Hello all, I have a question about CODA. Using my R code as bellow, I drew two graphs (the data comes from the example of the speed of light in the Gelman’s book “Bayesian Data Analysis (Second edition)” (page 77)). My R code is: library(R2WinBUGS) y=c(28, 26, 33, 24, 34, -44, 27, 16, 40, -2, 29, 22, 24, 21, 25, 30, 23, 29, 31, 19, 24, 20, 36, 32, 36, 28, 25, 21, 28, 29, 37, 25, 28, 26, 30, 32, 36, 26, 30, 22, 36, 23, 27, 27, 28, 27, 31, 27, 26, 33, 26, 32, 32, 24, 39, 28, 24, 25, 32, 25, 29, 27, 28, 29, 16, 23) n=length(y) data=list("n","y") inits=function() {list(mu=runif(1,-5,5),tau=runif(1,0.01,10))} parameters=c("mu","sigma") sim=bugs(data,inits,parameters,"U:/my BUGS code.txt",n.chains=3,n.iter=1000,debug=T) library(coda) y=sim$sims.array x1=mcmc(y[,1,]) #mu,sigma, and deviance from the chain 1 x2=mcmc(y[,2,]) #mu,sigma, and deviance from the chain 2 x3=mcmc(y[,3,]) #mu,sigma, and deviance from the chain 3 x=mcmc.list(x1,x2,x3) plot(x) gelman.plot(x)
# my BUGS code is (copy and save as a txt file): model { for(i in 1:n) { y[i]~dnorm(mu,tau) } mu~dnorm(0.0,0.001) tau~dgamma(0.001,0.001) sigma<-1/sqrt(tau) } As you see, I set 3 chains and 1000 iterations, so there should be 1500 simulation samples after removed the first 500 samples for each chain (burn in). But from the density graph, there indicated only N=500. Why N=500? But not 1500. From another graph produced by “gelman.plot”, we can see that the x axis is labeled as “last iteration in chain”. What is the last iteration in chain? I set 3 chains, which chain was the result calculated based on? Thank you very much. Legendy -- View this message in context: http://www.nabble.com/Question-about-R-graphs-tp20117061p20117061.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ 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.