plotAuto {scapeMCMC}R Documentation

Plot MCMC Autocorrelation

Description

Plot Markov-chain Monte Carlo autocorrelation over a range of lag values. This is a diagnostic plot for deciding whether a chain needs further thinning.

Usage

plotAuto(mcmc, thin=1, log=FALSE, base=10, main=NULL, xlab="Lag",
         ylab="Autocorrelation", lty=1, lwd=1, col="black", ...)

Arguments

mcmc MCMC chain(s) as a vector, data frame or mcmc object.
thin interval to subsample chain(s), or 1 to keep chain intact.
log whether values should be log-transformed.
base logarithm base.
main main title.
xlab x-axis label.
ylab y-axis label.
lty line type.
lwd line width.
col line colour.
... passed to autocorr.plot(), title() and axis().

Value

Null, but a plot is drawn on the current graphics device.

Note

The Args function from the gdata package is recommended for reviewing the arguments, instead of args.

Author(s)

Arni Magnusson arnima@u.washington.edu.

See Also

autocorr.plot, mcmc, window.mcmc.

scapeMCMC-package gives an overview of the package.

Examples

plotAuto(xmcmc$P$R0)
plotAuto(xmcmc$P$R0, thin=10)
plotAuto(xmcmc$P, lag.max=50, ann=FALSE, axes=FALSE)

[Package scapeMCMC version 1.0-3 Index]