Nothing
"plotD"<-function (y, dose, baseline, se = TRUE, line = TRUE,
meansOnly=FALSE,sem=NULL,clev = 0.9,
xlab='Dose',ylab='Response', logScale=FALSE)
{
cadj <- abs(qnorm((1 - clev)/2))
if(meansOnly && se && missing(sem))stop('sem must be specified with means only and se=TRUE')
if(meansOnly && !missing(baseline))stop('Covariate adjustment and means only cannot be specified')
if(meansOnly){
dord<-order(dose)
ym<-y[dord]
doselev<-dose[dord]
}else{
doselev <- sort(unique(dose))
if(missing(baseline)){
ym <- tapply(y, dose, mean, na.rm = TRUE)
sem <- sqrt(tapply(y, dose, var, na.rm = TRUE)/tapply(!is.na(y),
dose, sum, na.rm = TRUE))
}else{
anova.fit<-lm(y~baseline+factor(dose))
predat<-data.frame(dose=doselev,baseline=rep(mean(baseline),length(doselev)))
pred.anova<-predict(anova.fit,predat,se.fit= TRUE)
ym<-pred.anova$fit
sem<-pred.anova$se.fit
}
}
if(is.null(sem))sem<-numeric(length(ym))
chvec<-ym + cadj * sem
clvec<-ym - cadj * sem
if(!logScale){
ggp<-ggplot(data.frame(ym,doselev,chvec,clvec),aes(x=doselev,y=ym))
ggp<-ggp + geom_point(size=4,shape=8,color='red')
if (se == TRUE)
ggp<-ggp + geom_errorbar(aes(ymax=chvec,ymin=clvec))
if (line == TRUE)
ggp<-ggp + geom_line()
}else{
x0 <- doselev
if(sum(x0==0)){
doselevlog <- doselev
doselevlog[doselev==0] <- doselev[2]^2/doselev[3]
ggp<-ggplot(data.frame(ym,doselevlog,chvec,clvec),aes(x=log(doselevlog),y=ym))
ggp<-ggp + scale_x_continuous(breaks=log(doselevlog),
labels=c(format(round(doselev, 0), nsmall=0)))
ggp<-ggp + geom_point(size=4,shape=8,color='red')
if (se == TRUE)
ggp<-ggp + geom_errorbar(aes(ymax=chvec,ymin=clvec))
if (line == TRUE){
data <- data.frame(ym,doselevlog,chvec,clvec)
#data1 <- subset(data, data$doselevlog < doselevlog[2] & data$doselevlog >= doselevlog[1])
data2 <- subset(data, data$doselevlog >= doselevlog[2])
ggp<-ggp+geom_line(data=data, aes(x=log(doselevlog),ym),color='black',size=0.6, linetype="dashed")
ggp<-ggp+geom_line(data=data2, aes(x=log(doselevlog),ym),color='black',size=0.6, linetype="solid")
}
}else{
doselevlog <- doselev
ggp<-ggplot(data.frame(ym,doselevlog,chvec,clvec),aes(x=log(doselevlog),y=ym))
ggp<-ggp + scale_x_continuous(breaks=log(doselevlog),
labels=doselev)
ggp<-ggp + geom_point(size=4,shape=8,color='red')
if (se == TRUE)
ggp<-ggp + geom_errorbar(aes(ymax=chvec,ymin=clvec))
if (line == TRUE)
ggp<-ggp + geom_line()
}
}
ggp <- ggp +ylab(ylab) + xlab(xlab) + ggplot2::theme_bw()
## remove the vertical grid lines
ggp <- ggp+ ggplot2::theme(panel.grid.major.x=element_blank(),
panel.grid.minor.x=element_blank(),
panel.grid.major.y=element_line(size=0.1))
return(list(ggp = ggp, means = ym, se = sem))
}
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