On Tue, Feb 19, 2013 at 7:18 AM, Uwe Ligges <lig...@statistik.tu-dortmund.de > wrote:
> > > On 18.02.2013 05:24, Jia Liu wrote: > >> Hi all, >> >> I used both OpenBugs and R function bugs{R2WinBUGS} to run a linear mixed >> effects model based on the same data set and initial values. I got the >> same >> summary statistics but different posterior samples. However, if I order >> these two sets of samples, one is generated from OpenBugs and the other is >> generated from R, they turn to be the same. And the samples from R do not >> have any autocorrelation. I do not know why and how this R function >> destroy >> the orders of posterior samples. Have anyone ever met this situation >> before? Any idea is appreciated. >> > > Not sure what you are looking at, since there is no reproducible example > nor any code in your message. > Sorry for the inconvenience, I should have posted a sample code with it. > However, I guess you came across a specific design decision by Andrew > Gelman, who wrote some code of R2WinBUGS before it was turned into an R > package. That feature is documented on the ?bugs help page: > > "for convenience, the n.keep*n.chains simulations in sims.matrix and > sims.list (but NOT sims.array) have been randomly permuted". > > It is exactly what I asked. I noticed that the posterior sample have been randomly permuted. But I am curious the reason for doing that. So if the autocorrelation is of my interest, I should use sims.array, not sims.list. Thanks, Jia > Best, > Uwe Ligges > > > > > > > >> Thanks, >> >> Jia >> >> >> sessionInfo()R version 2.15.1 (2012-06-22) >>> >> Platform: x86_64-pc-mingw32/x64 (64-bit) >> >> locale: >> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United >> States.1252 >> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C >> [5] LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] R2WinBUGS_2.1-18 BRugs_0.8-0 coda_0.15-2 lattice_0.20-6 >> >> loaded via a namespace (and not attached): >> [1] grid_2.15.1 tools_2.15.1 >> >> [[alternative HTML version deleted]] >> >> ______________________________**________________ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/**listinfo/r-help<https://stat.ethz.ch/mailman/listinfo/r-help> >> PLEASE do read the posting guide http://www.R-project.org/** >> posting-guide.html <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.