Submit BUGS Script Options

This dialog can be used to set options for submitting scripts to WinBUGS or OpenBUGS.

In the Submit BUGS Script dialog click Options.
Set options as required then click OK to close this dialog.

Display

Specifies the output to be displayed.

Bugs log	Displays the contents of the log file produced by WinBUGS/OpenBUGS.
Node statistics	Summary statistics for the monitored nodes.
DIC	Deviance information criterion.

Application control

Controls how WinBUGS is run from Genstat.

Leave BUGS open after run	By default, WinBUGS automatically closes after the batch operation has been run from Genstat. The option can be selected to keep WinBUGS open once the Genstat generated script has run. However, if the wait for BUGS script to complete option is selected the Genstat server will be suspended until you close WinBUGS.
Wait for BUGS script to complete	When selected, the Genstat server is suspended until the script has been run within WinBUGS. If this option is not selected then the Genstat server will be available to receive other commands, but you will not be able to save the simulations for further analysis or plotting.

Thinning rate

Specifies a thinning rate where the samples from every kth iteration are stored.

Save CODA files

Each run of WinBUGS produces CODA output files containing the Markov Chain Monte Carlo output in CODA format. By default the CODA files are deleted, however, when this option is selected these can be saved in the working directory. The CODA files consist of an output file for each chain, showing the iteration number and value. In addition there is an index file containing a description of which lines of the output files correspond to which variable. The index file is saved using the name WBGCODAIndex.txt and the output files are saved as WBGCODA1.txt, WBGCODA2.txt, etc.

Seed

Specifies a seed to use for the random number generator in BUGS; default uses a pseudo-random number generated from the uniform distribution.

Graphics

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.

Save log file in

This specifies the filename to save the WinBUGS log in. You can browse for a filename by clicking

Action buttons

OK	Save the option settings 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.