Nothing
plot.meta4diag = function(x, var.type="var1", add=FALSE, overlay.prior = TRUE, save = FALSE, width=5, height=5, ...){
if(is.logical(save)){
if(save){
mainDir <- getwd()
subDir <- "meta4diagPlot"
if (file.exists(subDir)){
file.name = paste(subDir,"/",var.type,".pdf",sep="")
} else {
dir.create(file.path(mainDir, subDir))
file.name = paste(subDir,"/",var.type,".pdf",sep="")
}
}
}else{
if(is.character(save)){
mainDir <- getwd()
subDir <- "meta4diagPlot"
if (!file.exists(subDir)){
dir.create(file.path(mainDir, subDir))
}
name_temp = unlist(strsplit(basename(save), "[.]"))
fileform = name_temp[length(name_temp)]
if(fileform %in% c("pdf","eps","jpg","png")){
file.name = paste(subDir,"/",save,sep="")
}else{
stop("Please give the correct file name!")
}
}else{
stop("Argument \"save\" could be FALSE, TRUE or a file name.")
}
}
fixed.name = rownames(x$summary.fixed)
hyper.name = rownames(x$summary.hyperpar)
fullnames = c(fixed.name, hyper.name, "var1", "var2", "rho")
if(!(var.type %in% fullnames)){
stop(paste("Please give the correct \"type\" name, which should be ", paste(fullnames,collapse=", ")," var1, var2, rho.",sep=""))
}
if(var.type=="var1"){var.type="var_phi"}
if(var.type=="var2"){var.type="var_psi"}
if(var.type=="rho"){var.type="cor"}
fixed.prior = data.frame(x=seq(-10,10,len=100),y=dnorm(seq(-10,10,len=100),mean=0,sd=sqrt(1000)))
fullmarginals = append(x$marginals.fixed,x$marginals.hyperpar)
ind = which(fullnames==var.type)
if(var.type=="var_phi" || var.type=="var_psi"){
marginals.plot = fullmarginals[[ind]]
}else{
marginals.plot = INLA::inla.smarginal(fullmarginals[[ind]])
}
xlabnames = c(fixed.name, rownames(x$summary.hyperpar))
if(add){
lines(marginals.plot, ...)
}else{
if(is.logical(save)){
if(save){
pdf(file.name, width=width, height=height)
}
}else{
if(fileform=="eps"){
setEPS()
postscript(file.name, width=width, height=height)
}else if(fileform=="pdf"){
pdf(file.name, width=width, height=height)
}else if(fileform=="jpg"){
jpeg(filename = file.name,
width = width, height = height, units = "in")
}else{
png(filename = file.name,
width = width, height = height, units = "in")
}
}
plot(marginals.plot, type="l", xlab=xlabnames[ind], ylab="",xaxs = "r",xaxt="s",yaxt="s",bty="o",...)
if(!x$misc$wishart.flag){
if(overlay.prior){
if(var.type %in% c("var_phi","var_psi","cor")){
if(var.type=="var_phi"){
lines(x$priors.density[[1]],lty=2,col="darkgray")
}else if(var.type == "var_psi"){
lines(x$priors.density[[2]],lty=2,col="darkgray")
}else{
lines(x$priors.density[[3]],lty=2,col="darkgray")
}
}else{
lines(fixed.prior,lty=2,col="darkgray")
}
}
}
if(save==TRUE || is.character(save)==TRUE){
dev.off()
}
}
}
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