I'm currently using JAGS as my Bayesian program of choice due to working off of an older mac running OSX. I'd like to utilize some of the functions from R2WinBUGS, however. As such, I'm attempting to write something to go from coda output dumped by JAGS into the bugs object format - I've looked for functions that will convert from an mcmc object to a bugs object, but have had no luck as of yet. I've attempted to adapt Yu-Sung Su's method over at http:// yusung.blogspot.com/2007/01/analyzing-coda-statistics-produced- by.html . However, whenever I run it for a coda file set generated by jags, I get the following error:
Error in if (trans[i] == "log") { : missing value where TRUE/FALSE needed This is for a run whose jags.ind is as follows cypraea.effect 1 10000 intercept 10001 20000 sponge.sd 20001 30000 deviance 30001 40000 When I debuged R2WinBUGS:::monitor, which is where the whole thing borks, I found that trans is as follows cypraea.effect intercept sponge.sd deviance "" NA NA NA And the error comes when first looking at intercept, which is NA, not "". I am somewhat unclear as to why this is so. The code for the method is as follows. Any thoughts would be greatly appreciated, and if this works out, feel free to use it yourself! Could be quite useful! -Jarrett #note, the test run was something along the lines of c.bugs<-coda2bugs (n.burnin=1000) coda2bugs<-function(codafile="jags.out", indexfile="jags.ind", n.chains=1, n.iter=NA, n.burnin=NA, n.thin=1, DIC=FALSE, file.rm=T, ...){ require(R2WinBUGS) #first, split up the coda file for R2WinBUGS codaSplit(codafile, indexfile) #get the parameter names index.table<-read.table(indexfile) varNames<-as.vector(index.table[,1]) #determine the n.iter if(is.na(n.iter)){n.iter<-index.table[1,3]} #you will need to put the n.burnin in yourself #for the cypraea example, it is 1000 bugs.fit <- R2WinBUGS:::bugs.sims(varNames, n.chains=n.chains, n.iter=n.iter, n.burnin=n.burnin, n.thin=n.thin, DIC = DIC) class(bugs.fit)<-"bugs" bugs.fit$isDIC <- FALSE #clean up the new coda files if(file.rm==T){ file.remove("codaIndex.txt") for(i in rownames(index.table)){ file.remove(paste("coda",i,".txt",sep="")) } } return(bugs.fit) } codaSplit<-function(codafile="jags.out", indexfile="jags.ind"){ index.table<-read.table(indexfile) write.table(index.table, "codaIndex.txt", quote=F, row.names=F, col.names=F, sep="\t") coda.table<-read.table(codafile) #write the new coda files for(i in rownames(index.table)){ new.file=paste("coda",i,".txt", sep="") new.out<-coda.table[index.table[i,2]:index.table[i,3],] write.table(new.out, new.file, row.names=F, col.names=F, sep="\t") } } ______________________________________________ R-help@stat.math.ethz.ch 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.