R/traplot.R

traplot <- function(mcmcout, parms=NULL, regex=NULL, random=NULL, leaf.marker="[\\[_]", ylim=NULL, auto.layout=TRUE, mar=c(2.0, 2.0, 1.5, 0.25) + 0.1, col=NULL, lty=1, plot.title = NULL, main=NULL, greek = FALSE, style=c("gray", "plain"), ...){
    style <- match.arg(style)
    mcmcout <- convert.mcmc.list(mcmcout)
    nchains <- length(mcmcout)
    if (is.null(col)){
        col <- mcmcplotsPalette(nchains)
    }
    col <- rep(col, length.out=nchains)
    if (is.null(varnames(mcmcout))){
        warning("Argument 'mcmcout' did not have valid variable names, so names have been created for you.")
        varnames(mcmcout) <- varnames(mcmcout, allow.null=FALSE)
    }
    parnames <- parms2plot(varnames(mcmcout), parms, regex, random, leaf.marker)
    if (length(parnames)==0)
        stop("No parameters matched arguments 'parms' or 'regex'.")
    p <- length(parnames)
    ## parnames <- varnames(mcmcout)
    ## if (is.null(parnames)) stop("Argument 'mcmcout' must have valid variable names, chump!")
    ## parnames <- parms2plot(parnames, parms, regex, random)
    ## p <- length(parnames)
    if (auto.layout){
        op <- mult.fig(p, main=plot.title, mar=mar)$old.par
        on.exit(par(op))
    }
    if (is.null(main)){
        main <- parnames
        names(parnames) <- main
    }
    if (greek) {
      main <- .to.greek(main)
    }
    main <- rep(main, length.out=length(parnames))
    names(main) <- parnames
    for (pmtr in parnames){
        traplot1(mcmcout[, pmtr, drop=FALSE], col=col, lty=lty, ylim=ylim, xlab="", ylab="", main=main[pmtr], style=style, ...)
    }
    return(invisible(parnames))
}
s-mckay-curtis/mcmcplots documentation built on May 31, 2019, 5:13 p.m.