Scripts, Batch-mode and
ClassicBUGS
The Scripting Language
As an alternative to the menu / dialog box interface of WinBUGS a scripting language has been provided. This language can be useful for automating routine analysis. The language works in effect by writing values into fields and clicking on buttons in relevant dialog boxes. Note that it is possible to combine use of this scripting language with use of the menu / dialog box interface.
The scripting language is the same as the command line interface used in the ClassicBUGS flavour of OpenBUGS, with the exception that ClassicBUGS does not have any commands to produce graphic output. The script language is also very similar to the R interface to OpenBUGS called BRugs.
The translation between commands in the script language and the underlying Component Pascal procedures is in the file Bugs/Mod/Script.odc. There are two versions of each script command, the first for use with the graphical user interface and the second for use with ClassicBUGS (the second version can be empty). Commands marked with an asterixs produce graphics output and do not work in ClassicBUGS, or do not work with ClassicBUGS for some other reason.
To make use of the scripting language for a specific problem, a minimum of four files are required: the script itself; a file containing the BUGS language representation of the model; a file (or several) containing the data; and for each chain a file containing initial values. Each file may be in either native OpenBUGS format (.odc) or text format, in which case it must have a .txt extension.
Below is a list of currently implemented commands in the scripting language. Alongside each is a brief synopsis of its menu / dialog box equivalent: first we have the menu name (in bold) then the associated menu option or dialog box; then possibly a button in the dialog box, or the name of a dialog box field set equal to the value of the quantity on the other side of the equals sign. Script commands can take two types of arguments: strings and integers. If a string argument contains non-alpha-numeric characters (including space but excluding the period) the string must be enclosed in double quotes. If an argument is in italics it must be supplied by the user, other arguments will be set to default values if absent.
If the menu / dialog box equivalent of the specified script command would normally be greyed out, because of inappropriate timing, for example, then the script command will not execute and an error message will be produced instead.
script command menu / dialog box equivalent
modelCheck( string ) Model (Specification... )
modelData( string ) Model (Specification... )
modelEnableDynamic() Model (Specification... ) dynamic compilation = TRUE
modelDisableDynamic() Model (Specification... ) dynamic compilation = FALSE
modelCompile( int ) Model (Specification...)
num of chains = int
modelInits( string , int) Model (Specification...)
for chain = chain
modelGenInits() Model (Specification...)
_____________________________________________________________________
modelUpdate( int0 , int1, string) Model (Update...)
updates = int0,
thin = int1
over relax = string
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modelSaveState(string) Model (Save State) fileStem = string
_____________________________________________________________________
modelGetRN(int) Model (RN generator...) seed
modelSetRN(int0, int1 ) Model (RN generator...)
seed = int1
state = int0
_______________________________________________________________
modelOutput( string ) Model (Inout/Output options...)
Input options = window / log
modelPrecison( int ) Model (Inout/Output options...)
output precision = int
_____________________________________________________________________
modelDisable( string ) Model (Updater options...) disable = TRUE
methods = string
modelEnable( string ) Model (Updater options...) enable = TRUE
methods = string
modelSetAP( string , int ) Model (Updater option...) adaptive phase = int
methods = string
modelSetIts(string, int ) Model (Updater option...) iterations = int
methods = string
modelSetOR(string, int ) Model (Updater option...) over-relaxation = int
methods = string
_____________________________________________________________________
modelExternalize( string ) Model (Externalize) File name: = string
modelInternalise( string ) Model (Internalize) File name: = string
modelQuit() File (Exit)
modelSaveLog( string ) 1 File (Save As...)
File name: = string
_____________________________________________________________________
samplesBeg( int ) Inference (Samples...) beg = int
samplesEnd( int ) Inference (Samples... ) end = int
samplesFirstChain( int ) Inference (Samples...) chains = int
samplesLastChain( int ) Inference (Samples... ) to = int
samplesThin( int ) Inference (Samples...) thin = int
samplesSet( string ) Inference (Samples...)
node = string
samplesClear( string ) Inference (Samples...)
node = string
samplesStats( string ) Inference (Samples...)
node = string
*samplesDensity( string ) Inference (Samples...)
node = string
*samplesAutoC( string ) Inference (Samples...)
node = string
*samplesTrace( string ) Inference (Samples...)
node = string
*samplesHistory( string ) Inference (Samples...)
node = string
*samplesQuantiles( string ) Inference (Samples...)
node = string
*samplesBgr( string ) Inference (Samples...)
node = string
samplesCoda( string0 , string1) Inference (Samples...)
node = string0
fileStem = string1
______________________________________________________________
summarySet( string ) Inference (Summary...)
node = string
summaryStats( string ) Inference (Summary...)
node = string
summaryMean( string ) Inference (Summary...)
node = string
summaryClear( string ) Inference (Summary... )
node = string
_____________________________________________________________________
rankSet( string ) Inference (Rank... )
node = string
rankStats( string ) Inference (Rank... )
node = string
*rankHistrogram( string ) Inference (Rank...)
node = string
rankClear( string ) Inference (Rank...)
node = string
_____________________________________________________________________
dicSet() Inference (DIC...)
dicClear() Inference (DIC... )
dicStats() Inference (DIC... )
_____________________________________________________________________
infoNodeValues( string ) Info (Node info...)
node = string
infoNodeMethods( string ) Info (Node info...)
node = string
infoNodeTypes( string ) Info (Node info...)
node = string
_____________________________________________________________________
*infoUnitializedUpdaters() Info (Uninitialized Nodes)
infoUpdatersbyName() Info (Updaters(by name))
infoUpdatersbyDepth() Info (Updaters(by depth))
_____________________________________________________________________
infoModules() Info (Modules)
1 If the file ends with ".txt" the log window is saved to a text file (with all graphics, fonts, etc., stripped out); otherwise the log window is saved as is.
Batch-mode
The shortcut BackBUGS has been set up to run the commands contained in the script file script (in the root directory of OpenBUGS ) when it is double-clicked. Thus a OpenBUGS session may be embedded within any software component that can execute the BackBUGS shortcut.