[R] R, Coda, and OpenBUGS - Thanks!!

[Bill Halteman]

Worked perfectly.  Thanks very Much

Uwe Ligges wrote:
>
>
> Bill Halteman wrote:
>> Hi All,
>>
>>   I am trying to figure out how to use R-Coda with the output from 
>> OpenBugs. I have installed and loaded the packages BRugs and 
>> R2WinBUGS.  I have successfully run a simple Bayes model in WinBUGS 
>> using R2WinBUGS' "bugs" and have used "read.bugs" to build the coda 
>> object.  I can successfully switch to OpenBugs and run the same model 
>> and get the basic summary back.  However, I cannot build the coda 
>> object.  From what I have read "read.openbugs" should do the trick.  
>> However, I have discovered the current version of OpenBUGS (v 3.03) 
>> doesn't write any output files in spite of setting codaPkg=TRUE in 
>> the "bugs" call.  "Str(openbugs.object)" reveals a large collection 
>> of elements, one of which is an array that contains the MCMC chains.  
>> Is there a function to build the coda object?
>
>
> For BRugs: Sure, the function is called buildMCMC(). From the examples 
> of ?BRugs:
>
> library(BRugs) # loading BRugs
>
> ## Now setting the working directory to the examples' one:
> oldwd <- getwd()
> setwd(system.file("OpenBUGS", "Examples", package="BRugs"))
>
> ## some usual steps (like clicking in WinBUGS):
> modelCheck("ratsmodel.txt")          # check model file
> modelData("ratsdata.txt")            # read data file
> modelCompile(numChains=2)            # compile model with 2 chains
> modelInits(rep("ratsinits.txt", 2))  # read init data file
> modelUpdate(1000)                    # burn in
> samplesSet(c("alpha0", "alpha"))     # alpha0 and alpha should be 
> monitored
> modelUpdate(1000)                    # 1000 more iterations ....
>
>
> ##  now let's construct a coda object
> ## (of class mcmc.list, to be precise)
> ## for BUGS node "alpha":
>
> alpha <- buildMCMC("alpha")
>
>
> Best,
> Uwe Ligges
>
>
>> Thanks in advance for any suggestions,
>>
>> Bill Halteman
>>
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