Dear Virgilio, Many thanks for taking a look at it!
That 'debug = TRUE' is already set!!!! It doesn't make any difference!! I'm running R in Windows 7 through Parallels on a Macbook Pro (OSx Mavericks). I have shut down OsX and booted purely into windows and it doesn't make any difference. I've experienced this problem under both R 2.15 and R 3.01. It also happens both in R Studio and in the standard R interface. I have Openbugs version 3.2.2. Running latest version of the packages used. My thinking is that something is crashing OpenBugs when it attempts to open - but I cant' figure out how or why. I wonder is there a file size limit for passing things into OpenBugs ? Appreciate any help! James ________________________________________ From: Virgilio Gómez-Rubio [[email protected]] Sent: 27 November 2013 20:29 To: James Rooney Cc: [email protected] Subject: Re: [R-sig-Geo] Help - calling OpenBugs through R2OpenBugs problem Dear James, I'll be happy to look into this but I will need more information about your system. Also, could you run the code using 'debug=TRUE' as seen in the error message? Best wishes, Virgilio On mié, 2013-11-27 at 20:13 +0000, James Rooney wrote: > Hi everyone, > > Has anyone looked at this problem below ? > Even if nobody has an answer I'd be keen to know if the problem replicated > for others. > > Many thanks, > > James > > ________________________________________ > From: [email protected] [[email protected]] On > Behalf Of James Rooney [[email protected]] > Sent: 23 November 2013 16:30 > To: [email protected] > Subject: [R-sig-Geo] Help - caling OpenBugs thourgh R2OpenBugs problem > > Hi all, > > I am working on a Bayesian spatial smoothing project - and have implemented > the BYM model, similar to the description in Chapter 11 of the ASDAR book. > However, I have been having a huge problem calling OpenBugs from within R and > I cannot figure out why. I would veyr much liek to do this as it would speed > up the whole process. I'm stared at this for a omnth or two now to no avail > so I'm hoping that somebody might spot a mistake. Basically when I call > OpenBugs from R using the bugs command through R2OpenBugs - it throws a > non-specific error and tells me to heck the bugs log file. The problem is > Bugs does not generate one. This is made all the weirder by the fact that if > I manually start up bugs and start it running using the data and inits files > gnerated by R2OpenBugs - it runs fine without complaint. This is how I have > been working so far. But I want to parallelize Bugs using Snow - so I need > R2OpenBugs to work properly. I'm hoping someone here can help!!! > > I've made a simulation to recreate the problem. My apologies it is a little > complex, but I wanted to use the shapefile I'm actually working with which is > freely downloadable for those willing to take a look. > So here goes. > > 1. Go here for the shapefile: > http://www.cso.ie/en/census/census2011boundaryfiles/ > > 2. Click on the word "Disclaimer" to access the shapefiles (should you agree > with the disclaimer!!). After clicking through the Disclaimer stuff, the file > to download is: "Census2011_Electoral_Divisions_generalised20m.zip" > > 3. Set up a directory for this and save the shapefiles there. > > 4. You will need a bugs model. Cut and paste the below into a txt file and > save it to your directory under the name "spatial_CAR.txt" > > model > { > > for(i in 1:N) > { > observed[i]~dpois(mu[i]) > log(theta[i])<-alpha + u[i] + v[i] > mu[i]<-expected[i]*theta[i] > u[i] ~dnorm(0,tau) > } > > v[1:N]~car.normal(adj[],weights[],num[],precv) > > alpha ~dflat() > tau ~dgamma(0.001,0.001) > precv ~dgamma(0.1,0.1) > } > > 5. Now open R and paste in the R code below. Remember to set your working > directory to the same directory you saved the shapefiles and bugs model into. > Also you might need to modify the path to OpenBugs on your machine. > > 6. Run the code. For me the final line throws the error: > "Error in bugs.run(n.burnin, OpenBUGS.pgm, debug = debug, WINE = WINE, : > Look at the log file in C:......<SNIP>................./R2OpenBugs > Simulation and > try again with 'debug=TRUE' to figure out what went wrong within OpenBUGS." > > I cannot figure out why!!! The log file does not exist!! If you manually open > bugs and use the data and init files it works. Why ? No idea!!!! > Any and all help much appreciated!!! > Apologies for the length of this!! > > James > > > R Code: > > library(rgdal) > library(spdep) > library(R2OpenBUGS) > > setwd("....your working directory here......") > > #Read in Spatial Polygon Data Frame > SPolyDF<-readOGR(".","Census2011_Electoral_Divisions_generalised20m",TRUE) > > # Detect neighbours > nb<-poly2nb(SPolyDF,queen=T,snap=0.1) # snap at 100m distance > > # Create nb weights > nb.w<-nb2listw(nb,zero.policy=T,style="B") > > # Create BUGS CAR weights > nbBugs<-listw2WB(nb.w) > > # Simulate some count data for observed and expected cases > N<-nrow(SPolyDF) > SPolyDF$obs<-sample.int(100, N, TRUE) > SPolyDF$exp<-sample.int(100, N, TRUE) > > # Prep Data for OpenBugs > d<-list(N = N, observed = SPolyDF$obs, expected = SPolyDF$exp, > adj=nbBugs$adj, weights=nbBugs$weights, num=nbBugs$num) > > # Specify dir where bugs lives > BugsDir<-"C:/Program Files (x86)/OpenBUGS/OpenBUGS322" > > # Define initial values for bugs > inits<-list( > list(u=rep(0,N),v=rep(0,N),alpha=0,tau=0.0001,precv=0.002) > ,list(u=rep(0,N),v=rep(0,N),alpha=0.1,tau=0.0002,precv=0.001)) > > # Define working directory as current directory > wdir=getwd() > > # Openbugs call > MCMCres<-bugs(data=d,inits=inits,parameters.to.save > =c("theta","alpha","tau","precv"), > > n.iter=1000,model.file="spatial_CAR.txt",n.chains=2,n.burnin=100,n.thin=1, > OpenBUGS.pgm=BugsDir,working.directory=wdir,codaPkg=F,debug=T) > > _______________________________________________ > R-sig-Geo mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-geo > > _______________________________________________ > R-sig-Geo mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-geo _______________________________________________ R-sig-Geo mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-geo
