R/norm.plot.R

In isubirana/compareGroups: Descriptive Analysis by Groups

norm.plot<-function(x, file, var.label.x, z, n.breaks, ...)
{

  x<-x[!is.na(x)]
  if (length(unique(x))<5){
    return(NULL)
    warning(paste("too few valid different values for variable",var.label.x))
  }
  
  dots.args <- eval(substitute(alist(...))) 
  onefile <- FALSE
  if (!is.null(dots.args$onefile))
    onefile<- dots.args$onefile

  if (is.null(file))
    {} #dev.new()
  else {
    if (length(grep("bmp$",file)))
      bmp(file,...) 
    if (length(grep("png$",file)))
      png(file,...)  
    if (length(grep("tif$",file)))
      tiff(file,...)  
    if (length(grep("jpg$",file)))
      jpeg(file,...)  
    if (length(grep("pdf$",file)))
      if (!onefile)
        pdf(file,...)                             
  }

  mean<-mean(x,na.rm=TRUE)
  sd<-sd(x,na.rm=TRUE)
  Z.x<-(x-mean)/sd
  qqnorm<-qqnorm(Z.x,plot=FALSE)
  dif<-qqnorm$y-qqnorm$x
  
  par(mfrow=c(2,2),mar=c(3,3,3,1),mgp=c(2,0.5,0),oma=c(3,0,3,0))
  hist(x,probability=TRUE,main="Histogram",xlab="",ylab="",col="red",breaks=n.breaks)
  dens<-dnorm(seq(min(x),max(x),len=1000),mean,sd)
  lines(seq(min(x),max(x),len=1000),dens)
  mtext(paste("mean=",format2(mean)," SD=",format2(sd)))
  box()
  qqnorm(x,datax=TRUE,pch=19,cex=0.09)
  qqline(unclass(x),datax=TRUE)
  boxplot(x,main="Boxplot",pch=19,cex=0.09,outline=TRUE,col="red")
  plot(qqnorm$y*sd+mean,dif,pch=19,cex=0.01,xlab="",ylab="desv.",main="Standard deviation\nfrom normality")
	abline(h=c(-z,0,z),lty=c(2,4,2))
  p.sh<-try(shapiro.test(x)$p.value,silent=TRUE)
  title(paste("Normality plots of '",var.label.x,"'",sep=""), outer=TRUE, cex=2)
  if (!inherits(p.sh,"try-error")){
    mtext(paste("Shapiro-Wilks p-value: ",format2(p.sh,3),sep=""), side=1, outer=TRUE)
  } else {
    warning(paste0("p-value for normality in ",var.label.x," could not be calculated"))
  }
  par(mfrow=c(1,1))
  
  if (!is.null(file) && (length(grep("pdf$",file))==0 || !onefile))
    dev.off()

}