Traceplots of JAGS output

Displays a series of MCMC iteration plots for monitored parameter in a JAGS analysis, along with the calculated Rhat value.

traceplot(x, parameters=NULL, Rhat_min=NULL, layout=NULL, ask=NULL)

Arguments

x

A jagsUI object

parameters

A vector of names (as characters) of parameters to plot. Parameter names must match parameters included in the model. Calling non-scalar parameters without subsetting (e.g. alpha) will plot all values of alpha. If parameters=NULL, all parameters will be plotted.

Rhat_min

If provided, only plot parameters with Rhat values that exceed the provided value. A good min value to start with is 1.05.

layout

A length 2 vector with the number of rows and columns to display in the plot. The default is 3 x 3, or smaller if there are fewer parameters to plot.

ask

If TRUE, ask user for confirmation before generating each new plot; the default is to ask when output is going to the screen, not when it is going to a file.

Author

Ken Kellner contact@kenkellner.com.