plot.bmk {LaplacesDemon}

Plot Hellinger Distances

Description

This function plots Hellinger distances in an object of class bmk.

Usage

## S3 method for class 'bmk'
plot(x, col=colorRampPalette(c("black","red"))(100),
     title="", PDF=FALSE, Parms=NULL, ...)

Arguments

x

This required argument is an object of class bmk. See the BMK.Diagnostic function for more information.

col

This argument specifies the colors of the cells. By default, the colorRampPalette function colors large Hellinger distances as red, small as black, and provides 100 color gradations.

title

This argument specifies the title of the plot, and the default does not include a title.

PDF

Logical. When TRUE, the plot is saved as a .pdf file.

Parms

This argument accepts a vector of quoted strings to be matched for selecting parameters for plotting. This argument defaults to NULL and selects every parameter for plotting. Each quoted string is matched to one or more parameter names with the grep function. For example, if the user specifies Parms=c("eta", "tau"), and if the parameter names are beta[1], beta[2], eta[1], eta[2], and tau, then all parameters will be selected, because the string eta is within beta. Since grep is used, string matching uses regular expressions, so beware of meta-characters, though these are acceptable: ".", "[", and "]".

...

Additional arguments are unused.

Details

The plot.bmk function plots the Hellinger distances in an object of class bmk. This is useful for quickly finding portions of chains with large Hellinger distances, which indicates non-stationarity and non-convergence.

See Also

BMK.Diagnostic

Examples

library(LaplacesDemon)
N <- 1000 #Number of posterior samples
J <- 10 #Number of parameters
Theta <- matrix(runif(N*J),N,J)
colnames(Theta) <- paste("beta[", 1:J, "]", sep="")
for (i in 2:N) {Theta[i,1] <- Theta[i-1,1] + rnorm(1)}
HD <- BMK.Diagnostic(Theta, batches=10)
plot(HD, title="Hellinger distance between batches")