From: Wincent <ronggui.huang_at_gmail.com>

Date: Mon, 04 Apr 2011 14:09:02 +0800

Date: Mon, 04 Apr 2011 14:09:02 +0800

It turns out that when I use GUI (file-change dir) to set the working
directory, R will crash.

If I use setwd() instead, the example runs well.

Regards,

On 4 April 2011 00:17, Wincent <ronggui.huang_at_gmail.com> wrote:

*> OK, I dig into the problem and found that Chinese character in the path
**> should be blamed.
**> Once the path rename to English only, it works.
**>
**> Regards,
**>
**> On 3 April 2011 23:43, Douglas Bates <bates_at_stat.wisc.edu> wrote:
**>
**>> On Sun, Apr 3, 2011 at 9:53 AM, Wincent <ronggui.huang_at_gmail.com> wrote:
**>> > Does any one run the example without problem?
**>> > I download the example and try to run line and seeds from vol1. R
**>> crashes.
**>> >> library(rjags)
**>> > Loading required package: coda
**>> > Loading required package: lattice
**>> > module basemod loaded
*

>> > module bugs loaded

*>> >> sessionInfo()
**>> > R version 2.12.2 (2011-02-25)
**>> > Platform: i386-pc-mingw32/i386 (32-bit)
**>> > locale:
**>> > [1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936
**>> > [2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936
**>> > [3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936
**>> > [4] LC_NUMERIC=C
**>> > [5] LC_TIME=Chinese (Simplified)_People's Republic of China.936
**>> > attached base packages:
**>> > [1] stats graphics grDevices utils datasets methods base
**>> > other attached packages:
**>> > [1] rjags_2.2.0-4 coda_0.14-2 lattice_0.19-17
**>> > loaded via a namespace (and not attached):
**>> > [1] grid_2.12.2
**>>
**>> I didn't have any problem with the seeds examples
**>> > library(rjags)
**>> Loading required package: coda
**>> module basemod loaded
**>> module bugs loaded
**>> > setwd("/var/tmp/classic-bugs/vol1/seeds/")
**>> > source("../../R/Rcheck.R")
**>> > load.module("glm")
**>> module glm loaded
**>> > d <- read.jagsdata("seeds-data.R")
**>> > inits <- read.jagsdata("seeds-init.R")
**>> > m <- jags.model("seeds.bug", d, inits, n.chains=2, n.adapt=2500)
**>> Compiling model graph
**>> Resolving undeclared variables
**>> Allocating nodes
**>> Graph Size: 167
**>>
**>> > update(m, 2500)
**>> |**************************************************| 100%
**>> > x <- coda.samples(m, c("alpha0", "alpha1","alpha2","alpha12","sigma"),
**>> + n.iter=10000, thin=10)
**>> |**************************************************| 100%
**>> > source("bench-test1.R")
**>> > check.fun()
**>> alpha0 alpha1 alpha12 alpha2 sigma
**>> 0.027439417 -0.022922026 0.025170384 -0.065288678 0.001678632
**>> OK
**>> > m <- jags.model("seedszro.bug", d, inits, n.chains=2, n.adapt=2500)
**>> Compiling model graph
**>> Resolving undeclared variables
**>> Allocating nodes
**>> Graph Size: 190
**>>
**>> > update(m, 2500)
**>> |**************************************************| 100%
**>> > x <- coda.samples(m, c("alpha0", "alpha1","alpha2","alpha12","sigma"),
**>> + n.iter=10000, thin=10)
**>> |**************************************************| 100%
**>> > source("bench-test2.R")
**>> > check.fun()
**>> alpha0 alpha1 alpha12 alpha2 sigma
**>> -0.00216258 0.00196343 0.02732117 -0.01017020 -0.01976949
**>> OK
**>> > m <- jags.model("seedssig.bug", d, inits, n.chains=2, n.adapt=2500)
**>> Compiling model graph
**>> Resolving undeclared variables
**>> Allocating nodes
**>> Graph Size: 185
**>>
**>> |++++++++++++++++++++++++++++++++++++++++++++++++++| 100%
**>> > update(m, 2500)
**>> |**************************************************| 100%
**>> > x <- coda.samples(m, c("alpha0", "alpha1","alpha2","alpha12","sigma"),
**>> + n.iter=10000, thin=10)
**>> |**************************************************| 100%
**>> > source("bench-test3.R")
**>> > check.fun()
**>> alpha0 alpha1 alpha12 alpha2 sigma
**>> 0.06600343 -0.01107823 0.02933205 -0.04117105 -0.03376439
**>> OK
**>> > m <- jags.model("seedsuni.bug", d, inits, n.chains=2, n.adapt=2500)
**>> Compiling model graph
**>> Resolving undeclared variables
**>> Allocating nodes
**>> Graph Size: 186
**>>
**>> |++++++++++++++++++++++++++++++++++++++++++++++++++| 100%
**>> > update(m, 2500)
**>> |**************************************************| 100%
**>> > x <- coda.samples(m, c("alpha0", "alpha1","alpha2","alpha12","sigma"),
**>> + n.iter=10000, thin=10)
**>> |**************************************************| 100%
**>> > source("bench-test4.R")
**>> > check.fun()
**>> alpha0 alpha1 alpha12 alpha2 sigma
**>> -0.04482849 0.05603658 -0.01204552 0.03653643 -0.00798445
**>> OK
**>>
**>> > On 1 April 2011 04:00, Martyn Plummer <plummerM_at_iarc.fr> wrote:
**>> >>
**>> >> I'm sorry, the whole project is somewhat under-documented at the
**>> moment,
**>> >> but in addition the glm module is a work in progress.
**>> >>
**>> >> >From a user point of view, it should be fairly transparent. Using
**>> rjags,
**>> >> you type
**>> >>
**>> >> R> loadModule("glm")
**>> >>
**>> >> before calling jags.model(). If your model contains a GLM then JAGS
**>> >> should recognize it and provide samplers that do block updating of the
**>> >> parameters in the linear predictor.
**>> >>
**>> >> To see if it is working, call list.samplers(m) where m is the JAGS
**>> model
**>> >> object. The return value is a named list: the names correspond to the
**>> >> sampling method, and the values are the names of the nodes that are
**>> >> updated by that sampler. Samplers have names prefixed by the module
**>> >> name, so if you have any entries in the sampler list called "glm::*"
**>> >> then it is working.
**>> >>
**>> >> For some examples, you can download the classic bugs examples from
**>> >> http://sourceforge.net/projects/mcmc-jags/files/Examples/2.x/
**>> >>
**>> >> The subdirectories "epil", "oxford", and "seeds" (in vol1) contain R
**>> >> scripts that you can run using rjags, or scripts with the name
**>> test*.cmd
**>> >> that you can run using jags in batch mode.
**>> >>
**>> >> Under the hood, most of the samplers use data augmentation to reduce
**>> the
**>> >> model from a GLM to an LM, then the block updating relies on Tim
**>> Davis's
**>> >> libraries for sparse matrix algebra (Very much following your lead here
**>> >> but with a much more basic use of the sparse matrix algebra). Variance
**>> >> parameters for the random effects are still a problem and can show poor
**>> >> mixing even when everything else is working properly. As I said, it is
**>> >> a work in progress.
**>> >>
**>> >> I hope this helps.
**>> >> Martyn
**>> >>
**>> >> On Wed, 2011-03-30 at 13:11 -0500, Douglas Bates wrote:
**>> >> > In reading about the glm module in JAGS it seems that it is suitable
**>> >> > for sampling from the posterior distribution of the parameters in a
**>> >> > generalized linear mixed model. However, I haven't been able to find
**>> >> > documentation on how to use this module in particular. Section 5.6
**>> of
**>> >> > the JAGS User Manual for version 2.2.0 hints at abilities but doesn't
**>> >> > really expand on how to use them.
**>> >> >
**>> >> > Can anyone point me to further documentation or examples?
**>> >>
**>> >>
**>> >> -----------------------------------------------------------------------
**>> >> This message and its attachments are strictly
**>> confidenti...{{dropped:8}}
**>> >>
**>> >> _______________________________________________
**>> >> R-sig-mixed-models_at_r-project.org mailing list
**>> >> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
**>> >
**>> >
**>> >
**>> > --
**>> > Wincent Ronggui HUANG
**>> > Sociology Department of Fudan University
**>> > PhD of City University of Hong Kong
**>> > http://asrr.r-forge.r-project.org/rghuang.html
**>> >
**>>
**>
**>
**>
**> --
**> Wincent Ronggui HUANG
**> Sociology Department of Fudan University
**> PhD of City University of Hong Kong
**> http://asrr.r-forge.r-project.org/rghuang.html
**>
**>
*

-- Wincent Ronggui HUANG Sociology Department of Fudan University PhD of City University of Hong Kong http://asrr.r-forge.r-project.org/rghuang.html [[alternative HTML version deleted]] ______________________________________________ R-devel_at_r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-develReceived on Mon 04 Apr 2011 - 06:13:13 GMT

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