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authorJohannes Ranke <jranke@uni-bremen.de>2017-03-24 15:22:07 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2017-03-24 15:22:07 +0100
commitae13a2e7f373f697cdfb6acb7ae042d6e27d8967 (patch)
tree61bc66f752a81e9d50becf173d138ca9dfa80778
parentcd9d3e214233b0a6862200f60bf70a4214bc2115 (diff)
Add pkgdown docu, change package build directory
-rw-r--r--GNUmakefile16
-rw-r--r--docs/authors.html99
-rw-r--r--docs/index.html88
-rw-r--r--docs/jquery.sticky-kit.min.js9
-rw-r--r--docs/link.svg12
-rw-r--r--docs/pkgdown.css137
-rw-r--r--docs/pkgdown.js8
-rw-r--r--docs/reference/antifoul.html160
-rw-r--r--docs/reference/checkcontrols.html159
-rw-r--r--docs/reference/checkexperiment.html143
-rw-r--r--docs/reference/checksubstance.html176
-rw-r--r--docs/reference/drcfit.html251
-rw-r--r--docs/reference/drdata.html245
-rw-r--r--docs/reference/drfit-package-9.pngbin0 -> 20004 bytes
-rw-r--r--docs/reference/drfit-package.html141
-rw-r--r--docs/reference/drfit.html300
-rw-r--r--docs/reference/drplot.html268
-rw-r--r--docs/reference/index.html195
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 @@
+/*
+ Sticky-kit v1.1.2 | WTFPL | Leaf Corcoran 2015 | http://leafo.net
+*/
+(function(){var b,f;b=this.jQuery||window.jQuery;f=b(window);b.fn.stick_in_parent=function(d){var A,w,J,n,B,K,p,q,k,E,t;null==d&&(d={});t=d.sticky_class;B=d.inner_scrolling;E=d.recalc_every;k=d.parent;q=d.offset_top;p=d.spacer;w=d.bottoming;null==q&&(q=0);null==k&&(k=void 0);null==B&&(B=!0);null==t&&(t="is_stuck");A=b(document);null==w&&(w=!0);J=function(a,d,n,C,F,u,r,G){var v,H,m,D,I,c,g,x,y,z,h,l;if(!a.data("sticky_kit")){a.data("sticky_kit",!0);I=A.height();g=a.parent();null!=k&&(g=g.closest(k));
+if(!g.length)throw"failed to find stick parent";v=m=!1;(h=null!=p?p&&a.closest(p):b("<div />"))&&h.css("position",a.css("position"));x=function(){var c,f,e;if(!G&&(I=A.height(),c=parseInt(g.css("border-top-width"),10),f=parseInt(g.css("padding-top"),10),d=parseInt(g.css("padding-bottom"),10),n=g.offset().top+c+f,C=g.height(),m&&(v=m=!1,null==p&&(a.insertAfter(h),h.detach()),a.css({position:"",top:"",width:"",bottom:""}).removeClass(t),e=!0),F=a.offset().top-(parseInt(a.css("margin-top"),10)||0)-q,
+u=a.outerHeight(!0),r=a.css("float"),h&&h.css({width:a.outerWidth(!0),height:u,display:a.css("display"),"vertical-align":a.css("vertical-align"),"float":r}),e))return l()};x();if(u!==C)return D=void 0,c=q,z=E,l=function(){var b,l,e,k;if(!G&&(e=!1,null!=z&&(--z,0>=z&&(z=E,x(),e=!0)),e||A.height()===I||x(),e=f.scrollTop(),null!=D&&(l=e-D),D=e,m?(w&&(k=e+u+c>C+n,v&&!k&&(v=!1,a.css({position:"fixed",bottom:"",top:c}).trigger("sticky_kit:unbottom"))),e<F&&(m=!1,c=q,null==p&&("left"!==r&&"right"!==r||a.insertAfter(h),
+h.detach()),b={position:"",width:"",top:""},a.css(b).removeClass(t).trigger("sticky_kit:unstick")),B&&(b=f.height(),u+q>b&&!v&&(c-=l,c=Math.max(b-u,c),c=Math.min(q,c),m&&a.css({top:c+"px"})))):e>F&&(m=!0,b={position:"fixed",top:c},b.width="border-box"===a.css("box-sizing")?a.outerWidth()+"px":a.width()+"px",a.css(b).addClass(t),null==p&&(a.after(h),"left"!==r&&"right"!==r||h.append(a)),a.trigger("sticky_kit:stick")),m&&w&&(null==k&&(k=e+u+c>C+n),!v&&k)))return v=!0,"static"===g.css("position")&&g.css({position:"relative"}),
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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 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!-- Generator: Adobe Illustrator 19.2.1, SVG Export Plug-In . SVG Version: 6.00 Build 0) -->
+<svg version="1.1" id="Layer_1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" x="0px" y="0px"
+ viewBox="0 0 20 20" style="enable-background:new 0 0 20 20;" xml:space="preserve">
+<style type="text/css">
+ .st0{fill:#75AADB;}
+</style>
+<path class="st0" d="M4,11.3h1.3v1.3H4c-2,0-4-2.3-4-4.7s2.1-4.7,4-4.7h5.3c1.9,0,4,2.3,4,4.7c0,1.9-1.2,3.6-2.7,4.3v-1.5
+ C11.4,10.2,12,9.1,12,8c0-1.7-1.4-3.3-2.7-3.3H4C2.7,4.7,1.3,6.3,1.3,8S2.7,11.3,4,11.3z M16,7.3h-1.3v1.3H16c1.3,0,2.7,1.6,2.7,3.3
+ s-1.4,3.3-2.7,3.3h-5.3C9.4,15.3,8,13.7,8,12c0-1.1,0.6-2.2,1.3-2.8V7.7C7.9,8.4,6.7,10.1,6.7,12c0,2.4,2.1,4.7,4,4.7H16
+ c1.9,0,4-2.3,4-4.7S18,7.3,16,7.3z"/>
+</svg>
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);
+ flex-direction: column;
+}
+
+body > .container .row {
+ flex: 1;
+}
+
+footer {
+ margin-top: 45px;
+ padding: 35px 0 36px;
+ border-top: 1px solid #e5e5e5;
+ color: #666;
+ display: flex;
+}
+footer p {
+ margin-bottom: 0;
+}
+footer div {
+ flex: 1;
+}
+footer .pkgdown {
+ text-align: right;
+}
+footer p {
+ margin-bottom: 0;
+}
+
+img.icon {
+ float: right;
+}
+
+/* Section anchors ---------------------------------*/
+
+.hasAnchor {
+ margin-left: -30px;
+}
+
+a.anchor {
+ display:inline-block;
+ width: 30px;
+ height: 30px;
+ visibility: hidden;
+
+ background-image: url(./link.svg);
+ background-repeat: no-repeat;
+ background-size: 20px 20px;
+ background-position: center center;
+}
+
+.hasAnchor:hover a.anchor {
+ visibility: visible;
+}
+
+/* Fixes for fixed navbar --------------------------*/
+
+.contents h1, .contents h2, .contents h3, .contents h4 {
+ padding-top: 60px;
+ margin-top: -60px;
+}
+
+/* Sidebar --------------------------*/
+
+#sidebar {
+ margin-top: 30px;
+}
+#sidebar h2 {
+ font-size: 1.5em;
+ margin-top: 1em;
+}
+
+#sidebar h2:first-child {
+ margin-top: 0;
+}
+
+#sidebar .list-unstyled li {
+ margin-bottom: 0.5em;
+}
+
+/* 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%;}
+.ref-index .title {width: 60%;}
+
+.ref-index .alias {width: 40%;}
+.ref-index .title {width: 60%;}
+
+.ref-arguments th {text-align: right; padding-right: 10px;}
+.ref-arguments th, .ref-arguments td {vertical-align: top;}
+.ref-arguments .name {width: 20%;}
+.ref-arguments .desc {width: 80%;}
+
+/* Nice scrolling for wide elements --------------------------------------- */
+
+table {
+ display: block;
+ overflow: auto;
+}
+
+/* Syntax highlighting ---------------------------------------------------- */
+
+code {
+ background-color: #f7f7f7;
+ color: #333;
+}
+code a {
+ color: #375f84;
+}
+
+.warning { color: red; }
+.message { font-weight: bolder; }
+.error { color: red; font-weight: bolder; }
+
+.fl,.number {color:rgb(21,20,181);}
+.fu,.functioncall {color:#264D66 ;}
+.ch,.st,.string {color:#375D81 ;}
+.kw,.keyword {color:black;}
+.argument {color:#264D66 ;}
+.co,.comment {color: #777;}
+.formalargs {color: #264D66;}
+.eqformalargs {color:#264D66;}
+.slot {font-style:italic;}
+.symbol {color:black ;}
+.prompt {color:black ;}
+
+pre img {
+ background-color: #fff;
+ display: block;
+}
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() {
+ $("#sidebar").stick_in_parent({offset_top: 40});
+ $('body').scrollspy({
+ target: '#sidebar',
+ offset: 60
+ });
+
+});
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">
+<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>
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+ <span class="icon-bar"></span>
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+ </button>
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+ </div>
+ <div id="navbar" class="navbar-collapse collapse">
+ <ul class="nav navbar-nav">
+ <li>
+ <a href="../reference/index.html">Reference</a>
+</li>
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+
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+
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+ </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>
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+<meta http-equiv="X-UA-Compatible" content="IE=edge">
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+
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+
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+ </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">
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+
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+<script src="https://code.jquery.com/jquery-3.1.0.min.js" integrity="sha384-nrOSfDHtoPMzJHjVTdCopGqIqeYETSXhZDFyniQ8ZHcVy08QesyHcnOUpMpqnmWq" crossorigin="anonymous"></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>
+ </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>
+
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+</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 -->
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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>
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+
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+
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+ </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 @@
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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">
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+</li>
+ </ul>
+
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+
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+ </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 -->
+<!DOCTYPE html>
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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>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
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+
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+</div><!--/.navbar -->
+
+
+ </header>
+
+ <div class="row">
+ <div class="col-md-9 contents">
+ <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
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--- /dev/null
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@@ -0,0 +1,300 @@
+<!-- Generated by pkgdown: do not edit by hand -->
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+ <span class="icon-bar"></span>
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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>
+
+ </body>
+</html>
diff --git a/docs/reference/drplot.html b/docs/reference/drplot.html
new file mode 100644
index 0000000..eff1338
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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>
diff --git a/docs/reference/index.html b/docs/reference/index.html
new file mode 100644
index 0000000..d92d4dc
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@@ -0,0 +1,195 @@
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+ <h4>version&nbsp;0.7.1</h4>
+ </div>
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+ <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>
+
+ <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>
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