R help - Oct 2009 - R, Coda, and OpenBUGS

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?

Thanks in advance for any suggestions,

Bill Halteman

Have you tried the rjags package which uses the jags system?  It is much 
more integrated into R and works quite well.  It uses the same modeling 
language as BUGS.  It is also better supported than OpenBUGS.

Frank

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?
> 
> Thanks in advance for any suggestions,
> 
> Bill Halteman
> 
-- 
Frank E Harrell Jr   Professor and Chair           School of Medicine
                      Department of Biostatistics   Vanderbilt University

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
> 
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide 
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.