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author(no author) <(no author)@d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc>2004-07-27 07:36:01 +0000
committer(no author) <(no author)@d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc>2004-07-27 07:36:01 +0000
commit8154a03c79eb910c42dcff03fd8fa611cdc8cc9d (patch)
treec4e64967d78078a0fb0a8c9ec85307c35c9ec8f9
First version published on CRAN
git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@1 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
Diffstat
-rw-r--r--DESCRIPTION20
-rw-r--r--INDEX5
-rw-r--r--R/drfit.R370
-rw-r--r--chm/00Index.html24
-rw-r--r--chm/Rchm.css25
-rw-r--r--chm/antifoul.html49
-rw-r--r--chm/drdata.html146
-rw-r--r--chm/drfit.chmbin0 -> 22081 bytes
-rw-r--r--chm/drfit.hhp17
-rw-r--r--chm/drfit.html99
-rw-r--r--chm/drfit.toc51
-rw-r--r--chm/drplot.html131
-rw-r--r--chm/logo.jpgbin0 -> 8793 bytes
-rw-r--r--data/00Index2
-rw-r--r--data/antifoul.rda2410
-rw-r--r--man/antifoul.Rd20
-rw-r--r--man/drdata.Rd74
-rw-r--r--man/drfit.Rd59
-rw-r--r--man/drplot.Rd86
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diff --git a/DESCRIPTION b/DESCRIPTION
new file mode 100644
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--- /dev/null
+++ b/DESCRIPTION
@@ -0,0 +1,20 @@
+Package: drfit
+Version: 0.02-3
+Date: 2004-07-23
+Title: Dose-response data evaluation
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Maintainer: Johannes Ranke <jranke@uni-bremen.de>
+Depends: R,stats,RODBC
+Description: drfit provides basic functions for accessing the
+ dose-response data of the UFT Bremen, Department of Bioorganic Chemistry,
+ fitting dose-response curves to this and similar data, calculating some
+ (eco)toxicological parameters and plotting the results. Functions that are
+ fitted are the cumulative densitiy function of the lognormal distribution,
+ of the logistic distribution and a linea-logistic model, derived from the
+ latter, which is used to describe data showing stimulation at low doses
+ (hormesis). The author would be delighted if anyone would join in the
+ effort of creating useful and useable tools for dealing with dose-response
+ data from biological testing.
+License: GPL version 2 or newer
+URL: http://www.r-project.org,
+ http://www.uft.uni-bremen.de/chemie/ranke
diff --git a/INDEX b/INDEX
new file mode 100644
index 0000000..52fea7c
--- /dev/null
+++ b/INDEX
@@ -0,0 +1,5 @@
+antifoul Dose-Response data for TBT and Zink Pyrithione
+ in IPC-81 cells
+drdata Get dose-response data
+drfit Fit dose-response models
+drplot Plot dose-response data and dose-response models
diff --git a/R/drfit.R b/R/drfit.R
new file mode 100644
index 0000000..c3fc945
--- /dev/null
+++ b/R/drfit.R
@@ -0,0 +1,370 @@
+drdata <- function(substances, experimentator = "%", db = "cytotox",
+ celltype="IPC-81",whereClause="1",
+ ok="'ok'")
+{
+ library(RODBC)
+ cytotoxchannel <- odbcConnect("cytotox",uid="cytotox",pwd="cytotox",case="tolower")
+ slist <- paste(substances,collapse="','")
+ query <- paste("SELECT conc,viability,unit,experimentator,substance,celltype,",
+ "plate,ok FROM cytotox WHERE substance IN ('",
+ slist,"') AND experimentator LIKE '",
+ experimentator,"' AND celltype LIKE '",
+ celltype,"' AND ",
+ whereClause," AND ok in (",
+ ok,")",sep="")
+ data <- sqlQuery(cytotoxchannel,query)
+ names(data)[[1]] <- "dose"
+ names(data)[[2]] <- "response"
+ data$dosefactor <- factor(data$dose)
+ data$substance <- factor(data$substance,levels=substances)
+ return(data)
+}
+
+drfit <- function(data, startlogEC50 = NA, lognorm = TRUE, logis = FALSE,
+ linearlogis = FALSE, b0 = 2, f0 = 0)
+{
+ library(nls)
+ substances <- levels(data$substance)
+ unit <- levels(as.factor(data$unit))
+ logisf <- function(x,x0,b,k=1)
+ {
+ k / (1 + (x/x0)^b)
+ }
+ linearlogisf <- function(x,k,f,mu,b)
+ {
+ k*(1 + f*x) / (1 + ((2*f*(10^mu) + 1) * ((x/(10^mu))^b)))
+ }
+
+ ri <- 0 # an index over the result rows
+ rsubstance <- array() # the substance names in the results
+ rn <- vector() # number of dose-response curves
+ rlhd <- rlld <- vector() # highest and lowest doses tested
+ mtype <- array() # the modeltypes
+ logEC50 <- vector()
+ stderrlogEC50 <- vector()
+ slope <- vector()
+ b <- vector()
+ f <- vector()
+
+ splitted <- split(data,data$substance)
+ for (i in substances)
+ {
+ tmp <- splitted[[i]]
+ n <- round(length(tmp$response)/9)
+ if (is.na(startlogEC50[i])){
+ w <- 1/abs(tmp$response - 0.3)
+ startlogEC50[[i]] <- sum(w * log10(tmp$dose))/sum(w)
+ }
+ highestdose <- max(tmp$dose)
+ lowestdose <- min(tmp$dose)
+ lhd <- log10(highestdose)
+ lld <- log10(lowestdose)
+ responseathighestdose <- mean(subset(tmp,dose==highestdose)$response)
+ rix <- ri # rix is used late to check if any
+ # model result was appended
+ if (responseathighestdose < 0.5) {
+ if (lognorm)
+ {
+ m <- try(nls(response ~ pnorm(-log10(dose),-logEC50,slope),
+ data=tmp,
+ start=list(logEC50=startlogEC50[[i]],slope=1)))
+ if (!inherits(m, "try-error"))
+ {
+ ri <- ri + 1
+ rsubstance[[ri]] <- i
+ rn[[ri]] <- n
+ rlld[[ri]] <- log10(lowestdose)
+ rlhd[[ri]] <- log10(highestdose)
+ mtype[[ri]] <- "lognorm"
+ s <- summary(m)
+ logEC50[[ri]] <- coef(m)[["logEC50"]]
+ if (logEC50[[ri]] > rlhd[[ri]])
+ {
+ logEC50[[ri]] <- NA
+ slope[[ri]] <- NA
+ stderrlogEC50[[ri]] <- NA
+ } else
+ {
+ slope[[ri]] <- coef(m)[["slope"]]
+ stderrlogEC50[[ri]] <- s$parameters["logEC50","Std. Error"]
+ }
+ }
+ }
+
+ if (logis)
+ {
+ # Instead of plogis(), the function logisf() defined above
+ # could be used for regression against dose, not log10(dose)
+ m <- try(nls(response ~ plogis(-log10(dose),-logEC50,slope),
+ data=tmp,
+ start=list(logEC50=startlogEC50[[i]],slope=1)))
+ if (!inherits(m, "try-error"))
+ {
+ ri <- ri + 1
+ rsubstance[[ri]] <- i
+ rn[[ri]] <- n
+ rlld[[ri]] <- log10(lowestdose)
+ rlhd[[ri]] <- log10(highestdose)
+ mtype[[ri]] <- "logis"
+ s <- summary(m)
+ logEC50[[ri]] <- coef(m)[["logEC50"]]
+ if (logEC50[[ri]] > rlhd[[ri]])
+ {
+ logEC50[[ri]] <- NA
+ slope[[ri]] <- NA
+ stderrlogEC50[[ri]] <- NA
+ } else
+ {
+ slope[[ri]] <- coef(m)[["slope"]]
+ stderrlogEC50[[ri]] <- s$parameters["logEC50","Std. Error"]
+ }
+ }
+ }
+
+ if (linearlogis)
+ {
+ m <- try(nls(response ~ linearlogisf(dose,1,f,logEC50,b),
+ data=tmp,
+ start=list(f=f0,logEC50=startlogEC50[[i]],b=b0)))
+ if (!inherits(m, "try-error"))
+ {
+ ri <- ri + 1
+ rsubstance[[ri]] <- i
+ rn[[ri]] <- n
+ rlld[[ri]] <- log10(lowestdose)
+ rlhd[[ri]] <- log10(highestdose)
+ mtype[[ri]] <- "linearlogis"
+ s <- summary(m)
+#print(s)
+ logEC50[[ri]] <- coef(m)[["logEC50"]]
+ if (logEC50[[ri]] > rlhd[[ri]])
+ {
+ logEC50[[ri]] <- NA
+ stderrlogEC50[[ri]] <- NA
+ b[[ri]] <- NA
+ f[[ri]] <- NA
+ } else
+ {
+ stderrlogEC50[[ri]] <- s$parameters["logEC50","Std. Error"]
+ b[[ri]] <- coef(m)[["b"]]
+ f[[ri]] <- coef(m)[["f"]]
+ }
+ }
+ }
+ }
+ if (ri == rix) # if no entry was appended for this substance
+ {
+ ri <- ri + 1
+ rsubstance[[ri]] <- i
+ rn[[ri]] <- n
+ rlld[[ri]] <- log10(lowestdose)
+ rlhd[[i]] <- log10(highestdose)
+ mtype[[ri]] <- "none"
+ logEC50[[ri]] <- NA
+ stderrlogEC50[[ri]] <- NA
+ slope[[ri]] <- NA
+ b[[ri]] <- NA
+ f[[ri]] <- NA
+ }
+ }
+ results <- data.frame(rsubstance,rn, rlld, rlhd, mtype, logEC50, stderrlogEC50, unit)
+ names(results) <- c("Substance","n", "lld","lhd","mtype","logEC50","std","unit")
+ if (lognorm || logis) {
+ results$slope <- slope
+ }
+ if (linearlogis) {
+ results$b <- b
+ results$f <- f
+ }
+ return(results)
+}
+
+drplot <- function(drresults, data = FALSE, dtype = "std", alpha = 0.95,
+ path = "./", fileprefix = "drplot", overlay = FALSE,
+ postscript = FALSE,
+ color = TRUE,
+ colors = 1:8, fitcolors = "default")
+{
+ # Prepare plots
+ devices <- 1
+ if (postscript && !overlay) psdevices <- vector()
+ if (!postscript && !overlay) x11devices <- vector()
+
+ unit <- levels(as.factor(drresults$unit))
+
+ # Get the plot limits on the x-axis (log of the dose)
+ if(is.data.frame(data))
+ {
+ lld <- log10(min(data$dose))
+ lhd <- log10(max(data$dose))
+ hr <- max(data$response)
+ dsubstances <- levels(data$substance)
+ } else {
+ lld <- min(drresults[["logEC50"]],na.rm=TRUE) - 2
+ lhd <- max(drresults[["logEC50"]],na.rm=TRUE) + 2
+ if (length(subset(drresults,mtype=="linearlogis")$substance) != 0) {
+ hr <- 1.8
+ } else {
+ hr <- 1.0
+ }
+ }
+
+ # Prepare overlay plot if requested
+ if (overlay)
+ {
+ devices <- devices + 1
+ if (postscript) {
+ filename = paste(path,fileprefix,".eps",sep="")
+ postscript(file=filename,
+ paper="special",width=7,height=7,horizontal=FALSE,pointsize=12)
+ cat("Created File: ",filename,"\n")
+ } else {
+ x11(width=7,height=7,pointsize=12)
+ }
+
+ plot(0,type="n",
+ xlim=c(lld - 0.5, lhd + 2),
+ ylim= c(-0.1, hr + 0.2),
+ xlab=paste("Decadic Logarithm of the dose in ", unit),
+ ylab="Normalized response")
+ }
+
+ # Plot the data either as raw data or as error bars
+ if(is.data.frame(data))
+ {
+ splitted <- split(data,data$substance)
+ n <- 0
+ for (i in dsubstances)
+ {
+ # Prepare the single graphs if an overlay is not requested
+ if (!overlay)
+ {
+ devices <- devices + 1
+ if (postscript) {
+ filename = paste(path,fileprefix,sub(" ","_",gsub("([\(\) ])", "", i)),".eps",sep="")
+ postscript(file=filename,
+ paper="special",width=7,height=7,horizontal=FALSE,pointsize=12)
+ psdevices[[i]] <- devices
+ cat("Created File: ",filename,"\n")
+ } else {
+ x11(width=7,height=7,pointsize=12)
+ x11devices[[i]] <- devices
+ }
+
+ plot(0,type="n",
+ xlim=c(lld - 0.5, lhd + 2),
+ ylim= c(-0.1, hr + 0.2),
+ xlab=paste("Decadic Logarithm of the dose in ", unit),
+ ylab="Normalized response")
+ }
+ if (color == FALSE) colors <- rep("black",length(dsubstances))
+ n <- n + 1
+ if (!overlay) legend(lhd - 1, hr + 0.1, i,lty = 1, col = colors[[n]])
+ tmp <- splitted[[i]]
+ tmp$dosefactor <- factor(tmp$dose) # necessary because the old
+ # factor has all levels, not
+ # only the ones tested with
+ # this substance
+ if (dtype == "raw") {
+ points(log10(tmp$dose),tmp$response,col=colors[[n]])
+ } else {
+ splitresponses <- split(tmp$response,tmp$dosefactor)
+ means <- sapply(splitresponses,mean)
+ lengths <- sapply(splitresponses,length)
+ vars <- sapply(splitresponses,var)
+ standarddeviations <- sqrt(vars)
+ }
+ if (dtype == "std")
+ {
+ tops <- means + standarddeviations
+ bottoms <- means - standarddeviations
+ }
+ if (dtype == "conf")
+ {
+ confidencedeltas <- qt((1 + alpha)/2, lengths - 1) * sqrt(vars)
+ tops <- means + confidencedeltas
+ bottoms <- means - confidencedeltas
+ }
+ if (dtype != "raw")
+ {
+ x <- log10(as.numeric(levels(tmp$dosefactor)))
+ segments(x,bottoms,x,tops,col=colors[[n]])
+ points(x,means,col=colors[[n]])
+ smidge <- 0.05
+ segments(x - smidge,bottoms,x + smidge,bottoms,col=colors[[n]])
+ segments(x - smidge,tops,x + smidge,tops,col=colors[[n]])
+ }
+ }
+ }
+
+ # Plot the fitted dose response models from drresults
+ fits <- subset(drresults,!is.na(logEC50))
+ nf <- length(fits$Substance) # number of fits to plot
+ if (fitcolors[[1]] == "default")
+ {
+ defaultfitcolors <- rainbow(nf)
+ }
+ legendcolors <- vector()
+ for (i in 1:nf)
+ {
+ s <- as.character(fits[i,"Substance"]) # The substance name to display
+ if (!overlay && !is.data.frame(data))
+ {
+ devices <- devices + 1
+ if (postscript) {
+ filename = paste(path,fileprefix,sub(" ","_",gsub("([\(\) ])", "", s)),".eps",sep="")
+ postscript(file=filename,
+ paper="special",width=7,height=7,horizontal=FALSE,pointsize=12)
+ psdevices[[s]] <- devices
+ cat("Created File: ",filename,"\n")
+ } else {
+ x11(width=7,height=7,pointsize=12)
+ x11devices[[s]] <- devices
+ }
+
+ plot(0,type="n",
+ xlim=c(lld - 0.5, lhd + 2),
+ ylim= c(-0.1, hr + 0.2),
+ xlab=paste("Decadic Logarithm of the dose in ", unit),
+ ylab="Normalized response")
+ }
+ if (postscript && !overlay) {
+ dev.set(psdevices[[s]]) }
+ if (!postscript && !overlay) {
+ dev.set(x11devices[[s]]) }
+
+ if (color == FALSE) {
+ fitcolor <- "black"
+ } else {
+ if (fitcolors[[1]] == "default")
+ {
+ fitcolor <- defaultfitcolors[[i]]
+ } else {
+ fitcolor <- fitcolors[[i]]
+ }
+ }
+ if (!overlay) legend(lhd - 1, hr + 0.1, s,lty = 1, col = fitcolor)
+ legendcolors[[i]] <- fitcolor
+ logEC50 <- fits[i,"logEC50"]
+ mtype <- as.character(fits[i, "mtype"])
+ if (mtype == "lognorm")
+ {
+ slope <- fits[i,"slope"]
+ plot(function(x) pnorm(-x,-logEC50,slope),lld - 0.5, lhd + 2, add=TRUE,col=fitcolor)
+ }
+ if (mtype == "logis")
+ {
+ slope <- fits[i,"slope"]
+ plot(function(x) plogis(-x,-logEC50,slope),lld - 0.5, lhd + 2, add=TRUE,col=fitcolor)
+ }
+ }
+ if (overlay) {
+ legend(lhd - 1, hr + 0.1, as.vector(fits$Substance), lty = 1, col = legendcolors)
+ }
+ if (devices > 1 && postscript)
+ {
+ for (i in 2:devices) {
+ dev.off(i)
+ }
+ }
+}
diff --git a/chm/00Index.html b/chm/00Index.html
new file mode 100644
index 0000000..9958f5e
--- /dev/null
+++ b/chm/00Index.html
@@ -0,0 +1,24 @@
+<html><head><title>Dose-response data evaluation</title>
+<link rel="stylesheet" type="text/css" href="Rchm.css">
+</head><body>
+<h1>Dose-response data evaluation
+<img class="toplogo" src="logo.jpg" alt="[R logo]"></h1>
+
+<hr>
+
+<object type="application/x-oleobject" classid="clsid:1e2a7bd0-dab9-11d0-b93a-00c04fc99f9e">
+<param name="keyword" value=".. contents">
+</object>
+
+
+<table width="100%">
+<tr><td width="25%"><a href="antifoul.html">antifoul</a></td>
+<td>Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells</td></tr>
+<tr><td width="25%"><a href="drdata.html">drdata</a></td>
+<td>Get dose-response data</td></tr>
+<tr><td width="25%"><a href="drfit.html">drfit</a></td>
+<td>Fit dose-response models</td></tr>
+<tr><td width="25%"><a href="drplot.html">drplot</a></td>
+<td>Plot dose-response models</td></tr>
+</table>
+</body></html>
diff --git a/chm/Rchm.css b/chm/Rchm.css
new file mode 100644
index 0000000..badd579
--- /dev/null
+++ b/chm/Rchm.css
@@ -0,0 +1,25 @@
+BODY{ background: white;
+ color: black }
+
+A:link{ background: white;
+ color: blue }
+A:visited{ background: white;
+ color: rgb(50%, 0%, 50%) }
+
+H1{ background: white;
+ color: rgb(55%, 55%, 55%);
+ font-family: monospace;
+ font-size: large;
+ text-align: center }
+
+H2{ background: white;
+ color: rgb(0%, 0%, 100%);
+ font-family: monospace;
+ text-align: center }
+
+H3{ background: white;
+ color: rgb(40%, 40%, 40%);
+ font-family: monospace }
+
+IMG.toplogo{ vertical-align: middle }
+
diff --git a/chm/antifoul.html b/chm/antifoul.html
new file mode 100644
index 0000000..12ba527
--- /dev/null
+++ b/chm/antifoul.html
@@ -0,0 +1,49 @@
+<html><head><title>Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells</title>
+<link rel="stylesheet" type="text/css" href="Rchm.css">
+</head>
+<body>
+
+<table width="100%"><tr><td>antifoul(drfit)</td><td align="right">R Documentation</td></tr></table><object type="application/x-oleobject" classid="clsid:1e2a7bd0-dab9-11d0-b93a-00c04fc99f9e">
+<param name="keyword" value="R: antifoul">
+<param name="keyword" value=" Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells">
+</object>
+
+
+<h2>Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells</h2>
+
+
+<h3>Description</h3>
+
+<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>
+
+
+<h3>Usage</h3>
+
+<pre>data(rivers)</pre>
+
+
+<h3>Format</h3>
+
+<p>
+A dataframe containing 135 and 81 data points for concentrations and responses
+for TBT and Zink Pyrithione, respecitively. Additional data from the database is
+also present.
+</p>
+
+
+<h3>Source</h3>
+
+<p>
+<a href="http://www.uft.uni-bremen.de/chemie">http://www.uft.uni-bremen.de/chemie</a>
+</p>
+
+
+
+<hr><div align="center"><a href="00Index.html">[Package Contents]</a></div>
+
+</body></html>
diff --git a/chm/drdata.html b/chm/drdata.html
new file mode 100644
index 0000000..7dd4a2b
--- /dev/null
+++ b/chm/drdata.html
@@ -0,0 +1,146 @@
+<html><head><title>Get dose-response data</title>
+<link rel="stylesheet" type="text/css" href="Rchm.css">
+</head>
+<body>
+
+<table width="100%"><tr><td>drdata(drfit)</td><td align="right">R Documentation</td></tr></table><object type="application/x-oleobject" classid="clsid:1e2a7bd0-dab9-11d0-b93a-00c04fc99f9e">
+<param name="keyword" value="R: drdata">
+<param name="keyword" value=" Get dose-response data">
+</object>
+
+
+<h2>Get dose-response data</h2>
+
+
+<h3>Description</h3>
+
+<p>
+Get dose-response data from a remote mysql server
+</p>
+
+
+<h3>Usage</h3>
+
+<pre>
+ drdata(substances, experimentator = "%", db = "cytotox", celltype = "IPC-81",
+ whereClause = "1", ok = "'ok'")
+</pre>
+
+
+<h3>Arguments</h3>
+
+<table summary="R argblock">
+<tr valign="top"><td><code>substances</code></td>
+<td>
+A string or an array of strings with the substance names for
+which dose-response data is to be retrieved.</td></tr>
+<tr valign="top"><td><code>experimentator</code></td>
+<td>
+The name of the experimentator whose data is to be used.</td></tr>
+<tr valign="top"><td><code>db</code></td>
+<td>
+The database to be used. Currently only "cytotox" of the UFT Department of
+Bioorganic Chemistry is supported.</td></tr>
+<tr valign="top"><td><code>celltype</code></td>
+<td>
+Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are supported.</td></tr>
+<tr valign="top"><td><code>whereClause</code></td>
+<td>
+With this argument, additional conditions for the SQL query can be set,
+e.g. "where plate != 710". The default is 1 (in SQL syntax this means TRUE).</td></tr>
+<tr valign="top"><td><code>ok</code></td>
+<td>
+With the default value "'ok'", only data that has been checked and set to "ok"
+in the database is retrieved. Another sensible argument would be "'ok','?'", in
+order to additionally retrieve data which has not yet been checked.</td></tr>
+</table>
+
+<h3>Details</h3>
+
+<p>
+The function is currently only used for retrieving data from the
+mysql database "cytotox" of the UFT Department of Bioorganic Chemistry.
+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 &lsquo;<TT>/etc/odbcinst.ini</TT>&rsquo;
+containing:
+<table summary="Rd table">
+<tr>
+ <td align="left">[MySQL] </td> <td align="left"> </td> <td align="left"> </td>
+</tr>
+<tr>
+ <td align="left"> Description </td> <td align="left"> = </td> <td align="left"> MySQL driver for ODBC </td>
+</tr>
+<tr>
+ <td align="left"> Driver </td> <td align="left"> = </td> <td align="left"> /usr/local/lib/libmyodbc.so </td>
+</tr>
+<tr>
+ <td align="left"> Setup </td> <td align="left"> = </td> <td align="left"> /usr/lib/odbc/libodbcmyS.so </td>
+</tr>
+</table>
+<p>
+and the file &lsquo;<TT>/etc/odbc.ini</TT>&rsquo; containing:
+<table summary="Rd table">
+<tr>
+ <td align="left">[cytotox] </td> <td align="left"> </td> <td align="left"> </td>
+</tr>
+<tr>
+ <td align="left"> Description </td> <td align="left"> = </td> <td align="left"> Cytotoxicity database of the department of bioorganic chemistry, UFT Bremen </td>
+</tr>
+<tr>
+ <td align="left"> Driver </td> <td align="left"> = </td> <td align="left"> MySQL </td>
+</tr>
+<tr>
+ <td align="left"> Trace </td> <td align="left"> = </td> <td align="left"> Yes </td>
+</tr>
+<tr>
+ <td align="left"> TraceFile </td> <td align="left"> = </td> <td align="left"> /tmp/odbc.log </td>
+</tr>
+<tr>
+ <td align="left"> Database </td> <td align="left"> = </td> <td align="left"> cytotox </td>
+</tr>
+<tr>
+ <td align="left"> Server </td> <td align="left"> = </td> <td align="left"> eckehaat </td>
+</tr>
+<tr>
+ <td align="left"> Port </td> <td align="left"> = </td> <td align="left"> 3306 </td>
+</tr>
+</table>
+.
+</p>
+
+
+<h3>Value</h3>
+
+<table summary="R argblock">
+<tr valign="top"><td><code>data</code></td>
+<td>
+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.</td></tr>
+</table>
+
+<h3>Author(s)</h3>
+
+<p>
+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>
+</p>
+
+
+<h3>Examples</h3>
+
+<pre>
+# Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81 cells
+## Not run: data &lt;- drdata(c("TBT","Zn Pyrithion"))
+</pre>
+
+
+
+<hr><div align="center"><a href="00Index.html">[Package Contents]</a></div>
+
+</body></html>
diff --git a/chm/drfit.chm b/chm/drfit.chm
new file mode 100644
index 0000000..420ddab
--- /dev/null
+++ b/chm/drfit.chm
Binary files differ
diff --git a/chm/drfit.hhp b/chm/drfit.hhp
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index 0000000..f7e719a
--- /dev/null
+++ b/chm/drfit.hhp
@@ -0,0 +1,17 @@
+[OPTIONS]
+Auto Index=Yes
+Contents file=drfit.toc
+Compatibility=1.1 or later
+Compiled file=drfit.chm
+Default topic=00Index.html
+Display compile progress=No
+Full-text search=Yes
+Full text search stop list file=..\..\..\gnuwin32\help\R.stp
+
+
+[FILES]
+00Index.html
+antifoul.html
+drdata.html
+drfit.html
+drplot.html
diff --git a/chm/drfit.html b/chm/drfit.html
new file mode 100644
index 0000000..0c67eae
--- /dev/null
+++ b/chm/drfit.html
@@ -0,0 +1,99 @@
+<html><head><title>Fit dose-response models</title>
+<link rel="stylesheet" type="text/css" href="Rchm.css">
+</head>
+<body>
+
+<table width="100%"><tr><td>drfit(drfit)</td><td align="right">R Documentation</td></tr></table><object type="application/x-oleobject" classid="clsid:1e2a7bd0-dab9-11d0-b93a-00c04fc99f9e">
+<param name="keyword" value="R: drfit">
+<param name="keyword" value=" Fit dose-response models">
+</object>
+
+
+<h2>Fit dose-response models</h2>
+
+
+<h3>Description</h3>
+
+<p>
+Fit dose-response relationships to dose-response data and calculate
+biometric results for (eco)toxicity evaluation
+</p>
+
+
+<h3>Usage</h3>
+
+<pre>
+ drfit(data, startlogEC50 = NA, lognorm = TRUE, logis = FALSE,
+ linearlogis = FALSE, b0 = 2, f0 = 0)
+</pre>
+
+
+<h3>Arguments</h3>
+
+<table summary="R argblock">
+<tr valign="top"><td><code>data</code></td>
+<td>
+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 and a column
+"dose" with the numeric dose values. For later use of the
+<code><a href="drplot.html">drplot</a></code> function, a factor called "dosefactor" also has to be
+present, containing the dose as a factor.
+</td></tr>
+<tr valign="top"><td><code>startlogEC50</code></td>
+<td>
+Especially for the linearlogis model, a suitable log10 of the EC50 has to be given
+by the user, since it is not correctly estimated for data showing hormesis with
+the default estimation method.</td></tr>
+<tr valign="top"><td><code>lognorm</code></td>
+<td>
+A boolean defining if cumulative density curves of normal distributions
+are fitted to the data. Default ist TRUE.</td></tr>
+<tr valign="top"><td><code>logis</code></td>
+<td>
+A boolean defining if cumulative densitiy curves of logistic distributions
+are fitted to the data. Default is FALSE.</td></tr>
+<tr valign="top"><td><code>linearlogis</code></td>
+<td>
+A boolean defining if the linear-logistic function as defined by van Ewijk and Hoekstra
+1993 is fitted to the data. Default is FALSE.</td></tr>
+<tr valign="top"><td><code>b0,f0</code></td>
+<td>
+If the linearlogistic model is fitted, b0 and f0 give the possibility to
+adapt the starting values for the parameters b and f.</td></tr>
+</table>
+
+<h3>Value</h3>
+
+<table summary="R argblock">
+<tr valign="top"><td><code>results</code></td>
+<td>
+A data frame containing at least one line for each substance. If the data did not
+show a mean response &lt; 0.5 at the highest dose level, the modeltype is set to "none".
+Every successful fit is reported in one line. Parameters of the fitted curves are only
+reported if the fitted EC50 is not higher than the highest dose.</td></tr>
+</table>
+
+<h3>Author(s)</h3>
+
+<p>
+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>
+</p>
+
+
+<h3>Examples</h3>
+
+<pre>
+## Not run: data(antifoul)
+## Not run: r &lt;- drfit(antifoul)
+## Not run: format(r,digits=2)
+</pre>
+
+
+
+<hr><div align="center"><a href="00Index.html">[Package Contents]</a></div>
+
+</body></html>
diff --git a/chm/drfit.toc b/chm/drfit.toc
new file mode 100644
index 0000000..ceaaa27
--- /dev/null
+++ b/chm/drfit.toc
@@ -0,0 +1,51 @@
+<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML//EN">
+<HEAD></HEAD><HTML><BODY>
+<UL>
+<LI> <OBJECT type="text/sitemap">
+<param name="Name" value="Package drfit: Contents">
+<param name="Local" value="00Index.html">
+</OBJECT>
+<LI> <OBJECT type="text/sitemap">
+<param name="Name" value="Package drfit: R objects">
+</OBJECT>
+<UL>
+<LI> <OBJECT type="text/sitemap">
+<param name="Name" value="antifoul">
+<param name="Local" value="antifoul.html">
+</OBJECT>
+<LI> <OBJECT type="text/sitemap">
+<param name="Name" value="drdata">
+<param name="Local" value="drdata.html">
+</OBJECT>
+<LI> <OBJECT type="text/sitemap">
+<param name="Name" value="drfit">
+<param name="Local" value="drfit.html">
+</OBJECT>
+<LI> <OBJECT type="text/sitemap">
+<param name="Name" value="drplot">
+<param name="Local" value="drplot.html">
+</OBJECT>
+</UL>
+<LI> <OBJECT type="text/sitemap">
+<param name="Name" value="Package drfit: Titles">
+</OBJECT>
+<UL>
+<LI> <OBJECT type="text/sitemap">
+<param name="Name" value="Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells">
+<param name="Local" value="antifoul.html">
+</OBJECT>
+<LI> <OBJECT type="text/sitemap">
+<param name="Name" value="Fit dose-response models">
+<param name="Local" value="drfit.html">
+</OBJECT>
+<LI> <OBJECT type="text/sitemap">
+<param name="Name" value="Get dose-response data">
+<param name="Local" value="drdata.html">
+</OBJECT>
+<LI> <OBJECT type="text/sitemap">
+<param name="Name" value="Plot dose-response models">
+<param name="Local" value="drplot.html">
+</OBJECT>
+</UL>
+</UL>
+</BODY></HTML>
diff --git a/chm/drplot.html b/chm/drplot.html
new file mode 100644
index 0000000..34ae967
--- /dev/null
+++ b/chm/drplot.html
@@ -0,0 +1,131 @@
+<html><head><title>Plot dose-response models</title>
+<link rel="stylesheet" type="text/css" href="Rchm.css">
+</head>
+<body>
+
+<table width="100%"><tr><td>drplot(drfit)</td><td align="right">R Documentation</td></tr></table><object type="application/x-oleobject" classid="clsid:1e2a7bd0-dab9-11d0-b93a-00c04fc99f9e">
+<param name="keyword" value="R: drplot">
+<param name="keyword" value=" Plot dose-response models">
+</object>
+
+
+<h2>Plot dose-response models</h2>
+
+
+<h3>Description</h3>
+
+<p>
+Produce graphics of dose-response data and dose-response relationships
+either combined or separately, for one or more substances.
+</p>
+
+
+<h3>Usage</h3>
+
+<pre>
+ drplot(drresults, data, dtype, alpha, path, fileprefix, overlay,
+ postscript, color, colors, fitcolors)
+</pre>
+
+
+<h3>Arguments</h3>
+
+<table summary="R argblock">
+<tr valign="top"><td><code>drresults</code></td>
+<td>
+A data frame as returned from <code><a href="drfit.html">drfit</a></code>.
+</td></tr>
+<tr valign="top"><td><code>data</code></td>
+<td>
+A data frame as returned from <code><a href="drdata.html">drdata</a></code>. If data is to be
+plotted, 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. If plotting of the data is
+not required, data can be set to FALSE.
+</td></tr>
+<tr valign="top"><td><code>dtype</code></td>
+<td>
+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"). Of course, dtype only makes a difference, if a valid data
+object has been referenced.
+</td></tr>
+<tr valign="top"><td><code>alpha</code></td>
+<td>
+The confidence level, defaulting to 0.95, only used if dtype "conf" has been
+chosen.
+</td></tr>
+<tr valign="top"><td><code>path</code></td>
+<td>
+The path where graphic files should be put if any are produced. Defaults
+to "./" i.e. the current working directory of R.
+</td></tr>
+<tr valign="top"><td><code>fileprefix</code></td>
+<td>
+A string which will form the beginning of each filename, if graphic files are
+created. Defaults to "drplot".
+</td></tr>
+<tr valign="top"><td><code>overlay</code></td>
+<td>
+If TRUE, all output will be put into one graph, otherwise a separate graph
+will be created for each substance. In the latter case, on-screen display
+(postscript=FALSE) only works correctly for data plots. Dose-response models
+will all be put into the last graph in this case.
+</td></tr>
+<tr valign="top"><td><code>postscript</code></td>
+<td>
+If TRUE, (a) postscript graph(s) will be created. Otherwise, graphics will be
+displayed with a screen graphics device.
+</td></tr>
+<tr valign="top"><td><code>color</code></td>
+<td>
+If TRUE, a sensible selection of colors will be attempted. If false, everything
+will be drawn in black
+</td></tr>
+<tr valign="top"><td><code>colors</code></td>
+<td>
+This is a vector of colors, defaulting to 1:8, used for plotting the data.
+</td></tr>
+<tr valign="top"><td><code>fitcolors</code></td>
+<td>
+Here you can specify a palette for the colors of the dose-response fits. The
+default value is "default", which produces rainbow colors.
+</td></tr>
+</table>
+
+<h3>Value</h3>
+
+<table summary="R argblock">
+<tr valign="top"><td><code>results</code></td>
+<td>
+A data frame containing at least one line for each substance. If the data did not
+show a mean response &lt; 0.5 at the highest dose level, the modeltype is set to "none".
+Every successful fit is reported in one line. Parameters of the fitted curves are only
+reported if the fitted EC50 is not higher than the highest dose.</td></tr>
+</table>
+
+<h3>Author(s)</h3>
+
+<p>
+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>
+</p>
+
+
+<h3>Examples</h3>
+
+<pre>
+## Not run: data(antifoul)
+## Not run: r &lt;- drfit(antifoul)
+## Not run: format(r,digits=2)
+</pre>
+
+
+
+<hr><div align="center"><a href="00Index.html">[Package Contents]</a></div>
+
+</body></html>
diff --git a/chm/logo.jpg b/chm/logo.jpg
new file mode 100644
index 0000000..b8e2149
--- /dev/null
+++ b/chm/logo.jpg
Binary files differ
diff --git a/data/00Index b/data/00Index
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--- /dev/null
+++ b/data/00Index
@@ -0,0 +1,2 @@
+antifoul Dose-Response data for TBT and Zink Pyrithione
+ in IPC-81 cells
diff --git a/data/antifoul.rda b/data/antifoul.rda
new file mode 100644
index 0000000..5360fee
--- /dev/null
+++ b/data/antifoul.rda
@@ -0,0 +1,2410 @@
+RDA1
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+ 1.25
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+ 0.0195312
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+ 3 114
+ 3 115
+ 3 116
+ 3 117
+ 3 118
+ 3 119
+ 3 120
+ 3 121
+ 3 122
+ 3 123
+ 3 124
+ 3 125
+ 3 126
+ 3 127
+ 3 128
+ 3 129
+ 3 130
+ 3 131
+ 3 132
+ 3 133
+ 3 134
+ 3 135
+ 3 136
+ 3 137
+ 3 138
+ 3 139
+ 3 140
+ 3 141
+ 3 142
+ 3 143
+ 3 144
+ 3 145
+ 3 146
+ 3 147
+ 3 148
+ 3 149
+ 3 150
+ 3 151
+ 3 152
+ 3 153
+ 3 154
+ 3 155
+ 3 156
+ 3 157
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+ 3 159
+ 3 160
+ 3 161
+ 3 162
+ 3 163
+ 3 164
+ 3 165
+ 3 166
+ 3 167
+ 3 168
+ 3 169
+ 3 170
+ 3 171
+ 3 172
+ 3 173
+ 3 174
+ 3 175
+ 3 176
+ 3 177
+ 3 178
+ 3 179
+ 3 180
+ 3 181
+ 3 182
+ 3 183
+ 3 184
+ 3 185
+ 3 186
+ 3 187
+ 3 188
+ 3 189
+ 3 190
+ 3 191
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+ 3 194
+ 3 195
+ 3 196
+ 3 197
+ 3 198
+ 3 199
+ 3 200
+ 3 201
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+ 3 204
+ 3 205
+ 3 206
+ 3 207
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+ 3 210
+ 3 211
+ 3 212
+ 3 213
+ 3 214
+ 3 215
+ 3 216
+-1
+2 0 0
+1 0 0
+3
+-1
+16 0 0
+1
+ 10 data.frame
+-1
+-1
+-1
+-1
+-1
+-1
+-1
diff --git a/man/antifoul.Rd b/man/antifoul.Rd
new file mode 100644
index 0000000..2f4ae85
--- /dev/null
+++ b/man/antifoul.Rd
@@ -0,0 +1,20 @@
+\name{antifoul}
+\docType{data}
+\alias{antifoul}
+\title{Dose-Response data for TBT and Zink Pyrithione in IPC-81 cells}
+\description{
+ 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
+}
+\usage{data(rivers)}
+\format{
+ A dataframe containing 135 and 81 data points for concentrations and responses
+ for TBT and Zink Pyrithione, respecitively. Additional data from the database is
+ also present.
+}
+\source{
+ \url{http://www.uft.uni-bremen.de/chemie}
+}
+\keyword{datasets}
diff --git a/man/drdata.Rd b/man/drdata.Rd
new file mode 100644
index 0000000..b9f8660
--- /dev/null
+++ b/man/drdata.Rd
@@ -0,0 +1,74 @@
+\name{drdata}
+\alias{drdata}
+\title{Get dose-response data}
+\description{
+ Get dose-response data from a remote mysql server
+}
+\usage{
+ drdata(substances, experimentator = "\%", db = "cytotox", celltype = "IPC-81",
+ whereClause = "1", ok = "'ok'")
+}
+\arguments{
+ \item{substances}{
+ A string or an array of strings with the substance names for
+ which dose-response data is to be retrieved.}
+ \item{experimentator}{
+ The name of the experimentator whose data is to be used.}
+ \item{db}{
+ The database to be used. Currently only "cytotox" of the UFT Department of
+ Bioorganic Chemistry is supported.}
+ \item{celltype}{
+ Currently, only data for IPC-81, C6, NB4, HeLa, Jurkat and U937 are supported.}
+ \item{whereClause}{
+ With this argument, additional conditions for the SQL query can be set,
+ e.g. "where plate != 710". The default is 1 (in SQL syntax this means TRUE).}
+ \item{ok}{
+ With the default value "'ok'", only data that has been checked and set to "ok"
+ in the database is retrieved. Another sensible argument would be "'ok','?'", in
+ order to additionally retrieve data which has not yet been checked.}
+}
+\value{
+ \item{data}{
+ 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.}
+}
+\details{
+ The function is currently only used for retrieving data from the
+ mysql database "cytotox" of the UFT Department of Bioorganic Chemistry.
+ 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 \file{/etc/odbcinst.ini}
+ containing:
+ \tabular{lll}{
+ [MySQL] \tab \tab \cr
+ Description \tab = \tab MySQL driver for ODBC \cr
+ Driver \tab = \tab /usr/local/lib/libmyodbc.so \cr
+ Setup \tab = \tab /usr/lib/odbc/libodbcmyS.so \cr
+ }
+ and the file \file{/etc/odbc.ini} containing:
+ \tabular{lll}{
+ [cytotox] \tab \tab \cr
+ Description \tab = \tab Cytotoxicity database of the department of bioorganic chemistry, UFT Bremen \cr
+ Driver \tab = \tab MySQL \cr
+ Trace \tab = \tab Yes \cr
+ TraceFile \tab = \tab /tmp/odbc.log \cr
+ Database \tab = \tab cytotox \cr
+ Server \tab = \tab eckehaat \cr
+ Port \tab = \tab 3306 \cr
+ }.
+}
+\examples{
+# Get cytotoxicity data for Tributyltin and zinc pyrithione, tested with IPC-81 cells
+\dontrun{data <- drdata(c("TBT","Zn Pyrithion"))}
+}
+\author{
+ Johannes Ranke
+ \email{jranke@uni-bremen.de}
+ \url{http://www.uft.uni-bremen.de/chemie/ranke}
+}
+\keyword{IO}
+\keyword{database}
diff --git a/man/drfit.Rd b/man/drfit.Rd
new file mode 100644
index 0000000..6e39032
--- /dev/null
+++ b/man/drfit.Rd
@@ -0,0 +1,59 @@
+\name{drfit}
+\alias{drfit}
+\title{Fit dose-response models}
+\description{
+ Fit dose-response relationships to dose-response data and calculate
+ biometric results for (eco)toxicity evaluation
+}
+\usage{
+ drfit(data, startlogEC50 = NA, lognorm = TRUE, logis = FALSE,
+ linearlogis = FALSE, b0 = 2, f0 = 0)
+}
+\arguments{
+ \item{data}{
+ A data frame as returned from \code{\link{drdata}}. 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 and a column
+ "dose" with the numeric dose values. For later use of the
+ \code{\link{drplot}} function, a factor called "dosefactor" also has to be
+ present, containing the dose as a factor.
+ }
+ \item{startlogEC50}{
+ Especially for the linearlogis model, a suitable log10 of the EC50 has to be given
+ by the user, since it is not correctly estimated for data showing hormesis with
+ the default estimation method.}
+ \item{lognorm}{
+ A boolean defining if cumulative density curves of normal distributions
+ are fitted to the data. Default ist TRUE.}
+ \item{logis}{
+ A boolean defining if cumulative densitiy curves of logistic distributions
+ are fitted to the data. Default is FALSE.}
+ \item{linearlogis}{
+ A boolean defining if the linear-logistic function as defined by van Ewijk and Hoekstra
+ 1993 is fitted to the data. Default is FALSE.}
+ \item{b0,f0}{
+ If the linearlogistic model is fitted, b0 and f0 give the possibility to
+ adapt the starting values for the parameters b and f.}
+}
+\value{
+ \item{results}{
+ A data frame containing at least one line for each substance. If the data did not
+ show a mean response < 0.5 at the highest dose level, the modeltype is set to "none".
+ Every successful fit is reported in one line. Parameters of the fitted curves are only
+ reported if the fitted EC50 is not higher than the highest dose.}
+
+}
+\examples{
+\dontrun{data(antifoul)}
+\dontrun{r <- drfit(antifoul)}
+\dontrun{format(r,digits=2)}
+}
+\author{
+ Johannes Ranke
+ \email{jranke@uni-bremen.de}
+ \url{http://www.uft.uni-bremen.de/chemie/ranke}
+}
+\keyword{models}
+\keyword{regression}
+\keyword{nonlinear}
diff --git a/man/drplot.Rd b/man/drplot.Rd
new file mode 100644
index 0000000..bb4826e
--- /dev/null
+++ b/man/drplot.Rd
@@ -0,0 +1,86 @@
+\name{drplot}
+\alias{drplot}
+\title{Plot dose-response models}
+\description{
+ Produce graphics of dose-response data and dose-response relationships
+ either combined or separately, for one or more substances.
+}
+\usage{
+ drplot(drresults, data, dtype, alpha, path, fileprefix, overlay,
+ postscript, color, colors, fitcolors)
+}
+\arguments{
+ \item{drresults}{
+ A data frame as returned from \code{\link{drfit}}.
+ }
+ \item{data}{
+ A data frame as returned from \code{\link{drdata}}. If data is to be
+ plotted, 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. If plotting of the data is
+ not required, data can be set to FALSE.
+ }
+ \item{dtype}{
+ 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"). Of course, dtype only makes a difference, if a valid data
+ object has been referenced.
+ }
+ \item{alpha}{
+ The confidence level, defaulting to 0.95, only used if dtype "conf" has been
+ chosen.
+ }
+ \item{path}{
+ The path where graphic files should be put if any are produced. Defaults
+ to "./" i.e. the current working directory of R.
+ }
+ \item{fileprefix}{
+ A string which will form the beginning of each filename, if graphic files are
+ created. Defaults to "drplot".
+ }
+ \item{overlay}{
+ If TRUE, all output will be put into one graph, otherwise a separate graph
+ will be created for each substance. In the latter case, on-screen display
+ (postscript=FALSE) only works correctly for data plots. Dose-response models
+ will all be put into the last graph in this case.
+ }
+ \item{postscript}{
+ If TRUE, (a) postscript graph(s) will be created. Otherwise, graphics will be
+ displayed with a screen graphics device.
+ }
+ \item{color}{
+ If TRUE, a sensible selection of colors will be attempted. If false, everything
+ will be drawn in black
+ }
+ \item{colors}{
+ This is a vector of colors, defaulting to 1:8, used for plotting the data.
+ }
+ \item{fitcolors}{
+ Here you can specify a palette for the colors of the dose-response fits. The
+ default value is "default", which produces rainbow colors.
+ }
+}
+\value{
+ \item{results}{
+ A data frame containing at least one line for each substance. If the data did not
+ show a mean response < 0.5 at the highest dose level, the modeltype is set to "none".
+ Every successful fit is reported in one line. Parameters of the fitted curves are only
+ reported if the fitted EC50 is not higher than the highest dose.}
+
+}
+\examples{
+\dontrun{data(antifoul)}
+\dontrun{r <- drfit(antifoul)}
+\dontrun{format(r,digits=2)}
+}
+\author{
+ Johannes Ranke
+ \email{jranke@uni-bremen.de}
+ \url{http://www.uft.uni-bremen.de/chemie/ranke}
+}
+\keyword{models}
+\keyword{regression}
+\keyword{nonlinear}

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