Yes I unzip the folder to no avail


On Thu, Nov 28, 2013 at 1:56 PM, James Rooney <ROONEYJ4@tcd.ie> wrote:

> Hi Yuster,
>
> Did you unzip the file? Sorry I forgot to say that in instructions. You
> need to put the unzipped file into that directory.
> James
> ________________________________________
> From: Yuster Ronoh [yuster0@gmail.com]
> Sent: 28 November 2013 10:21
> To: James Rooney
> Cc: r-sig-geo@r-project.org
> Subject: Re: [R-sig-Geo] Help - calling OpenBugs through R2OpenBugs problem
>
> 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 <ROONEYJ4@tcd.ie<mailto:
> ROONEYJ4@tcd.ie>> 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 [yuster0@gmail.com<mailto:yuster0@gmail.com>]
> Sent: 28 November 2013 09:11
> To: James Rooney
> Cc: r-sig-geo@r-project.org<mailto:r-sig-geo@r-project.org>
> 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 <ROONEYJ4@tcd.ie<mailto:
> ROONEYJ4@tcd.ie><mailto:ROONEYJ4@tcd.ie<mailto:ROONEYJ4@tcd.ie>>> 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 [virgilio.gomez@uclm.es<mailto:
> virgilio.gomez@uclm.es><mailto:virgilio.gomez@uclm.es<mailto:
> virgilio.gomez@uclm.es>>]
> Sent: 27 November 2013 20:29
> To: James Rooney
> Cc: r-sig-geo@r-project.org<mailto:r-sig-geo@r-project.org><mailto:
> r-sig-geo@r-project.org<mailto:r-sig-geo@r-project.org>>
> 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: r-sig-geo-bounces@r-project.org<mailto:
> r-sig-geo-bounces@r-project.org><mailto:r-sig-geo-bounces@r-project.org
> <mailto:r-sig-geo-bounces@r-project.org>> [r-sig-geo-bounces@r-project.org
> <mailto:r-sig-geo-bounces@r-project.org><mailto:
> r-sig-geo-bounces@r-project.org<mailto:r-sig-geo-bounces@r-project.org>>]
> On Behalf Of James Rooney [ROONEYJ4@tcd.ie<mailto:ROONEYJ4@tcd.ie><mailto:
> ROONEYJ4@tcd.ie<mailto:ROONEYJ4@tcd.ie>>]
> > Sent: 23 November 2013 16:30
> > To: r-sig-geo@r-project.org<mailto:r-sig-geo@r-project.org><mailto:
> r-sig-geo@r-project.org<mailto:r-sig-geo@r-project.org>>
> > 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$obs<-sample.int<http://sample.int><http://sample.int>(100, N,
> TRUE)
> > SPolyDF$exp<-sample.int<http://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
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> R-sig-Geo@r-project.org<mailto:R-sig-Geo@r-project.org>>
> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >
> > _______________________________________________
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> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
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