[R] R2WinBUGS: Data loading error

Uwe Ligges ligges at statistik.uni-dortmund.de
Thu Sep 22 16:08:44 CEST 2005

Hadassa Brunschwig wrote:

> Hi R-Help!
> I am trying to use R2WinBUGS but I get the following error message in WinBUGS
> (and there must be something wrong with my R statement as I tried it directly in
> WinBUGS and it worked):
> display(log)
> check(C:/Documents and Settings/Daikon/Roche/pop_model.txt)
> model is syntactically correct
> data(C:/Documents and Settings/Daikon/Roche/data.txt)
> expected key word structure
> compile(7)
> ...(and of course nothing works after that)
> and when I close WinBUGS i get:
> Error in file(file, "r") : unable to open connection
> In addition: Warning message:
> cannot open file 'codaIndex.txt' 
> Does anyone know what this 'expected key word structure' means?
> This is my R code (and I guess my model file is ok):
> modelA     <- c("C:/Documents and Settings/Daikon/Roche/pop_model.txt")
> n          <- length(unique(subsetA$subject))    #number of subjects
> nt         <- 13                                 #number of days
> Y          <- subsetA$concentr                   #concentration per day/subject
> t          <- 1:13                               #days
> dataA      <- list("n","nt","Y","t")
> parameters <- c("tau","C0","st90","C0.pop","st90.pop","tau.cpop","tau.stpop")
> inits      <-
> list(tau=c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1),C0=5,st90=4,C0.pop=5,st90.pop=4,tau.cpop=0.2,tau.stpop=1)
> mcmcA      <-
> bugs(dataA,inits,parameters,modelA,debug=T,n.chains=7,bugs.directory="c:/Program
> Files/WinBUGS14",working.directory="C:/Documents and Settings/Daikon/Roche")

Which versions of R, WinBUGS and R2WinBUGS?
Your example is not reproducible for us.

I'd take a look whether dimensions are OK and whether subsetA$concentr 
is in appropriate object, but without data and model file I am unable to 
help for the data part.

For the inits part, please see ?bugs:

inits: a list with n.chains elements; each element of the list is itself 
a list of starting values for the WinBUGS model, or a function creating 
(possibly random) initial values. Alternatively, if inits = NULL, 
initial values are generated by WinBUGS

Looks like you want to have the same inits for each chain. In order not 
to repeat the inits 7 times, you might want to specify them simply as a 
function such as:

  inits <- function(){
    list(tau = rep(1, 17), C0 = 5, st90 = 4, C0.pop = 5, st90.pop = 4,
         tau.cpop = 0.2, tau.stpop = 1)

Uwe Ligges

[Further correspondence on this particular topic, please respond to to 
the package maintainer (Sibylle) and me directly rather than to R-help.]

> Thanks so much...
> Hadassa

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