a></code> </p>
+          </td>
+          <td><p>Check raw data from a specified experiment or microtiter plate</p></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>
+            <p><code><a href="drdata.html">drdata</a></code> </p>
+          </td>
+          <td><p>Get dose-response data via RODBC</p></td>
+        </tr><tr>
+          <!--  -->
+          <td>
+            <p><code><a href="drfit-package.html">drfit-package</a></code> </p>
+          </td>
+          <td><p>Dose-response data evaluation</p></td>
+        </tr><tr>
+          <!--  -->
+          <td>
+            <p><code><a href="drfit.html">drfit</a></code> </p>
+          </td>
+          <td><p>Fit dose-response models</p></td>
+        </tr><tr>
+          <!--  -->
+          <td>
+            <p><code><a href="drplot.html">drplot</a></code> </p>
+          </td>
+          <td><p>Plot dose-response models</p></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>
+            <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>
+            <p><code><a href="linlogitf.html">linlogitf</a></code> </p>
+          </td>
+          <td><p>Linear-logistic function</p></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>
+            <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>
+      </table>
+    </div>
+  </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-all-functions">All functions</a></li>
+    </ul>
+  </div>
+</div>
+
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+      <div class="copyright">
+  <p>Developed by Johannes Ranke.</p>
+</div>
+
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+  <p>Site built with <a href="http://hadley.github.io/pkgdown/">pkgdown</a>.</p>
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author	Johannes Ranke <jranke@uni-bremen.de>	2017-03-24 15:22:07 +0100
committer	Johannes Ranke <jranke@uni-bremen.de>	2017-03-24 15:22:07 +0100
commit	ae13a2e7f373f697cdfb6acb7ae042d6e27d8967 (patch)
tree	61bc66f752a81e9d50becf173d138ca9dfa80778
parent	cd9d3e214233b0a6862200f60bf70a4214bc2115 (diff)