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

[chaogai]

Hi,

For me running winbugs through wine just works. Even when I do not specify  
any directories.
The example they give in the bugs helpfile was my starting point.
Setup is suse 11.1, latest Wine, R, R2WinBUGS & winbugs.
I assume you first tried without specifying directories?
The directories you use do not work for me, with WINEPATH the culprit.
If you do not have the latest wine I advise to upgrade & not specify  
directories.

Good luck,
Kees

On Wed, 18 Feb 2009 01:27:18 +0100, Paul Heinrich Dietrich  
<paul.heinrich.dietrich at gmail.com> wrote:

>
> 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)
>
> The output says:
>
> ERROR:
>   cannot open the connection
>
> 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.
>
> Please help if I've done something wrong.  Thanks.



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