Anyone used jags.parallel in latest version of R2jags?
Ubuntu Oneiric, just ran updates in R to get latest R2jags package which
supposedly has added jags.parallel command to send chains to multiple
cores ... but when I submit, I get:
test <- jags.parallel(d, inits, param, model.file="rats.bug",
n.chains=3, n.iter=2000)
Error: could not find function "jags.parallel"
checked sessionInfo() to be sure I did actually have the udpated version:
R version 2.14.1 (2011-12-22)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] R2jags_0.03-02 rjags_3-5 arm_1.4-14 abind_1.4-0
[5] R2WinBUGS_2.1-18 coda_0.14-6 lme4_0.999375-42 Matrix_1.0-2
[9] lattice_0.20-0 MASS_7.3-16
loaded via a namespace (and not attached):
[1] grid_2.14.1 nlme_3.1-102 stats4_2.14.1
And then checked the library information and see that the jags.parallel
command doesn't actually appear:
> library(help=R2jags)
Information on package ?R2jags?
Description:
Package: R2jags
Version: 0.03-02
Date: 2012-1-12
Title: A Package for Running jags from R
Author: Yu-Sung Su <suyusung at tsinghua.edu.cn>, Masanao
Yajima <yajima at stat.columbia.edu>,
Maintainer: Yu-Sung Su <suyusung at tsinghua.edu.cn>
Depends: methods, R (>= 2.14.0), coda (>= 0.13),
R2WinBUGS, rjags (>= 3-3), parallel
SystemRequirements: jags (>= 3.3.0)
Description: Using this package to call jags from R.
License: GPL (>= 2)
Packaged: 2012-01-12 07:54:55 UTC; yusung
Repository: CRAN
Date/Publication: 2012-01-12 09:39:14
Built: R 2.14.1; ; 2012-01-13 15:09:30 UTC; unix
Index:
attach.jags Attach/detach elements of jags objects to
search path
autojags Function for auto-updating jags until the model
converges
jags Run jags from R
jags2bugs Read jags output files in CODA format
recompile Function for recompiling rjags object
traceplot Trace plot of bugs object
-------------------------
any tips would be much appreciated!
Thanks,
Liz Tighe
On 01/13/2012 11:29 AM, Elizabeth Tighe wrote:> > Anyone used jags.parallel in latest version of R2jags? > > Ubuntu Oneiric, just ran updates in R to get latest R2jags package which > supposedly has added jags.parallel command to send chains to multiple > cores ... but when I submit, I get: > > test <- jags.parallel(d, inits, param, model.file="rats.bug", > n.chains=3, n.iter=2000) > > Error: could not find function "jags.parallel" > > checked sessionInfo() to be sure I did actually have the udpated version: >Liz, I checked the code for R2Jags, and jags.parallel does exist. It appears that the author neglected to add jags.parallel to the export list in the package, which means you can't call it unless you know it is there. This is a bug that needs to be fixed. The workaround until it is fixed it to call it via: R2jags:::jags.parallel as in: test <- R2jags:::jags.parallel(d, inits, param, model.file="rats.bug",n.chains=3, n.iter=2000) That should work. I will notify the author and get the newer versions of R2jags up on the repositories. Michael -- Dr. Michael A. Rutter School of Science Penn State Erie, The Behrend College Station Road Erie, PA 16563 http://math.bd.psu.edu/faculty/rutter