BUGS plots

This dialog can be used to produce plots for output and diagnostics from Markov Chain Monte Carlo (MCMC) simulations calculated using the Submit BUGS Script dialog.

In the Submit BUGS Script dialog enter a name to save the simulations and run the analysis. This will enable the Graphics button.
Click Graphics. Set options as required then click Run.

Type of plot

Specifies the graphical output to be displayed.

Trace plot

Produces a trace plot for each monitored node, where every chain for the monitored nodes is superimposed on the same plot.

Density plot

Produces a kernel density smooth for each monitored node.

Bandwidth

Specify the bandwidth for the density plot. Leave this blank if you want Genstat to form the bandwidth automatically.

Autocorrelation plot

Generates an autocorrelation plot for each monitored node, where every chain for the monitored node is superimposed on the same plot.

Maximum lag

Specify the maximum lag for which the autocorrelation is calculated (default 50).

Gelman-Rubin plot

Produces the Gelman-Rubin “Potential Scale Reduction Factor” (PSRF) diagnostic. The PSRF compares the between and within variances of multiple chains. When selected a plot of the PSRF, and a second plot of the between and within variances are produced. The method used for the diagnostic can be controlled using either the Gelman-Rubin option which uses the original Gelman-Rubin PSRF diagnostic, or the Gelman-Rubin-Brooks setting which uses the Gelman-Rubin-Brooks version (as used in WinBUGS), which interprets the diagnostic as a ratio of interval lengths rather than a variance ratio.

Bin width	Specifies the number of values in each bin of the plot (default 50).
Use all samples	Usually the first half of the observations is discarded in the Gelman-Rubin plot, but you can set this option to use them all.
Display summary	Displays the PSRF convergence diagnostic.

Arrangement

Controls how the plots are produced. You can choose to display each plot separately by selecting the Single setting or four within the same plot by selecting the Multiple setting.

Use iterations

Lets you select a subset of the iterations to use in the plot.

Start	Start iteration to be used in the plots.
End	End iteration to be used in the plots.

Action buttons

Run	Produce the plots and close the dialog.
Cancel	Close the dialog without making any changes.
Defaults	Reset the options to their default settings.

Action Icons

	Clear	Clear all fields and list boxes.
	Help	Open the Help topic for this dialog.