I have used linbugs with the rbugs package for a recent work. It might be
worthwhile trying.
Jun
On 5/1/06, Uwe Ligges <[EMAIL PROTECTED]> wrote:
>
> Paul Johnson wrote:
>
> > Thank you very much. With the insertion of WINEPATH declaration, then
> > the following example program does run. And really fast, too!
> >
> >
> >
> >
> >
> > library(R2WinBUGS)
> >
> > WINEPATH <- "/usr/bin/winepath"
>
>
> Will be fixed in the package real soon now.
> Gregor, many thanks for the patches.
>
> Best,
> Uwe Ligges
>
>
> > # An example model file is given
> in:
> > model.file <- system.file(package = "R2WinBUGS", "model", "schools.txt")
> > # Let's take a look:
> > file.show(model.file)
> >
> > # Some example data (see ?schools for details):
> > data(schools)
> > schools
> >
> > J <- nrow(schools)
> > y <- schools$estimate
> > sigma.y <- schools$sd
> > data <- list ("J", "y", "sigma.y")
> > inits <- function(){
> > list(theta = rnorm(J, 0, 100), mu.theta = rnorm(1, 0, 100),
> > sigma.theta = runif(1, 0, 100))
> > }
> > parameters <- c("theta", "mu.theta", "sigma.theta")
> >
> >
> > schools.sim <- bugs(data, inits, parameters, model.file, n.chains = 3,
> > n.iter = 1000,bugs.directory = "/usr/local/share/WinBUGS14/",
> > working.directory = "/tmp", clearWD = FALSE, useWINE=T, newWINE=T,
> > WINE="/usr/bin/wine",WINEPATH=WINEPATH)
> >
> >
> >
> >
> > On 4/30/06, Gregor Gorjanc <[EMAIL PROTECTED]> wrote:
> >
> >>Hello Paul,
> >>
> >>thank you very much for this report. You caught a bug in R2WinBUGS that
> >>was introduced by me. I added support for winepath in 1.1-1 version.
> >>Since I switch between Windows and Linux I always set WINEPATH and then
> >>use it in bugs(). That's why I forgot to add it in further calls in
> >>bugs(). How silly :( This actually means that nobody else beside you
> >>tried to run R2WinBUGS under Linux. To bad. Please report summary to
> >>BUGS list as you have also asked there for help and I did not had time
> >>to answer you. I have been successfully running R2WinBUGS under Linux
> >>for quite some time now.
> >>
> >>Now you have the following options:
> >>
> >>A Set WINEPATH before you call bugs()
> >>
> >>i.e.
> >>
> >>WINEPATH <- "/usr/bin/winepath"
> >>
> >>bugs(..., WINEPATH=WINEPATH)
> >>
> >>This is the fastest approach for you.
> >>
> >>B Apply the following diffs, build and install R2WinBUGS by yourself
> >>
> >>I am also sendind them to maintainer of the package. So this should be
> >>fixed soon also on CRAN. Uwe?
> >>
> >>--- R2WinBUGSOrig/R/bugs.R 2006-04-29 21:44:59.000000000 +0200
> >>+++ R2WinBUGS/R/bugs.R 2006-04-30 12:52:36.000000000 +0200
> >>@@ -44,7 +44,7 @@
> >> } else new.model.file <- model.file
> >> bugs.script(parameters.to.save, n.chains, n.iter, n.burnin, n.thin,
> >> bugs.directory, new.model.file, debug=debug, is.inits=!is.null
> (inits),
> >>- bin = bin, DIC = DIC, useWINE = useWINE, newWINE = newWINE)
> >>+ bin = bin, DIC = DIC, useWINE = useWINE, newWINE = newWINE,
> >>WINEPATH=WINEPATH)
> >> #if (useWINE && missing(bugs.directory))
> >> # bugs.directory <- winedriveTr(bugs.directory)
> >> bugs.run(n.burnin, bugs.directory, WINE = WINE)
> >>
> >>--- R2WinBUGSOrig/R/bugs.script.R 2006-04-29 21:44:59.000000000+0200
> >>+++ R2WinBUGS/R/bugs.script.R 2006-04-30 12:52:12.000000000 +0200
> >>@@ -1,7 +1,7 @@
> >> "bugs.script" <-
> >> function (parameters.to.save, n.chains, n.iter, n.burnin,
> >> n.thin, bugs.directory, model.file, debug=FALSE, is.inits, bin,
> >>- DIC = FALSE, useWINE = FALSE, newWINE = FALSE){
> >>+ DIC = FALSE, useWINE = FALSE, newWINE = FALSE, WINEPATH=NULL){
> >>
> >>
> >>>I'm back!
> >>>
> >>>I've just learned that, on a fully updated Fedora Core Linux5 sytem,
> >>>the working solution to access Winbugs under wine via the R package
> >>>"rbugs" no longer works. Here was my last post on this topic (with
> >>>the formerly working solution) from January.
> >>>
> >>>http://finzi.psych.upenn.edu/R/Rhelp02a/archive/68497.html
> >>>
> >>>Currently, what happens is that WinBUGS starts up, but just sits there
> >>>doing nothing. I do not know if the problem is due to a change in
> >>>wine or rbugs, and since both of them are updated, it is hard to say.
> >>>I'm thinking it is a wine or perhaps even a kernel related problem.
> >>>Inside WinBUGS running under wine, it does not even work to manually
> >>>open the bugs.script file and then choose "Model/Script". it just
> >>>returns a screen full of errors saying the commands fail. I don't
> >>>think rbugs gets even that far, however, since the WinBUGS window does
> >>>pop up, but nothing happens.
> >>>
> >>>rbugs has been retooled to emphasize use of linbugs, the
> >>>OpenBUGS-based thing for linux, but I can't get linbugs to run at all
> >>>on my system, and the linbugs program itself appears to have been
> >>>removed from OpenBUGS distribution altogether. (I'm following that
> >>>with separate email to the OpenBUGS group).
> >>>
> >>>I think JAGS is the right long term solution, but currently I'm in the
> >>>middle of a semester trying to teach about Bayesian stats and the
> >>>students have some familiarity with WinBUGS and I'm interested in
> >>>making it work. So while I'm learning more about JAGS and the bayesmix
> >>>package that supports access to it from R, I still would like a way to
> >>>interact with Winbugs through Wine.
> >>>
> >>>If anybody has rbugs working in current Linux, please tell me
> >>>how--give me a working example?
> >>>
> >>>In the meanwhile, I've noticed that nightly updates have successfully
> >>>installed R2WinBUGS on linux systems and I've got a small test case
> >>>that I'd like to ask about. Since rbugs is a linux adaptation of
> >>>R2WinBUGS, and R2WinBUGS is now buildable on Linux, it looks like
> >>>R2WinBUGS may be the way to go. But it fails. The error centers
> >>>around the "WINEPATH" setting. I've learned that wine has a function
> >>>"winepath" that returns information that programs can use, and I've
> >>>fiddled this lots of ways, but it fails, saying
> >>>
> >>>
> >>>Error in paste(WINEPATH, "-w", x) : object "WINEPATH" not found
> >>>library(R2WinBUGS)
> >>>
> >>>I hope that by giving you this small not-yet-working example, you can
> >>>spot where I'm going wrong.
> >>>
> >>>##Paul Johnson 2006-04-29
> >>>
> >>>
> >>>library(R2WinBUGS)
> >>># Copied from Prof Andrew Gelman's example
> >>>model.file <- system.file(package = "R2WinBUGS", "model", "schools.txt
> ")
> >>>#
> >>>file.show(model.file)
> >>>data(schools)
> >>>schools
> >>>
> >>>J <- nrow(schools)
> >>>y <- schools$estimate
> >>>sigma.y <- schools$sd
> >>>data <- list ("J", "y", "sigma.y")
> >>>inits <- function(){
> >>> list(theta = rnorm(J, 0, 100), mu.theta = rnorm(1, 0, 100),
> >>> sigma.theta = runif(1, 0, 100))
> >>>}
> >>>parameters <- c("theta", "mu.theta", "sigma.theta")
> >>>
> >>>
> >>>schools.sim <- bugs(data, inits, parameters, model.file, n.chains = 3,
> >>>n.iter = 1000,bugs.directory = "/usr/local/share/WinBUGS14/",
> >>>working.directory = "/tmp", clearWD = FALSE, useWINE=T, newWINE=T,
> >>>WINE="/usr/bin/wine",WINEPATH="/usr/bin/winepath")
> >>>
> >>>
> >>>
> >>>I do have the binary "/usr/bin/winepath", but can't tell how to give
> >>>R2WinBUGS what it wants. Many failed efforts below:
> >>>
> >>>
> >>>
> >>>
> >>>>>schools.sim <- bugs(data, inits, parameters, model.file, n.chains =
> 3, n.iter = 1000,bugs.directory = "/usr/local/share/WinBUGS14/",
> working.directory = "/tmp", clearWD = FALSE, useWINE=T, newWINE=T,
> WINE="/usr/bin/wine",WINEPATH="/usr/bin/")
> >>>
> >>>Error in paste(WINEPATH, "-w", x) : object "WINEPATH" not found
> >>>
> >>>
> >>>>>schools.sim <- bugs(data, inits, parameters, model.file, n.chains =
> 3, n.iter = 1000,bugs.directory = "/usr/local/share/WinBUGS14/",
> working.directory = "/tmp", clearWD = FALSE, useWINE=T, newWINE=T,
> WINE="/usr/bin/wine")
> >>>
> >>>Error in if (!nchar(WINEPATH)) { : argument is of length zero
> >>>
> >>>
> >>>>>schools.sim <- bugs(data, inits, parameters, model.file, n.chains =
> 3, n.iter = 1000,bugs.directory = "/usr/local/share/WinBUGS14/",
> working.directory = "/tmp", clearWD = FALSE, useWINE=T, newWINE=T,
> WINE="/usr/bin/wine",WINEPATH="/usr/bin")
> >>>
> >>>Error in paste(WINEPATH, "-w", x) : object "WINEPATH" not found
> >>>
> >>>
> >>>
> >>>I know there are many unknowns here, but hope somebody has at least
> >>>one working example that we can build on.
> >>
> >>
> >>--
> >>Lep pozdrav / With regards,
> >> Gregor Gorjanc
> >>
> >>----------------------------------------------------------------------
> >>University of Ljubljana PhD student
> >>Biotechnical Faculty
> >>Zootechnical Department URI: http://www.bfro.uni-lj.si/MR/ggorjan
> >>Groblje 3 mail: gregor.gorjanc <at> bfro.uni-lj.si
> >>
> >>SI-1230 Domzale tel: +386 (0)1 72 17 861
> >>Slovenia, Europe fax: +386 (0)1 72 17 888
> >>
> >>----------------------------------------------------------------------
> >>"One must learn by doing the thing; for though you think you know it,
> >> you have no certainty until you try." Sophocles ~ 450 B.C.
> >>----------------------------------------------------------------------
> >>
> >>
> >>
> >
> >
> >
> > --
> > Paul E. Johnson
> > Professor, Political Science
> > 1541 Lilac Lane, Room 504
> > University of Kansas
> >
> > ______________________________________________
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>
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