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