diff options
| -rw-r--r-- | DESCRIPTION | 4 | ||||
| -rw-r--r-- | R/drfit.R | 177 | ||||
| -rw-r--r-- | man/drfit.Rd | 10 | ||||
| -rw-r--r-- | man/drplot.Rd | 32 | ||||
| -rw-r--r-- | man/linearlogisf.Rd | 6 |
5 files changed, 118 insertions, 111 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index 15ffa95..69f3d1d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: drfit -Version: 0.03-13 -Date: 2005-02-24 +Version: 0.03-16 +Date: 2005-02-25 Title: Dose-response data evaluation Author: Johannes Ranke <jranke@uni-bremen.de> Maintainer: Johannes Ranke <jranke@uni-bremen.de> @@ -38,7 +38,8 @@ linearlogisf <- function(x,k,f,mu,b) drfit <- function(data, startlogEC50 = NA, chooseone=TRUE,
lognorm = TRUE, logis = FALSE,
- linearlogis = FALSE, b0 = 2, f0 = 0)
+ linearlogis = FALSE, linearlogisWrong = NA,
+ b0 = 2, f0 = 0)
{
substances <- levels(data$substance)
unit <- levels(as.factor(data$unit))
@@ -67,6 +68,7 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE, } else {
nodata = FALSE
}
+ rix <- ri
if (!nodata) {
if (is.na(startlogEC50[i])){
w <- 1/abs(tmp$response - 0.3)
@@ -77,11 +79,11 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE, lhd <- log10(highestdose)
lld <- log10(lowestdose)
responseathighestdose <- mean(subset(tmp,dose==highestdose)$response)
- rix <- ri
if (responseathighestdose < 0.5) {
inactive <- FALSE
- if (linearlogis) {
+ if (linearlogis &&
+ length(subset(linearlogisWrong,linearlogisWrong == i))==0) {
m <- try(nls(response ~ linearlogisf(dose,1,f,logEC50,b),
data=tmp,
start=list(f=f0,logEC50=startlogEC50[[i]],b=b0)))
@@ -223,8 +225,7 @@ drplot <- function(drresults, data, dtype = "std", alpha = 0.95, }
# Get the plot limits on the x-axis (log of the dose)
- if(is.data.frame(data))
- {
+ if(is.data.frame(data)) {
if (min(data$dose == 0)) {
cat("At least one of the dose levels is 0 - this is not a valid dose.")
} else {
@@ -277,94 +278,98 @@ drplot <- function(drresults, data, dtype = "std", alpha = 0.95, for (i in dsubstances) {
n <- n + 1
tmp <- splitted[[i]]
- color <- colors[[n]]
- # Prepare the single graphs if an overlay is not requested
- if (!overlay)
- {
- if (postscript) {
- filename = paste(path,fileprefix,sub(" ","_",gsub("([\(\) ])", "", i)),".eps",sep="")
- postscript(file=filename,
- paper="special",width=7,height=7,horizontal=FALSE,pointsize=12)
- cat("Created File: ",filename,"\n")
- }
- if (png) {
- filename = paste(path,fileprefix,sub(" ","_",gsub("([\(\) ])", "", i)),".png",sep="")
- png(filename=filename,
- width=500, height=500,pointsize=12)
- cat("Created File: ",filename,"\n")
- }
- if (!postscript && !png) {
- 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")
- }
- if (!overlay) legend(lhd - 1, hr + 0.1, i,lty = 1, col = color)
- tmp$dosefactor <- factor(tmp$dose) # necessary because the old
- # factor has all levels, not
- # only the ones tested with
- # this substance
- # Plot the data, if requested
- if (dtype != "none") {
- if (dtype == "raw") {
- points(log10(tmp$dose),tmp$response,col=color)
- } 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")
+ if (length(tmp$response) != 0) {
+ color <- colors[[n]]
+ # Prepare the single graphs if an overlay is not requested
+ if (!overlay)
{
- confidencedeltas <- qt((1 + alpha)/2, lengths - 1) * sqrt(vars)
- tops <- means + confidencedeltas
- bottoms <- means - confidencedeltas
- }
- if (dtype != "raw")
- {
- x <- log10(as.numeric(levels(tmp$dosefactor)))
- segments(x,bottoms,x,tops,col=color)
- points(x,means,col=color)
- smidge <- 0.05
- segments(x - smidge,bottoms,x + smidge,bottoms,col=color)
- segments(x - smidge,tops,x + smidge,tops,col=color)
+ if (postscript) {
+ filename = paste(path,fileprefix,sub(" ","_",gsub("([\(\) ])", "", i)),".eps",sep="")
+ postscript(file=filename,
+ paper="special",width=7,height=7,horizontal=FALSE,pointsize=12)
+ cat("Created File: ",filename,"\n")
+ }
+ if (png) {
+ filename = paste(path,fileprefix,sub(" ","_",gsub("([\(\) ])", "", i)),".png",sep="")
+ png(filename=filename,
+ width=500, height=500,pointsize=12)
+ cat("Created File: ",filename,"\n")
+ }
+ if (!postscript && !png) {
+ 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 fits, if there are any
- fits <- subset(drresults,Substance == i)
- nf <- length(fits$Substance) # number of fits to plot
- if (nf > 0) {
- for (j in 1:nf)
- {
- logEC50 <- fits[j,"logEC50"]
- mtype <- as.character(fits[j, "mtype"])
- if (mtype == "lognorm") {
- slope <- fits[j,"slope"]
- plot(function(x) pnorm(-x,-logEC50,slope),lld - 0.5, lhd + 2, add=TRUE,col=color)
+ if (!overlay) legend(lhd - 1, hr + 0.1, i,lty = 1, col = color)
+ tmp$dosefactor <- factor(tmp$dose) # necessary because the old
+ # factor has all levels, not
+ # only the ones tested with
+ # this substance
+ # Plot the data, if requested
+ if (dtype != "none") {
+ if (dtype == "raw") {
+ points(log10(tmp$dose),tmp$response,col=color)
+ } else {
+ splitresponses <- split(tmp$response,tmp$dosefactor)
+ means <- sapply(splitresponses,mean)
+ lengths <- sapply(splitresponses,length)
+ vars <- sapply(splitresponses,var)
+ standarddeviations <- sqrt(vars)
+ }
+ if (dtype == "std")
+ {
+ tops <- means + standarddeviations
+ bottoms <- means - standarddeviations
+ }
+ if (dtype == "conf")
+ {
+ confidencedeltas <- qt((1 + alpha)/2, lengths - 1) * sqrt(vars)
+ tops <- means + confidencedeltas
+ bottoms <- means - confidencedeltas
}
- if (mtype == "logis") {
- slope <- fits[j,"slope"]
- plot(function(x) plogis(-x,-logEC50,slope),lld - 0.5, lhd + 2, add=TRUE,col=color)
+ if (dtype != "raw")
+ {
+ x <- log10(as.numeric(levels(tmp$dosefactor)))
+ segments(x,bottoms,x,tops,col=color)
+ points(x,means,col=color)
+ smidge <- 0.05
+ segments(x - smidge,bottoms,x + smidge,bottoms,col=color)
+ segments(x - smidge,tops,x + smidge,tops,col=color)
}
- if (mtype == "linearlogis") {
- plot(function(x) linearlogisf(10^x,1,fits[j,"f"],fits[j,"logEC50"],fits[j,"b"]),
- lld - 0.5, lhd + 2,
- add=TRUE,col=color)
+ }
+
+ # Plot the fits, if there are any
+ fits <- subset(drresults,Substance == i)
+ nf <- length(fits$Substance) # number of fits to plot
+ if (nf > 0) {
+ for (j in 1:nf)
+ {
+ logEC50 <- fits[j,"logEC50"]
+ mtype <- as.character(fits[j, "mtype"])
+ if (mtype == "lognorm") {
+ slope <- fits[j,"slope"]
+ plot(function(x) pnorm(-x,-logEC50,slope),lld - 0.5, lhd + 2, add=TRUE,col=color)
+ }
+ if (mtype == "logis") {
+ slope <- fits[j,"slope"]
+ plot(function(x) plogis(-x,-logEC50,slope),lld - 0.5, lhd + 2, add=TRUE,col=color)
+ }
+ if (mtype == "linearlogis") {
+ plot(function(x) linearlogisf(10^x,1,fits[j,"f"],fits[j,"logEC50"],fits[j,"b"]),
+ lld - 0.5, lhd + 2,
+ add=TRUE,col=color)
+ }
}
}
+ if (!overlay && (postscript || png)) dev.off()
+ } else {
+ cat("No data for ",i,"\n")
}
- if (!overlay && (postscript || png)) dev.off()
}
}
if (overlay) legend(lhd - 1, hr + 0.1, dsubstances,lty = 1, col = colors)
diff --git a/man/drfit.Rd b/man/drfit.Rd index 30f3fd4..ddcf80b 100644 --- a/man/drfit.Rd +++ b/man/drfit.Rd @@ -7,7 +7,7 @@ } \usage{ drfit(data, startlogEC50 = NA, chooseone = TRUE, lognorm = TRUE, logis = FALSE, - linearlogis = FALSE, b0 = 2, f0 = 0) + linearlogis = FALSE, linearlogisWrong = NA, b0 = 2, f0 = 0) } \arguments{ \item{data}{ @@ -30,8 +30,12 @@ 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.} + A boolean defining if the linear-logistic function + \code{\link{linearlogisf}} as defined by van Ewijk and Hoekstra 1993 is + fitted to the data. Default is FALSE.} + \item{linearlogisWrong}{ + An optional vector containing the names of the substances for which the + linearlogis function produces a wrong fit.} \item{chooseone}{ If TRUE (default), the models are tried in the order linearlogis, logis and lognorm, and the first model that produces a valid fit is used. Usually this will be the one diff --git a/man/drplot.Rd b/man/drplot.Rd index 418de15..784b65b 100644 --- a/man/drplot.Rd +++ b/man/drplot.Rd @@ -7,7 +7,7 @@ } \usage{ drplot(drresults, data, dtype, alpha, path, fileprefix, overlay, - postscript, color, datacolors, fitcolors) + postscript, png, bw, colors) } \arguments{ \item{drresults}{ @@ -46,23 +46,21 @@ 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 + If TRUE, (a) postscript graph(s) will be created. Otherwise, and if + the png argument is also FALSE, 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{png}{ + If TRUE, (a) png graph(s) will be created. Otherwise, and if the + postscript argument is also FALSE, graphics will be displayed with a + screen graphics device. } - \item{datacolors}{ - This is a vector of colors, defaulting to 1:8, used for plotting the data. + \item{bw}{ + A boolean deciding if the plots will be black and white or not. Default + is TRUE. } - \item{fitcolors}{ - Here you can specify a palette for the colors of the dose-response fits. The - default value is "default", which produces the default palette, if the - number of fits to be plotted is 8 or less. Otherwise, rainbow colors - will be plotted. Unless there is more than one fit per substance to be plotted, - or the number of fits is larger than 8, the fitcolors will match the - datacolors. + \item{colors}{ + This is a vector of colors, defaulting to 1:8, used for plotting the data. } } \value{ @@ -73,9 +71,9 @@ } \note{ - Turn off the colors if you don't like them and don't want to fiddle with - them. Treatment of legends is quite bad. Be sure all devices are closed - (e.g. by calling \code{dev.off()}) before calling \code{drplot} again. + Treatment of legends is not really well solved. Be sure all devices are + closed (e.g. by calling \code{dev.off()}) before calling \code{drplot} + again after a failure. } \examples{ data(antifoul) diff --git a/man/linearlogisf.Rd b/man/linearlogisf.Rd index d49dc9a..1ebe8be 100644 --- a/man/linearlogisf.Rd +++ b/man/linearlogisf.Rd @@ -23,9 +23,9 @@ \value{ The response at dose x. } -\examples{ - -} +\references{ + van Ewijk, P. H. and Hoekstra, J. A. (1993) \emph{Ecotox Environ Safety} + \bold{25} 25-32} \author{ Johannes Ranke \email{jranke@uni-bremen.de} |