[R-sig-Geo] BYM Model Problem

[Peter Larson]

Hello,

I can get the example in the book to work fine, but it will not work 
with my data. I have loaded a shp file in using the code below but don't 
know if I can attach it to the whole list or not.

What could be going wrong?

Thank you very much for your help,

Pete


nc <- readShapePoly("LynchingHotSpots.shp",  proj4string=llCRS)

statesWanted <- c("Alabama","Mississippi","Louisiana","Georgia","Kentucky",
"North Carolina","South Carolina","Florida","Arkansas","Tennessee")

nc <- nc[nc at data$STATE_NAME %in% statesWanted,]

#names(nc)#Variables in the dataset

nc$Observed<-nc$Lynchings
nc$Population<-nc$POP1990   #Population at risk
r<-sum(nc$Observed)/sum(nc$Population)
nc$Expected<-nc$Population*r

#Computed Standardised Mortality Ratio
nc$SMR<-nc$Observed/nc$Expected

#######BESAG

nc.nb <- nb2WB(nc)
nc$nwprop <- nc$Lynchings/nc$POP1990
d<-list(N=N, observed=nc$Observed, expected=nc$Expected,
   nonwhite=nc$nwprop,#log(nwprop/(1-nwprop)),
   adj=nc.nb$adj,  weights=nc.nb$weights, num=nc.nb$num)

dwoutcov<-list(N=N, observed=nc$Observed, expected=nc$Expected,
   adj=nc.nb$adj,  weights=nc.nb$weights, num=nc.nb$num)

inits<-list(u=rep(0,N), v=rep(0,N), alpha=0, beta=0, precu=.001, 
precv=.001)
#inits$v[d$num==0]<-NA


#### Winbugs ####

  bymmodelfile<-paste(getwd(), "/besag.txt", sep="")
  wdir<-paste(getwd(), "/BYM", sep="")
  if(!file.exists(wdir)){dir.create(wdir)}
  BugsDir <- "C:/Users/Pete/Downloads/WinBUGS14"
  MCMCres<- bugs(data=d, inits=list(inits),
  working.directory=wdir,
  parameters.to.save=c("theta", "alpha", "beta", "u", "v", "sigmau", 
"sigmav"),
  n.chains=1, n.iter=30000, n.burnin=20000, n.thin=10,
  model.file=bymmodelfile,
  bugs.directory=BugsDir,
  WINEPATH="/usr/bin/winepath")
      save(file="BYM.RData", list=c("d", "inits", "MCMCres") )
#Load the data obtained by running WinBUGS in Windows
nc$BYMmean<-MCMCres$mean$theta
#nc$BYMmedian<-MCMCres$median$theta
nc$BYMumean<-MCMCres$mean$u
#nc$BYMumedian<-MCMCres$median$u
nc$BYMvmean<-MCMCres$mean$v
#nc$BYMvmedian<-MCMCres$median$v
On 2010/05/31 14:20, Virgilio Gomez Rubio wrote:

On 2010/05/31 14:20, Virgilio Gomez Rubio wrote:
> Dear Peter,
>
>
>    
>> I am working through the examples in Applied Spatial Data Analysis with
>> R using my own data.
>>
>> When I attempt to run the Besage-York-Mollie model in Chapter 11, I get
>> an index out of range error in WinBugs.
>>
>> How should I go about finding where the problem is?
>>      
> PLease, could you provide more information? In particular, are you
> trying to reproduce the example in the book or adapting it to your own
> data set? In that case, could you provide the code and data that you are
> using (in a private e-mail, if you prefer)?
>
> The error usually happens when there is some mismatch between the index
> in the loop exceeds some vector size(i.e., looping over 20 areas when
> there are just 15).
>
> Best,
>
> Virgilio
>