R/mcmcplot1.R

In s-mckay-curtis/mcmcplots: Create Plots from MCMC Output

mcmcplot1 <- function(x, col=mcmcplotsPalette(n), lty=1, xlim=NULL, ylim=NULL, style=c("gray", "plain"), greek = FALSE){
    x <- convert.mcmc.list(x)
    style <- match.arg(style)
    n <- length(x)
    parname <- varnames(x)
    label <- parname
    if (greek) {
      label <- .to.greek(label)
    }
    ## layout(matrix(c(1, 1, 2, 3), 2, 2, byrow=TRUE))
    opar <- par(mar=c(5, 4, 2, 1) + 0.2, oma=c(0, 0, 2, 0) + 0.1)
    on.exit(par(opar))
    layout(matrix(c(1, 2, 1, 3, 4, 4), 3, 2, byrow=TRUE))
    denoverplot1(x, col=col, lty=lty, xlim=xlim, ylim=ylim, style=style, xlab=label, ylab="Density")
    autplot1(x, style=style)
    rmeanplot1(x, style=style)
    ## autplot1(x, style=style, partial=TRUE)
    traplot1(x, col=col, lty=lty, style=style, ylab=label, xlab="Iteration")
    if (greek) {
        ## title(parse(text=paste("paste('Diagnostics for ', ", parname, ")")), cex.main=1.5, outer=TRUE)
        title(parse(text=paste("paste('Diagnostics for ', ", label, ")")), cex.main=1.5, outer=TRUE)
    } else {
        title(paste("Diagnostics for ", parname, sep=""), cex.main=1.5, outer=TRUE)
    }
}