mcmcplot1: MCMC Diagnostics Plots for one Model Parameter
In mcmcplots: Create Plots from MCMC Output

Description Usage Arguments Value Note Author(s) References See Also Examples

Creates a graph window containing three different plots—a trace plot, a density plot, and an autocorrelation plot—for one parameter in an MCMC run. This function is used by mcmcplot to construct an html file of MCMC diagnostics. This function is intended for internal use only.

1 2	mcmcplot1(x, col = mcmcplotsPalette(n), lty = 1, xlim = NULL, ylim = NULL, style = c("gray", "plain"), greek = FALSE)

`x`	an `mcmc` object with a single variable.
`col`	colors for plotting each parallel chain. The default is `seq(nchains)+1` where `nchains` is the number of parallel chains in `mcmcout`. If there is only one parallel chain, then the default is 1.
`lty`	line types for plotting each parallel chain. The default is 1 for all parallel chains.
`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.

Creates a plot.

Only the first parallel chain is used to create the autocorrelation plot. This function is used by mcmcplot to create html output for all the parameters of an MCMC simulation.

S. McKay Curtis

No references.

mcmcplot

## Create fake MCMC output
fakemcmc <- coda::as.mcmc.list(coda::mcmc(sapply(1:5, function(dum) rnorm(1000))))
coda::varnames(fakemcmc) <- c("gamma[1,1]", "gamma[1,2]", "gamma[1,3]", "sigma[1]", "sigma[2]")

mcmcplot1(fakemcmc[, "sigma[1]", drop=FALSE])
mcmcplot1(fakemcmc[, "gamma[1,3]", drop=FALSE], style="plain")