#
#	This is the BUGS scripting language
#
#	There are two vesions of the CP code in the scripting language
#
#	The first is used within the GUI interface, the second with Linux and ClassicBUGS
#
#	The GUI version of the script language manipulates the GUI's dialog box and can be used in
#	conjunction with the GUI
#
#	The commands in the script language can take integer valued parameters denoted by i and string
#	value parameters denoted by s. If there are more than one parameter of one type the posfix 0, 1 etc
#	is added in a left to right order
#



#	check model in file s
modelCheck(s)
"BugsCmds.SetFilePath('^0' ); BugsCmds.ParseGuard; BugsCmds.ParseFile"
"BugsEmbed.SetFilePath( '^0' ); BugsEmbed.ParseGuard; BugsEmbed.Parse"

#	load data in files s
modelData(s)
"BugsCmds.SetFilePath( '^0' ); BugsCmds.LoadDataGuard; BugsCmds.LoadDataFile"
"BugsEmbed.SetFilePath( '^0' ); BugsEmbed.LoadDataGuard; BugsEmbed.LoadData"

#	compile model using 1 chain
modelCompile ()	
"BugsCmds.CompileGuard; BugsCmds.specificationDialog.numChains := ^0; BugsCmds.Compile"
"BugsEmbed.CompileGuard; BugsEmbed.numChains := 1; BugsEmbed.Compile"
  
#	compile model using i chains
modelCompile(i)
"BugsCmds.CompileGuard;BugsCmds.specificationDialog.numChains  := ^0;BugsCmds.Compile"
"BugsEmbed.CompileGuard; BugsEmbed.numChains := ^0; BugsEmbed.Compile"  

#	load initial values for current chain from file s
modelInits(s)	
"BugsCmds.SetFilePath( '^0' ); BugsCmds.LoadInitsGuard; BugsCmds.LoadInitsFile"
"BugsEmbed.SetFilePath('^0' ); BugsEmbed.LoadInitsGuard; BugsEmbed.LoadInits"

#	load initial values for chaini  from file s
modelInits(s,i)	
"BugsCmds.SetFilePath( '^0' );BugsCmds.LoadInitsGuard; BugsCmds.specificationDialog.chain := ^1; BugsCmds.LoadInitsFile"
"BugsEmbed.SetFilePath( '^0' ); BugsEmbed.LoadInitsGuard ; BugsEmbed.chain := ^1; BugsEmbed.LoadInits"
 
#	generate initial values
modelGenInits()	
"BugsCmds.GenerateInitsGuard;BugsCmds.GenerateInits"
"BugsEmbed.GenerateInitsGuard;BugsEmbed.GenerateInits" 
 
#	update model i iterations
modelUpdate(i)	
"BugsCmds.UpdateGuard;BugsCmds.updateDialog.updates  := ^0;BugsCmds.Update"
"BugsEmbed.UpdateGuard ; BugsEmbed.updates := ^0; BugsEmbed.Update"
 
#	update model i0 iteration with prospective thin of i1
modelUpdate(i, i)
"BugsCmds.UpdateGuard ;BugsCmds.updateDialog.updates  := ^0; BugsCmds.updateDialog.thin := ^1; BugsCmds.Update"
"BugsEmbed.UpdateGuard ; BugsEmbed.updates := ^0 ; BugsEmbed.thin  := ^1; BugsEmbed.Update" 

#	update model i iteration with over-relaxation s
modelUpdate(i, s)
"BugsCmds.UpdateGuard ;BugsCmds.updateDialog.updates  := ^0; BugsCmds.updateDialog.overRelax := ^1; BugsCmds.Update"
"BugsEmbed.UpdateGuard ; BugsEmbed.updates := ^0 ; BugsEmbed.overRelax  := ^1; BugsEmbed.Update" 
 
#	update model i0 iteration with prospective thin of i1 and over-relaxation s
modelUpdate(i, i, s)	
"BugsCmds.UpdateGuard ;BugsCmds.updateDialog.updates  := ^0;BugsCmds.updateDialog.thin := ^1; 
BugsCmds.updateDialog.overRelax := ^2; BugsCmds.Update"
"BugsEmbed.UpdateGuard ; BugsEmbed.updates := ^0; BugsEmbed.thin  := ^1; BugsEmbed.overRelax  := ^2; BugsEmbed.Update" 

#	writes out current state of sampler to windowsin WinBUGS, does nothing in ClassicBUGS
modelChains()
"BugsEmbed.UpdateGuard ; BugsCmds.WriteChains"
""

#	writes out current state of sampler to files with stem name s
modelChains(s)	
"BugsEmbed.UpdateGuard ;BugsEmbed.WriteChains('^0')"
"BugsEmbed.UpdateGuard ;BugsEmbed.WriteChains('^0')"

#	sets the first seed of the random number generator to i
modelSetRN(i)	
"BugsCmds.rnDialog.index := 1; BugsCmds.rnDialog.new := ^0; BugsCmds.SetRNGuard; BugsCmds.SetRNState"
"BugsEmbed.index := 1; BugsEmbed.new := ^0; BugsEmbed.SetRNGuard; BugsEmbed.SetRNState"

#	sets the i0 seed of the random number generator to i1
modelSetRN(i, i)	
"BugsCmds.rnDialog.index := ^0; BugsCmds.rnDialog.new := ^1; BugsCmds.SetRNGuard; BugsCmds.SetRNState"
"BugsEmbed.index := ^0; BugsEmbed.new := ^1;BugsEmbed.SetRNGuard; BugsEmbed.SetRNState"

#	gets the state of the random number generator
modelGetRN(i)	
"BugsCmds.rnDialog.index := ^0; BugsCmds.GetRNState"
"BugsEmbed.index := ^0; BugsEmbed.GetRNState"

#	sets where output is sent to s for WinBUGS, does nothing for ClassicBUGS
modelDisplay(s)	
"BugsCmds.SetDisplay('^0')"
""

#	sets the precision to which real numbers are output
modelPrecision(i)
"BugsCmds.displayDialog.precision :=  ^0; BugsMappers.SetPrec(^0)"
"BugsMappers.SetPrec(^0)"

#	causes the BUGS program to close
modelQuit()
"HostMenus.Exit "
"BugsEmbed.Quit"

#	displays the modules of the BUGS software currently loaded
modelModules()
"BugsCmds.Modules"
"BugsEmbed.Modules"

#	saves a log of output to file s
modelSaveLog(s)	
"BugsCmds.SaveLog('^0' )"
"BugsFiles.SaveLog('^0' )"

#	runs a script of commands stored in file s
modelScript(s)
"BugsEmbed.Script('^0')
"BugsEmbed.Script('^0')

#	sets the adaptive phase of updaters created by factory s to i
modelSetAP(s, i)
"UpdaterMethods.SetFactory('^0');UpdaterMethods.AdaptivePhaseGuard;UpdaterMethods.SetAdaptivePhase(^1)"
"UpdaterMethods.SetFactory('^0');UpdaterMethods.AdaptivePhaseGuard;UpdaterMethods.SetAdaptivePhase(^1)"

#	sets the number of iterations allowed in updaters created by factory s to i
modelSetIts(s, i)
"UpdaterMethods.SetFactory('^0');UpdaterMethods.IterationsGuard;UpdaterMethods.SetIterations(^1)"
"UpdaterMethods.SetFactory('^0');UpdaterMethods.IterationsGuard;UpdaterMethods.SetIterations(^1)"

#	sets the amount of over-relaxation used by updaters created by factory s to i
modelSetOR(s, i)
"UpdaterMethods.SetFactory('^0');UpdaterMethods.OverRelaxationGuard;UpdaterMethods.SetOverRelaxation(^1)"
"UpdaterMethods.SetFactory('^0');UpdaterMethods.OverRelaxationGuard;UpdaterMethods.SetOverRelaxation(^1)"

#	enables factory s to create updaters
modelEnable(s)
"UpdaterMethods.SetFactory('^0');UpdaterMethods.Enable"
"UpdaterMethods.SetFactory('^0');UpdaterMethods.Enable"

#	disables factory s creating updaters
modelDisable(s)
"UpdaterMethods.SetFactory('^0');UpdaterMethods.Disable"
"UpdaterMethods.SetFactory('^0');UpdaterMethods.Disable"

#	sets the begin iteration for sample monitors to i
samplesBeg(i)	
"SamplesCmds.dialog.beg :=  ^0"
"SamplesEmbed.beg :=  ^0"
 
#	sets the end iteration for sample monitors to i
samplesEnd(i)	
"SamplesCmds.dialog.end := ^0"
"SamplesEmbed.end := ^0"

#	sets the retrospective thin for sample monitors to i
samplesThin(i )	
"SamplesCmds.dialog.thin :=  ^0"
"SamplesEmbed.thin :=  ^0" 

#	sets the first chain for sample monitors to i
samplesFirstChain(i)	
"SamplesCmds.dialog.firstChain :=  ^0"
"SamplesEmbed.firstChain :=  ^0" 
 
#	sets the last chain for sample monitors to i
samplesLastChain(i)	
"SamplesCmds.dialog.lastChain := ^0"
"SamplesEmbed.lastChain := ^0"

#	sets a sample monitor for variable s
samplesSet(s)	
"SamplesCmds.SetVariable('^0');SamplesCmds.SetGuard;SamplesCmds.Set"
"SamplesEmbed.SetVariable('^0');SamplesEmbed.SetGuard;SamplesEmbed.Set"

#	clears the sample monitor for variable s
samplesClear(s)	
"SamplesCmds.SetVariable('^0');SamplesCmds.HistoryGuard;SamplesCmds.Clear" 
"SamplesEmbed.SetVariable('^0');SamplesEmbed.HistoryGuard;SamplesEmbed.Clear"

#	displays summary statistics for sample monitor s
samplesStats(s)	
"SamplesCmds.SetVariable('^0');SamplesCmds.StatsGuard;SamplesCmds.Stats"  
"SamplesEmbed.SetVariable('^0');SamplesEmbed.StatsGuard;SamplesEmbed.Stats"  

#	displays CODA output for sample monitor s in WinBUGS, does nothing in ClassicBUGS
samplesCoda(s)
"SamplesCmds.SetVariable('^0');SamplesCmds.StatsGuard;SamplesCmds.CODA()"
""

#	writes CODA output for sample monitor s0 to files with stem name s1
samplesCoda(s, s)	
"SamplesCmds.SetVariable('^0');SamplesCmds.StatsGuard;SamplesCmds.CODAFiles('^1')"
"SamplesEmbed.SetVariable('^0');SamplesEmbed.StatsGuard;SamplesEmbed.CODA ('^1')"

#	displays density estimates for sample monitor s in WinBUGS, does nothing in ClassicBUGS
samplesDensity(s)	
"SamplesCmds.SetVariable('^0' );SamplesCmds.StatsGuard;SamplesDensity.Install;SamplesCmds.Plot('Density')"
""

#	displays auto correlation for sample monitor s in WinBUGS, does nothing in ClassicBUGS
samplesAutoC(s)	
"SamplesCmds.SetVariable('^0');SamplesCmds.StatsGuard;SamplesCorrelat.Install;SamplesCmds.Plot('AutoC')"
""

#	displays dynamic traces for sample monitor s in WinBUGS, does nothing in ClassicBUGS
samplesTrace(s)	
"SamplesCmds.SetVariable('^0');SamplesCmds.StatsGuard;SamplesTrace.Install;SamplesCmds.Plot('Trace')"
""
 
#	displays history plots for sample monitor s in WinBUGS, does nothing in ClassicBUGS
samplesHistory(s)	
"SamplesCmds.SetVariable('^0');SamplesCmds.StatsGuard;SamplesHistory.Install;SamplesCmds.Plot('History')"
""

#	displays culmative quantile plots for sample monitor s in WinBUGS, does nothing in ClassicBUGS
samplesQuantiles(s)	
"SamplesCmds.SetVariable('^0');SamplesCmds.StatsGuard;SamplesQuantiles.Install;SamplesCmds.Plot('Quantiles')"
""
 
#	displays bgr convergence diagnostic plots for sample monitor s in WinBUGS, does nothing in ClassicBUGS
samplesBgr(s)	
"SamplesCmds.SetVariable('^0');SamplesCmds.BGRGuard;SamplesDiagnostics.Install;SamplesCmds.Plot('BGR diagnostic')"
""  

#	sets summary monitor for variable s
summarySet(s)	
"SummaryCmds.SetVariable('^0');SummaryCmds.SetGuard;SummaryCmds.Set"
"SummaryEmbed.SetVariable('^0');SummaryEmbed.SetGuard;SummaryEmbed.Set" 
 
#	displays summary statistics for summary monitor s
summaryStats(s)	
"SummaryCmds.SetVariable('^0' );SummaryCmds.StatsGuard;SummaryCmds.Stats"
"SummaryEmbed.SetVariable('^0' );SummaryEmbed.StatsGuard;SummaryEmbed.Stats" 
 
#	displays mean for summary monitor s
summaryMean(s)	
"SummaryCmds.SetVariable('^0');SummaryCmds.StatsGuard;SummaryCmds.Means"
"SummaryEmbed.SetVariable('^0');SummaryEmbed.StatsGuard;SummaryEmbed.Means" 
 
#	clears summary monitor s
summaryClear(s)	
"SummaryCmds.SetVariable('^0');SummaryCmds.StatsGuard;SummaryCmds.Clear"
"SummaryEmbed.SetVariable('^0');SummaryEmbed.StatsGuard;SummaryEmbed.Clear"

#	sets ranks monitor for variable s
ranksSet(s)	
"RanksCmds.SetVariable('^0');RanksCmds.SetGuard;RanksCmds.Set "
"RanksEmbed.SetVariable('^0');RanksEmbed.SetGuard;RanksEmbed.Set"

#	displays rank information for ranks monitor for variable s
ranksStats(s)	
"RanksCmds.SetVariable('^0' );RanksCmds.StatsGuard;RanksCmds.Stats"
"RanksEmbed.SetVariable('^0' );RanksEmbed.StatsGuard;RanksEmbed.Stats" 

#	clears ranks monitor s
ranksClear(s)	
"RanksCmds.SetVariable('^0');RanksCmds.StatsGuard;RanksCmds.Clear"
"RanksEmbed.SetVariable('^0');RanksEmbed.StatsGuard;RanksEmbed.Clear"
 
#	displays histograms for ranks monitor for variable s in WinBUGS, does nothing in ClassicBUGS
ranksHistogram(s)	
"RanksCmds.SetVariable('^0');RanksDialog.StatsGuard;RanksCmds.Draw"
"" 

#	sets monitor for DIC
dicSet()	
"DevianceCmds.SetVariable('*'); DevianceCmds.SetGuard; DevianceCmds.Set"
"DevianceEmbed.SetVariable('*'); DevianceEmbed.SetGuard ; DevianceEmbed.Set "

#	displays DIC statistics
dicStats()	
"DevianceCmds.SetVariable('*'); DevianceCmds.StatsGuard; DevianceCmds.Stats"
"DevianceEmbed.SetVariable('*');DevianceEmbed.StatsGuard; DevianceEmbed.Stats" 

#	clears monitor fro DIC
dicClear ()
"DevianceCmds.SetVariable('*'); DevianceCmds.StatsGuard ; DevianceCmds.Clear"
"DevianceEmbed.SetVariable('*'); DevianceEmbed.StatsGuard ; DevianceEmbed.Clear"

END

