[R] How to connect R and WinBUGS/OpenBUGS/LinBUGS in Linux in Feb. 2009

[Paul Heinrich Dietrich]

Hi Uwe,
Thank you for your guidance.  I have installed R2WinBUGS and WinBUGS14 under
wine.  Using ?bugs for help, it tells me:

useWINE: logical; attempt to use the Wine emulator to run 'WinBUGS',
defaults to 'FALSE' on Windows, and 'TRUE' otherwise. Not available in
S-PLUS.

WINE: character, path to 'wine' binary file, it is tried hard (by a guess
and the utilities 'which' and 'locate')  to get the information
automatically if not given.

newWINE: Use new versions of Wine that have 'winepath' utility

WINEPATH: character, path to 'winepath' binary file, it is tried hard (by a
guess and the utilities 'which' and 'locate')  to get the information
automatically if not given.

..and the following code is a simple Bayesian version of a t-test...

############################  Directory Paths  ############################
MyModelPath <- "/home/me/Compound/R/WinBUGS/"
MyBUGSPath <- "/home/me/.wine/drive_c/Program Files/WinBUGS14/"
MyModelFile <- paste(MyModelPath, "model.bug", sep="")
WINEPATH <- "/usr/bin/wine"

############################  Create Data Set  ############################
# Here is some fake data
n_draws <- 50
x <- round(runif(n_draws, 1, 2))
y <- ifelse(x == 1, rnorm(n_draws, 1, 1), rnorm(n_draws, 1.2, 0.8))
MyData <- as.data.frame(cbind(y, x))
y.n <- NROW(MyData$y)
x.j <- length(unique(x))
summary(MyData)

######################  Format Data for WinBUGS  ##########################
MyBUGSData <- list(y=MyData$y, x=MyData$x, n=y.n, x.j=x.j)
MyBUGSData

##########################  WinBUGS Model File  ###########################
library(R2WinBUGS)
cat("model
	{
	for (i in 1:n)
		{
		y[i] ~ dnorm(mu[i], tau)
		mu[i] <- alpha + beta[x[i]]
		}
	### STZ (Sum-To-Zero) Constraints
	beta[1] <- -sum(beta[2:x.j])
	### Priors
	alpha ~ dnorm(0.0, 1.0E-4)
	for (i in 2:x.j)
		{
		beta[i] ~ dnorm(0.0, 1.0E-4)
		}
	tau ~ dgamma(0.01, 0.01)
	precision <- sqrt(1/tau)
	}",
file=MyModelFile)
file.show(MyModelFile)

#############################  WinBUGS Model  #############################
MyModel <- bugs(MyBUGSData, inits=NULL,
	model.file=MyModelFile, 
	parameters.to.save=c("alpha", "beta", "precision"), 
	n.chains=3, n.iter=2000, n.burnin=1000, n.thin=1, codaPkg=TRUE,
	bugs.directory = MyBUGSPath, working.directory=MyModelPath, 
	useWINE=TRUE, WINEPATH=WINEPATH, debug=TRUE)

If I don't log in to R as the super-user (by just typing R in the terminal),
then the output says:

ERROR:  
  cannot open the connection

If I type sudo R to enter R, then it says:

ERROR:  
  Look at the log file and
try again with 'debug=TRUE' to figure out what went wrong within Bugs.

Now, the above error message occurs in the console window of R Commander,
but the terminal also has the following message occurs 11 times from one
try:

wine: /home/me/.wine is not owned by you
wine: /home/me/.wine is not owned by you
wine: /home/me/.wine is not owned by you
wine: /home/me/.wine is not owned by you
wine: /home/me/.wine is not owned by you
wine: /home/me/.wine is not owned by you
wine: /home/me/.wine is not owned by you
wine: /home/me/.wine is not owned by you
wine: /home/me/.wine is not owned by you
wine: /home/me/.wine is not owned by you
wine: /home/me/.wine is not owned by you

I'm wondering if I've misinterpreted how to set my paths with wine, because
I can go to the following path, double-click on WinBUGS14.exe, and open it
just fine: /home/me/.wine/drive_c/Program Files/WinBUGS14/

I can also go to Applications > Wine > Browse C:\ Drive and navigate to
WinBUGS.

Is this all about wine permissions, instead?  If so, how do I change them to
be what they need to be?

Please help if I've done something wrong.  Thanks.
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