This function produces trace plots from an MCMC simulation on a single plot for all parameters (by default) or those parameters indicated by the parms argument.
an object that can be coerced to an mcmc or mcmc.list object
parms
character vector specifying which subsets of parameters to plot. If NULL, mcmcplot will plot all parameters. Regular expressions are used to strip all numbers and punctuation out of the parameter names to find the parameters that match the character strings in parms.
regex
character vector of regular expressions denoting groups of parameters to plot.
random
an integer indicating the maximum number of parameters to randomly select for plotting from each group of parameters as specified by the parms argument.
leaf.marker
a regular expression with a character class that marks the beginning of the “leaf” portion of a parameter name. The default character class includes [ and _
ylim
limits for the y-axis.
auto.layout
automatically creates a plot layout using mult.fig if TRUE.
mar
argument passed to multi.fig if auto.layout=TRUE
col
colors to be used in plotting the densities. Default is mcmcplotsPalette(nchains).
lty
line types to be used in plotting.
plot.title
title to put in the outer margin. Default is no title.
main
main title for the plots. Default is to use parameter names.
greek
if TRUE, the names of greek letters in the labels will be displayed as greek characters on the plot.
style
if "gray", then the plotting region is printed with a gray background, otherwise the default plotting region is used.
...
further arguments passed to the plotting function.
Value
Creates a plot.
Author(s)
S. McKay Curtis
See Also
denplot, parms2plot
Examples
## Create fake MCMC output
nc <- 10; nr <- 1000
pnames <- c(paste("alpha[", 1:5, "]", sep=""), paste("gamma[", 1:5, "]", sep=""))
means <- rpois(10, 20)
fakemcmc <- coda::as.mcmc.list(
lapply(1:3,
function(i) coda::mcmc(matrix(rnorm(nc*nr, rep(means,each=nr)),
nrow=nr, dimnames=list(NULL,pnames)))))
## Plot traces of the fake MCMC output
traplot(fakemcmc)
traplot(fakemcmc, style="plain")
traplot(fakemcmc, "gamma", greek=TRUE)
## What happens with NULL varnames?
coda::varnames(fakemcmc) <- NULL
traplot(fakemcmc)
## Not run:
## traplot works on bugs objects too
library(R2WinBUGS)
example("openbugs", "R2WinBUGS")
## from the help file for openbugs:
schools.sim <- bugs(data, inits, parameters, model.file,
n.chains = 3, n.iter = 5000,
program = "openbugs", working.directory = NULL)
traplot(schools.sim, "theta")
## End(Not run)