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.
Produces a trace plot for each monitored node, where every chain for the monitored nodes is superimposed on the same 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.|
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).|
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.|
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.
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.|
|Run||Produce the plots and close the dialog.|
|Cancel||Close the dialog without making any changes.|
|Defaults||Reset the options to their default settings.|
|Clear||Clear all fields and list boxes.|
|Help||Open the Help topic for this dialog.|