mcmcplot: Diagnostics Plots for MCMC in HTML format
In s-mckay-curtis/mcmcplots: Create Plots from MCMC Output

Description Usage Arguments Details Value Author(s) See Also Examples

Creates an HTML file that displays diagnostic plots (trace, density, autocorrelation) from an MCMC simulation. When the number of parameters in an MCMC simulation is large, viewing all plots in a web browser is much easier than clicking through R graph windows.

mcmcplot(mcmcout, parms = NULL, regex = NULL, random = NULL,
leaf.marker = "[\\[_]", dir = tempdir(), filename = "MCMCoutput",
extension = "html", title = NULL,
heading = title, col = NULL, lty = 1,
xlim = NULL, ylim = NULL,
style=c("gray", "plain"), greek = FALSE)

`mcmcout`	posterior draws. This argument will be coerced to an `mcmc` object.
`parms`	character vector specifying subsets of parameters to plot. If `parms=NULL` and `regex=NULL`, `mcmcplot` will plot all parameters.
`regex`	character vector of regular expressions denoting groups of parameters to plot.
`random`	integer specifying how many parameters from each group will be randomly selected for plotting. This argument is useful when `mcmcout` has a large number of parameters (e.g., from a hierarchical model). If `NULL`, `mcmcplot` will plot all parameters.
`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 `_`
`dir`	string containing the directory where the plots and the main html file will be stored. This directory must exist or the function will throw an error.
`filename`	string containing the name of the main html file which will contain code to display each plot produced by `mcmcplot`.
`extension`	string containing the extension to be used for the html file.
`title`	string containing the title to be included in the html file. Default is to use the name of object passed as the `mcmcout` argument prepended with the string "MCMC Output: ".
`heading`	string containing the heading to be used for the html file. Default is to use the `title`.
`col`	vector of colors. This will determine the colors that will be used to plot each chain in the traceplots and density plots. Default is `mcmcplotsPalette(nchains)`.
`lty`	vector of line types. This will determine the line types that will be used to plot each chain in the traceplots and density plots. If missing, `mcmcplot` will use 1 for all line types.
`xlim`	limits for the x axis of the density plot.
`ylim`	limits for the y axis of the density plot.
`style`	if "gray", then the plotting region is printed with a gray background, otherwise the default plotting region is used.
`greek`	if `TRUE`, the names of greek letters in the `labels` will be displayed as greek characters on the plot.
`browse`	if `TRUE`, the html file will be opened up in a browser window using `browseURL`

The mcmcplot function generates an html file that contains diagnostics plots – trace plots, autocorrelation plots, and density plots – for parameters from an MCMC simulation. When an MCMC simulation contains a large number of parameters, it is no longer convenient to view plots in a small graph window. Viewing the plots in a web browser gives the user the ability to scroll through and examine a large number of plots in a more convenient manner.

See documentation for parms2plot for more information on how to “smartly” select parameters to plot using the parms, regex, and random arguments.

Invisibly returns a string containing the path to filename.

S. McKay Curtis and Ilya Goldin

parms2plot, plotting functions in the coda package.

## Not run: 
## 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)))))

## Use mcmcplot to plot
## the fake MCMC output
mcmcplot(fakemcmc)
mcmcplot(fakemcmc, greek=TRUE)
mcmcplot(fakemcmc, xlim=range(fakemcmc)) # put the densities on the same scale
mcmcplot(fakemcmc, "gamma")
mcmcplot(fakemcmc, regex="alpha\\[[12]", style="plain")
mcmcplot(fakemcmc, "gamma", regex="alpha\\[[12]")
mcmcplot(fakemcmc, random=2)
mcmcplot(fakemcmc, random=c(2, 3))

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

## mcmcplot 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)
mcmcplot(schools.sim)

## End(Not run)