plotCumu {scapeMCMC}R Documentation

Plot MCMC Cumulative Quantiles

Description

Plot Markov-chain Monte Carlo cumulative quantiles. This is a diagnostic plot for deciding whether the chain has converged.

Usage

plotCumu(mcmc, probs=c(0.025,0.975), div=1, log=FALSE, base=10,
         main=NULL, xlab="Iterations", ylab="Value", lty.median=1,
         lwd.median=2, col.median="black", lty.outer=2, lwd.outer=1,
         col.outer="black", ...)

Arguments

mcmc MCMC chain(s) as a vector, data frame or mcmc object.
probs outer quantiles to draw, a vector of length 2.
div denominator to shorten values on the y axis.
log whether values should be log-transformed.
base logarithm base.
main main title.
xlab x-axis label.
ylab y-axis label.
lty.median line type of median.
lwd.median line width of median.
col.median colour of median.
lty.outer line type of outer quantiles.
lwd.outer line width of outer quantiles.
col.outer colour of outer quantiles.
... passed to cumuplot(), 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

cumuplot, quantile.

scapeMCMC-package gives an overview of the package.

Examples

plotCumu(xmcmc$P$R0, main="R0")
plotCumu(xmcmc$P$cSfull, main="cSfull")
plotCumu(xmcmc$P, probs=c(0.25,0.50,0.75), ann=FALSE, axes=FALSE)

[Package scapeMCMC version 1.0-3 Index]