search for: r2jag

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.ite...

Hi, I'm trying to install rjags and R2jags with R version 2.14.1 (2011-12-22) on Linux Mint 12 machine using software repository: deb http://cran.fhcrc.org/bin/linux/ubuntu oneiric/ jags seems to install OK, but rjags gives a weird error about not finding fprec symbol. Here is a history of the problem including several attempts to wo...

Hi, I'm trying to generate a GLMM for Y following a negative binomial distribution. The first step I'm taking as a beginner in the use of R2Jags is to generate a GLM for Y following a Poisson distribution (I heard it's good in order to get used to the coding language), so here I am and here I face the first error message for which I can't find any mistake of spelling. Could you please give me your opinion about it? I'm modelli...

Dear R users, I am having problems in trying to run R2jags on a Linux Cluster. When I tried to run the model given in the R2jags manual I get the following error error message: Error in FUN(X[[3L]], ...) : object 'J' not found Can any one help me with this problem? Looking to hear from you all. Regards, -- Luwis Diya, Leuven Biostatistics a...

.... I'm running with latest versions of R and all packages, and latest version of JAGS running under Windows 7. Here's the problem. I have some source code. It's given below - standard stuff - seeds example from BUGS volume 1. I'm using R2WinBUGS only to create the model file, and R2jags as a front end to JAGS. I have the same problem whether or not I use R2jags. 1. If I start RGUI and source the code from a source file. R crashes when it tries to execute jags(). Problem Event Name: APPCRASH Application Name: Rgui.exe Application Version: 2.131.56322.0 Application...

Hi All, I have a user who is receiving this error after running the following: library(rjags) library(R2jags) x = c(1.6907, 1.7242, 1.7552, 1.7842, 1.8113, 1.8369, 1.8610, 1.8839) n = c(59, 60, 62, 56, 63, 59, 62, 60) r = c(6, 13, 18, 28, 52, 53, 61, 60) N = 8 data=list("x","n","r","N") inits=function(){ list(alpha.star=0,beta=0) } parameters=c("alpha",&q...

...uncate the file to zero. Now that I write that it really seems like a 'mis-feature'. On a Unix system I would probably compare inodes, but I don't know if there's a good system-independent way to test file identity ... $ ls -i tmp.dat 114080 tmp.dat $ ls -i /home/bolker/R/pkgs/r2jags/pkg/tests/tmp.dat 114080 /home/bolker/R/pkgs/r2jags/pkg/tests/tmp.dat Would normalizePath() work for this ... ? > normalizePath("tmp.dat") [1] "/mnt/hgfs/bolker/Documents/R/pkgs/r2jags/pkg/tests/tmp.dat" sincerely Ben Bolker

...ing 'R CMD BATCH --no-save filename.R &' (have an alias set to subr='R CMD BATCH --no-save") and am having a problem of sometimes the process ending without the R commands contained in the batch file actually having finished running. We're running Bayesian models using R2jags jags.parallel and it ends during the jags run, so it might be something funky with that package, but am curious to know if the general issue of R process ending unceremoniously is anything anyone has run into. Thanks, Liz

All R experts, How do I fit a dynamic Random effects model with a binary dependent variable in R Thanks JCM [[alternative HTML version deleted]]

Frank (or anyone else), can you offer any comments comparing runjags, R2jags, rjags ? I couldn't find any vignettes, nothing except a brief mention on Task Views. Kevin On Wed, Oct 7, 2009 at 7:48 AM, Frank E Harrell Jr <f.harrell@vanderbilt.edu > wrote: > Have you tried the rjags package which uses the jags system? It is much > more integrated into R...

I am generating 1000 replicate data sets in R, each data set is then analyzed with WinBUGS in batch mode using R2WinBUGS. Unfortunately, occasionally some data sets lead WinBUGS to open a "trap" window; and the simulations are interrupted as result of the message. Is there any ways to set R2WinBUGS so that it would ignore the trap message and proceed with the simulations? Cheers

Hello there, is there a way to update a model, which was called by "bugs()"? For instance starting with few iterations and then updating more and more, as is possible inside the WinBUGS-window. If set "debug=TRUE", then the window remains open and updating is possible, but it is no longer written into the R-object. Is it generally impossible? Thanks, Frederic

Hello ALL! I am running Linux, Fedora 15 64-bits, and R on it. I need to use WinBUGS and R2WinBUGS, but as far as I read, WinBUGS is closed project, to be continued with/as OpenBUGS. Thus, I have found R2OpenBUGS on OpenBUGS Contributed Code (http://openbugs.info/w/UserContributedCode), not on CRAN. Author(s) states that it is equivalent for R2WinBUGS. I tried briefly, and realized few minor

Hi all, I'd like to fit different models using a loop together with the jags package. to do this, I load the following packages "runjags", "R2jags" and "coda" and use the function "jags" to fit my models. The problem is that the following a windowx with the following message appear between each model fitting inside my loop : the following objects in .GlobalEnv will mask objects in the attached database: deviance....

CRAN (and crantastic) updates this week New packages ------------ * Bergm (1.0) Alberto Caimo http://crantastic.org/packages/Bergm Functions implementing Bayesian estimation for exponential random graph models via exchange algorithm Updated packages ---------------- lmtest (0.9-26), logcondens (1.3.5), MTSKNN (0.0-4), pmml (1.2.21), r2lUniv (0.9.4), rattle (2.5.11), rgdal (0.6-23),

May I request that Dirk's package for jags be added to the CRAN archives for Debian and Ubuntu? Installing the rjags package for R requires specific versions of jags to be present on the system. The current version of rjags requires jags version 2.2.0 or later but the version on the Ubuntu archives at Canonical (i.e. not the CRAN archives) is 2.1.0-2 I can always install Dirk's package

I'm new to bugs, so please bear with me. Can someone tell me if the following two models are doing the same thing? The reason I ask is that with the same data, the first (based on 4 separate coeffs a1--a4) takes about 50 secs, while the second (based on a vectorized form, a[]) takes about 300. The means are about the same, though R-hat's in the second version are quite a bit better.

...d (0.9-30), pgirmess (1.4.4), phyclust (0.1-5), picante (1.0-1), plotrix (2.8-3), plsdof (0.2-0), pmg (0.9-42), portfolio (0.4-5), portfolioSim (0.2-6), prefmod (0.8-19), PropCIs (0.1-5), PwrGSD (1.16), pyramid (1.2), qpcR (1.2-6), QRMlib (1.4.5), qvcalc (0.8-5), R.filesets (0.8.0), R2HTML (2.0.0), R2jags (0.02-02), randomSurvivalForest (3.6.2), rattle (2.5.24), rbenchmark (0.3), RcmdrPlugin.MAc (1.0.6), RcmdrPlugin.MAc (1.0.5), Rcpp (0.7.8), Rcpp (0.7.9), relations (0.5-7), reporttools (1.0.5), REQS (0.8-6), RFLPtools (1.1), RFOC (1.0-9), RGtk2DfEdit (0.5.4), rimage (0.5-8.1), rms (2.2-0), RQDA (0...

CRAN (and crantastic) updates this week New packages ------------ * bdoc (1.0) Michael Anderson http://crantastic.org/packages/bdoc This package contains a function that will classify DNA barcodes as well as a few test and reference data sets. * bdsmatrix (1.0) Terry Therneau http://crantastic.org/packages/bdsmatrix This is a special case of sparse matrices, used by coxme and

...2-11), psych (1.0-89), PtProcess (3.2-4), QCA3 (0.0-3), qcc (2.0.1), qpcR (1.2-8), qtl (1.16-6), QTLNetworkR (0.1-7), quadprog (1.5-3), qualV (0.2-5), quantreg (4.50), qvalue (1.22.0), qvcalc (0.8-7), R.filesets (0.8.2), R.matlab (1.3.1), R.oo (1.7.3), R.utils (1.4.3), r2dRue (1.0.1), R2HTML (2.1), R2jags (0.02-08), r2lh (0.6.1), R2wd (1.3.0), r4ss (1.06), rainbow (2.0), rake (1.1), random.polychor.pa (1.1.1), randomForest (4.5-35), randomLCA (0.7-3), randomSurvivalForest (3.6.3), rangeMapper (0.0-4), Rassoc (1.03), rattle (2.5.35), rbugs (0.4-3), rcdk (2.9.23), rcdklibs (1.3.4.2), Rcmdr (1.5-6), R...