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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