Nothing
plotTrace <- function(mcmc, axes=FALSE, same.limits=FALSE,
between=list(x=axes,y=axes), div=1, span=1/4, log=FALSE,
base=10, main=NULL, xlab=NULL, ylab=NULL, cex.main=1.2,
cex.lab=1, cex.axis=0.8, cex.strip=0.8,
col.strip="gray95", las=0, tck=0.5, tick.number=5,
lty.trace=1, lwd.trace=1, col.trace="gray", lty.median=1,
lwd.median=1, col.median="black", lty.loess=2,
lwd.loess=1, col.loess="black", plot=TRUE, ...)
{
## 1 Define functions
panel.trace <- function(x, y, ...)
{
panel.xyplot(x, y, type="l", lty=lty.trace, lwd=lwd.trace, col=col.trace)
if(any(is.finite(y)) && var(y)>0)
{
panel.xyplot(range(x), rep(median(y),2), type="l",
lty=lty.median, lwd=lwd.median, col=col.median)
suppressWarnings(panel.loess(x, y, span=span, lty=lty.loess,
lwd=lwd.loess, col=col.loess, ...))
}
}
## 2 Parse args
relation <- if(same.limits) "same" else "free"
## 3 Prepare data (rearrange, transform)
if(is.null(dim(mcmc))) # vector or mcmc(vector)
{
mcmc.name <- tail(as.character(substitute(mcmc)),1)
mcmc <- matrix(mcmc, dimnames=list(NULL,mcmc.name))
}
mcmc <- if(log) log(mcmc/div,base=base) else mcmc/div
mcmc <- as.data.frame(mcmc)
n <- nrow(mcmc)
p <- ncol(mcmc)
x <- data.frame(Factor=ordered(rep(names(mcmc),each=n),names(mcmc)),
Draw=rep(1:n,p), Value=as.vector(as.matrix(mcmc)))
## 4 Prepare plot (set pars, create list args)
ocol <- trellis.par.get("strip.background")$col
trellis.par.set(strip.background=list(col=col.strip))
on.exit(trellis.par.set(strip.background=list(col=ocol)))
mymain <- list(label=main, cex=cex.main)
myxlab <- list(label=xlab, cex=cex.lab)
myylab <- list(label=ylab, cex=cex.lab)
myrot <- switch(as.character(las), "0"=90, "1"=0, "2"=0, "3"=90)
myscales <- list(x=list(draw=FALSE),
y=list(draw=axes,relation=relation,cex=cex.axis,
tck=tck,tick.number=tick.number,rot=myrot))
mystrip <- list(cex=cex.strip)
## 5 Create trellis object
graph <- xyplot(Value~Draw|Factor, panel=panel.trace, data=x, as.table=TRUE,
between=between, main=mymain, xlab=myxlab, ylab=myylab,
par.strip.text=mystrip, scales=myscales, ...)
## 6 Finish
if(plot)
{
print(graph)
invisible(x)
}
else
{
invisible(graph)
}
}
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