denplot: Density Plots for MCMC Parameters on a Single Plot

In mcmcplots: Create Plots from MCMC Output

Description

Creates a plot of densities for specified parameters from an MCMC simulation in a single plot or plots densities for those parameters as indicated by the parms and regex.

Usage

denplot(mcmcout, parms = NULL, regex = NULL, random = NULL,
leaf.marker="[\\[_]", ci = NULL, xlim = NULL,
ylim = NULL, auto.layout = TRUE, mar=c(2.0, 2.0, 1.5, 0.25) + 0.1, col =
NULL, lty = 1, xlab = "", ylab = "", plot.title = NULL, main = NULL,
greek = FALSE, collapse = FALSE, style=c("gray", "plain"), ...)

Arguments

mcmcout	an object that can be coerced to an mcmc or mcmc.list object
parms	a vector of character strings that identifies which variables in mcmcout should be plotted. If parms and regex are both NULL, all parameters will be plotted.
regex	a vector of character strings with regular expressions that identify which variables in mcmcout should be plotted.
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 _
ci	if non NULL, plots (100*ci)% credible interval limits on the density plots. The default (NULL) is not to plot the intervals.
xlim	limits of the x-axis.
ylim	limits of the y-axis.
auto.layout	if TRUE, denplot automatically creates a plot layout using mult.fig from the sfsmisc package.
mar	argument passed to multi.fig if auto.layout=TRUE
col	colors to be used in plotting the densities.
lty	line types to be used in plotting.
xlab	label for the x-axis.
ylab	label for the y-axis.
plot.title	title to put in the outer margin. Default is no title.
main	character vector of titles for each individual plot. If NULL, then the names of the parameters are used.
greek	if TRUE, the names of greek letters in the labels will be displayed as greek characters on the plot.
collapse	if TRUE, all parallel chains are collapsed into one chain before plotting. If FALSE, parallel chains are plotted with colors as specified in col.
style	if "gray", then the plotting region is printed with a gray background, otherwise the default plotting region is used.
...	further arguments to be passed to the plotting function.

Value

Creates a plot.

Author(s)

S. McKay Curtis

See Also

mcmcplot, 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 densities of the fake MCMC output
denplot(fakemcmc)
denplot(fakemcmc, style="plain")
denplot(fakemcmc, collapse=TRUE, greek=TRUE, ci=0.95)
denplot(fakemcmc, xlim=range(unlist(fakemcmc)),
        plot.title="Density plots of fake data. Yawn.")
denplot(fakemcmc, "gamma")
denplot(fakemcmc, "gamma", "alpha\\[[12]]$") # all gamma and alpha[1] and alpha[2]

## What happens with NULL varnames?
coda::varnames(fakemcmc) <- NULL
denplot(fakemcmc)

## Not run: 
## denplot 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)
denplot(schools.sim, "theta")

## End(Not run)

mcmcplots documentation built on May 2, 2019, 1:29 p.m.