R/plot.Diffepoce.R

In lcmm: Extended Mixed Models Using Latent Classes and Latent Processes

#' @rdname plot.pred.accuracy
#' @export
plot.Diffepoce <- function(x,...)
{
	if (!inherits(x, "Diffepoce")) stop("use only with \"Diffepoce\" objects")

	#if (is.null(ylim) & all(is.na(x$DiffEPOCE[,3]))|all(is.na(x$DiffEPOCE[,4]))) stop("can't produce the plot with missing differences in EPOCE")
   if (all(is.na(x$DiffEPOCE[,3]))|all(is.na(x$DiffEPOCE[,4]))) stop("can't produce the plot with missing differences in EPOCE")

   dots <- list(...)

        if(length(list(...)$add))
            {
                add <- eval(dots$add)
            }
        else
            add <- FALSE

   if(length(list(...)$main)) 
   {
    title1 <- as.character(eval(dots$main))
    dots <- dots[setdiff(names(dots),"main")]
   }
   else title1 <- "Difference in EPOCE estimates"  
   
   if(length(list(...)$col)) 
   {
    color <- as.vector(eval(dots$col))
    dots <- dots[-which(names(dots)=="col")]
   }
   else  color <- c("black","black","black","lightgrey")                             

   if(length(list(...)$type))    
   {
    type1 <- eval(dots$type)
    dots <- dots[-which(names(dots)=="type")]
   }
   else  type1 <- c("o","o","o","l")

   if(length(list(...)$pch))    
   {
    pch1 <- eval(dots$pch)
    dots <- dots[-which(names(dots)=="pch")]
   }
   else  pch1 <- c(18,18,18,NA)

   if(length(list(...)$lty))    
   {
    lty1 <- eval(dots$lty)
    dots <- dots[-which(names(dots)=="lty")]
   }
   else  lty1 <- c(1,3,3,1)

   if(length(list(...)$ylim)) 
   {
    ylim1 <- eval(dots$ylim)
    dots <- dots[setdiff(names(dots),"ylim")]
   }
   else ylim1 <- c(min(x$DiffEPOCE[!(is.na(x$DiffEPOCE[,2])),2],x$DiffEPOCE[!(is.na(x$DiffEPOCE[,3])),3]),max(x$DiffEPOCE[!(is.na(x$DiffEPOCE[,2])),2],x$DiffEPOCE[!(is.na(x$DiffEPOCE[,4])),4]))
   
   if(length(list(...)$xlab)) 
   {
    xlab1 <- as.character(eval(dots$xlab))
    dots <- dots[setdiff(names(dots),"xlab")]
   }
   else xlab1 <- "prediction time"

   if(length(list(...)$ylab)) 
   {
    ylab1 <- as.character(eval(dots$ylab))
    dots <- dots[setdiff(names(dots),"ylab")]
   }
   else 
   {
  	if(x$new.data==FALSE) 
    {
		 ylab1 <- expression(Delta(CVPOL))
	  }
    else
    {
		 ylab1 <- expression(Delta(MPOL))	
    }
   }   


#ylim1 <- ylim
#if (is.null(ylim)){
#ylim1 <- c(min(x$DiffEPOCE[!(is.na(x$DiffEPOCE[,2])),2],x$DiffEPOCE[!(is.na(x$DiffEPOCE[,3])),3]),max(x$DiffEPOCE[!(is.na(x$DiffEPOCE[,2])),2],x$DiffEPOCE[!(is.na(x$DiffEPOCE[,4])),4]))	
#}
#xlim1 <- xlim
#if (is.null(xlim)){
#xlim1 <- c(min(x$DiffEPOCE[,1]),max(x$DiffEPOCE[,1]))
#}
#
#plot(x$DiffEPOCE[,1],x$DiffEPOCE[,2],pch=18,lty=1,type="o",xlab="prediction time",ylab=title,main=,bty="l",ylim=ylim1,xlim=xlim1,...)
#par(new=T)
#plot(x$DiffEPOCE[,1],x$DiffEPOCE[,3],pch=18,type="o",lty=3,xlab="prediction time",ylab=title,main="Difference in EPOCE estimates",bty="l",ylim=ylim1,xlim=xlim1,...)
#par(new=T)
#plot(x$DiffEPOCE[,1],x$DiffEPOCE[,4],pch=18,type="o",lty=3,xlab="prediction time",ylab=title,main="Difference in EPOCE estimates",bty="l",ylim=ylim1,xlim=xlim1,...)
#par(new=T)
#plot(x$DiffEPOCE[,1],rep(0,length(x$DiffEPOCE[,1])),lty=1,type="l",col="lightgrey",xlab="prediction time",ylab=title,bty="l",ylim=ylim1,xlim=xlim1,...)
#

   
  names.plot <- c("adj","ann","asp","axes","bg","bty","cex","cex.axis","cex.lab","cex.main","cex.sub","col","col.axis",
  "col.lab","col.main","col.sub","crt","err","family","fig","fin","font","font.axis","font.lab","font.main","font.sub",
  "frame.plot","lab","las","lend","lheight","ljoin","lmitre","lty","lwd","mai","main","mar","mex","mgp","mkh","oma",
  "omd","omi","pch","pin","plt","ps","pty","smo","srt","sub","tck","tcl","type","usr","xaxp","xaxs","xaxt","xlab",
  "xlim","xpd","yaxp","yaxs","yaxt","ylab","ylbias","ylim") 
  dots.plot <- dots[intersect(names(dots),names.plot)]

        if(add==FALSE)
            {
                do.call("matplot",c(dots.plot,list(x=x$DiffEPOCE[,1],y=cbind(x$DiffEPOCE[,2:4], 0),xlab=xlab1,ylab=ylab1,main=title1,type=type1,col=color,pch=pch1,lty=lty1,ylim=ylim1)))
            }
        else
            {
                title1 <- ""
                xlab1 <- ""
                ylab1 <- ""

                do.call("matpoints",c(dots.plot,list(x=x$DiffEPOCE[,1],y=x$DiffEPOCE[,2:4],xlab=xlab1,ylab=ylab1,main=title1,type=type1,col=color,pch=pch1,lty=lty1,ylim=ylim1)))
            }
}