How about require(coda) data(line) str(line) cline <- as.mcmc(do.call(rbind,line)) str(cline)
# Thus HPDinterval(cline) # (or any FUN.mcmc) sum(cline[,'alpha'] >= median(cline[,'alpha']))/nrow(cline) Cheers On Thu, Oct 4, 2012 at 12:22 PM, NORRIS Paul <p.nor...@ed.ac.uk> wrote: > Dear all, > > I'm not 100% sure if this question is best directed at the r-list, or a > mailing list concerned with Bayesian analysis, so please accept my > apologies if another audience may be more appropriate. > > I have been using the rjags package to run Jags models with multiple > chains and store the results in a Coda based mcmc list. For instance, > having created a jags model and done initial adapting and updating, I run > the following command: > > coda_odp_gini_only <- coda.samples(odp_gini_only, > variable.names=c("beta","sigma2.u2", > "deviance"), > n.iter=itercount, thin=thincount) > > This create an object with 4 separate chains as requested in my initial > call to Jags which created the object "odp_gini_only". I then use the > Coda package to look at the results stored in "coda_odp_gini_only". Prior > to running any analysis with Coda, I used the command, > > coda.options(combine.plots=TRUE, combine.stats=TRUE) > > to ask for results that combine the four separate chains. Sure enough, if > I enter "summary(coda_odp_gini_only)", I am given a single set of output > combining the four chains. However, if I enter > "HPDinterval(coda_odp_gini_only)" I receive 4 sets of HPD figures, one for > each chain. Is it possible to combine the four chains together to receive > a single set of HPD estimates? > > In a similar vein, is it possible to use the Coda object to estimate the > proportion of a given parameters distribution which is above (or below) a > given value, for instance, the proportion of the distribution of beta[1] > greater than zero? Again, in doing so, is it possible to combine the > results of the four chains into a single estimate? > > Kind regards, and many thanks in advance for any advice anyone can offer > me. > > Paul > Dr Paul Norris > Lecturer in Social Policy > University of Edinburgh > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > ______________________________________________ > R-help@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. > [[alternative HTML version deleted]] ______________________________________________ R-help@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.