traplot: Traceplots of Multiple Parameters.

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

Description

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.

Usage

traplot(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"), ...)

Arguments

mcmcout	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)

s-mckay-curtis/mcmcplots documentation built on May 31, 2019, 5:13 p.m.