R: Plot Hellinger Distances

plot.bmk {LaplacesDemon} | R Documentation

## 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")

[Package LaplacesDemon version 16.1.1 Index]