Hi James I Downloaded the correct file from http://www.cso.ie/en/census/census2011boundaryfiles/ as Census2011_Electoral_Divisions_generalised20m zipfolder of 4mb data size ,I set working Directory as("C:/Users/Public/shapefile") in shapefile i pasted the downloaded folder as zip file I try to both was first SPolyDF<-readOGR("C:/Users/Public/shapefile","Census2011_Electoral_Divisions_generalised20m",TRUE) and for second time SPolyDF<-readOGR(".","Census2011_Electoral_Divisions_generalised20m",TRUE)returning the same error message.
On Thu, Nov 28, 2013 at 12:17 PM, James Rooney <[email protected]> wrote: > Hi Yuster, > > Did you download the correct shapefile into "C:/Users/Public/shapefile" ?? > There are alot of files there and I could not link directly to the file due > to the "Disclaimer" page. > > The other thing I find if I am having these kinds of errors from readOGR, > is to paste the full pathway in quote into the readOGR instead of "." > In other words for your pathway if you are sure the right file is in the > folder try this: > > > SPolyDF<-readOGR("C:/Users/Public/shapefile","Census2011_Electoral_Divisions_generalised20m",TRUE) > > James > > ________________________________________ > From: Yuster Ronoh [[email protected]] > Sent: 28 November 2013 09:11 > To: James Rooney > Cc: [email protected] > Subject: Re: [R-sig-Geo] Help - calling OpenBugs through R2OpenBugs problem > > Hi All > I try to follow the above example but i got stuck in reading Spatial Data > Frame any Idea or Help? > Here are my R codes with error. I am using RStudio Version 3.0.2 ,Windows > 7 32Bit > > > Loading required package: sp > > library(rgdal) > rgdal: version: 0.8-12, (SVN revision 492) > Geospatial Data Abstraction Library extensions to R successfully loaded > Loaded GDAL runtime: GDAL 1.9.2, released 2012/10/08 > Path to GDAL shared files: C:/Users/symon/R/win-library/3.0/rgdal/gdal > GDAL does not use iconv for recoding strings. > Loaded PROJ.4 runtime: Rel. 4.7.1, 23 September 2009, [PJ_VERSION: 470] > Path to PROJ.4 shared files: C:/Users/symon/R/win-library/3.0/rgdal/proj > > library(spdep) > Loading required package: Matrix > Loading required package: lattice > > library(R2OpenBUGS) > > setwd("C:/Users/Public/shapefile") > > #Read in Spatial Polygon Data Frame > > > SPolyDF<-readOGR(".","Census2011_Electoral_Divisions_generalised20m",TRUE) > Error in ogrInfo(dsn = dsn, layer = layer, encoding = encoding, use_iconv > = use_iconv) : > Cannot open file > > > > On Thu, Nov 28, 2013 at 12:13 AM, James Rooney <[email protected]<mailto: > [email protected]>> wrote: > 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]<mailto: > [email protected]>] > Sent: 27 November 2013 20:29 > To: James Rooney > Cc: [email protected]<mailto:[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]<mailto: > [email protected]> [[email protected]<mailto: > [email protected]>] On Behalf Of James Rooney [ > [email protected]<mailto:[email protected]>] > > Sent: 23 November 2013 16:30 > > To: [email protected]<mailto:[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$obs<-sample.int<http://sample.int>(100, N, TRUE) > > SPolyDF$exp<-sample.int<http://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]<mailto:[email protected]> > > https://stat.ethz.ch/mailman/listinfo/r-sig-geo > > > > _______________________________________________ > > R-sig-Geo mailing list > > [email protected]<mailto:[email protected]> > > https://stat.ethz.ch/mailman/listinfo/r-sig-geo > > _______________________________________________ > R-sig-Geo mailing list > [email protected]<mailto:[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 > [[alternative HTML version deleted]]
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