Paul Johnson
2006-Jan-16 22:13 UTC
[R] Current state of support for BUGS access for Linux users?
Greetings: I'm going to encourage some students to try Bayesian ideas for hierarchical models. I want to run the WinBUGS and R examples in Tony Lancaster's An Introduction to Modern Bayesian Econometrics. That features MS Windows and "bugs" from R2WinBUGS. Today, I want to ask how people are doing this in Linux? I have found a plethora of possibilities, some of which are not quite ready, some of which work only under MS Windows. Right now I just want to know "what actually works". Here's where I stand now in Fedora Core 4 Linux. 1. OpenBUGS-2.1.1 runs in Linux. I can run "linbugs" (the console version similar to the old BUGS) and also I can run--under wine--the newest version of "winbugs.exe" that is circulated with OpenBUGS. As far as I can tell, the graphical interface in wine/winbugs works in almost all elements. A few things seem not quite right in the GUI (can't initialize more than one chain, difficult to specify variables for monitoring), but it does work. It is easier to install and work with OpenBUGS's version of winbugs.exe than with Winbugs-1.4 because the Open version does not have that annoying license registration and "winbugs.exe" is not wrapped inside an installation script. I'm a little confused about WinBUGS versions because the BRugs documents http://www.biostat.umn.edu/~brad/software/BRugs/BRugs_install.html refer to WinBUGS-1.5, which refers to http://www.biostat.umn.edu/~brad/software/BRugs/WinBUGS15.zip, which can be downloaded without any of the registration steps, but WinBUGS15 is not mentioned in the WinBUGS site (where 1.4.1 appears to be the newest). Supposing I get the winbugs.exe question settled: 2. How to most dependably send jobs from R to "linbugs" or "winbugs.exe"? The BRugs package is preferred? For a long time, R2WinBUGS was Windows-only, but toward the end of last fall I noticed that R2WinBUGS now does compile and install under R in Linux. however, its help still says: SystemRequirements: WinBUGS 1.4 on Windows I'd appreciate any advice. -- Paul E. Johnson Professor, Political Science 1541 Lilac Lane, Room 504 University of Kansas
Uwe Ligges
2006-Jan-17 07:50 UTC
[R] Current state of support for BUGS access for Linux users?
Paul Johnson wrote:> Greetings: > > I'm going to encourage some students to try Bayesian ideas for > hierarchical models. > I want to run the WinBUGS and R examples in Tony Lancaster's An > Introduction to Modern Bayesian Econometrics. That features MS > Windows and "bugs" from R2WinBUGS. > > Today, I want to ask how people are doing this in Linux? I have found > a plethora of possibilities, some of which are not quite ready, some > of which work only under MS Windows. Right now I just want to know > "what actually works". > > Here's where I stand now in Fedora Core 4 Linux. > 1. OpenBUGS-2.1.1 runs in Linux. I can run "linbugs" (the console > version similar to the old BUGS) and also I can run--under wine--the > newest version of "winbugs.exe" that is circulated with OpenBUGS. As > far as I can tell, the graphical interface in wine/winbugs works in > almost all elements. A few things seem not quite right in the GUI > (can't initialize more than one chain, difficult to specify variables > for monitoring), but it does work. > > It is easier to install and work with OpenBUGS's version of > winbugs.exe than with Winbugs-1.4 because the Open version does not > have that annoying license registration and "winbugs.exe" is not > wrapped inside an installation script. I'm a little confused about > WinBUGS versions because the BRugs documents > http://www.biostat.umn.edu/~brad/software/BRugs/BRugs_install.html > refer to WinBUGS-1.5, which refers to > http://www.biostat.umn.edu/~brad/software/BRugs/WinBUGS15.zip, which > can be downloaded without any of the registration steps, but WinBUGS15 > is not mentioned in the WinBUGS site (where 1.4.1 appears to be the > newest). > > Supposing I get the winbugs.exe question settled: > > 2. How to most dependably send jobs from R to "linbugs" or "winbugs.exe"? > > The BRugs package is preferred? > > For a long time, R2WinBUGS was Windows-only, but toward the end of > last fall I noticed that R2WinBUGS now does compile and install under > R in Linux. > > however, its help still says: > SystemRequirements: WinBUGS 1.4 on Windows > > I'd appreciate any advice.[resend to less recipients in order to save Martin's spare time to approve message; CCing Andrew Thomas, Bob O'Hara and Sibylle Sturtz separately] Re BUGS: WinBUGS-1.5 never got really released, AFAIK - Andrew or Bob might want to correct me. It has been renamed to OpenBUGS. The current version is the GPL'ed OpenBUGS 2.1.1 available from http://mathstat.helsinki.fi/openbugs/. Re R packages: - R2WinBUGS is compatible with WinBUGS-1.4.x only, its newest version can speak with WinBUGS under wine thanks to user contributions. But it still depends on WinBUGS-1.4.x, hence Windows only (considering wine as Windows). - BRugs contains the BRugs interface, R functions and the whole OpenBUGS installation. Unfortunately, due to serious compiler problems, we were not able to get a Linux version running using the interface. Hence it was not possible to release any non-Windows version up to now. I haven't tested BRugs under wine yet (in which case R has to run under wine as well, of course) ... and I do not know if there are any serious performance penalties. Note that even in the long term, OpenBUGS will only run on x86 based platforms. Due to the much more flexibile interface, I prefer BRugs. BTW: "Real programmers" won't consider R2WinBUGS to be an "interface" at all - it might be useful, though. ;-) Uwe Ligges> -- > Paul E. Johnson > Professor, Political Science > 1541 Lilac Lane, Room 504 > University of Kansas > > ______________________________________________ > R-help at stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Gregor Gorjanc
2006-Jan-17 23:18 UTC
[R] Current state of support for BUGS access for Linux users?
Hello!> Re R packages: > - R2WinBUGS is compatible with WinBUGS-1.4.x only, its newest version > can speak with WinBUGS under wine thanks to user contributions. But it > still depends on WinBUGS-1.4.x, hence Windows only (considering wine as > Windows).However Andrew Gelman, has added also support[1] for OpenBUGS so this might be also a good news for Linux if wine is used. Changelog can be found at [2]. [1]http://www.stat.columbia.edu/~gelman/bugsR/ [2]http://www.stat.columbia.edu/~gelman/bugsR/bugs.R -- 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.
Gregor Gorjanc
2006-Jan-18 06:44 UTC
[R] Current state of support for BUGS access for Linux users?
Paul Johnson wrote:> Do you mean to say that you have actually made OpenBUGS run with > R2WinBUGS in Linux? >No, I did not say this.> Gelman's page seems to state that OpenBUGS support is brought in from > BRugs, which is still Windows-only.Well, Gelman changed his site a bit. Few days (weeks?) ago there was a red text at the top of [1] stating that bugs.R was accomodated to work with OpenBUGS. Since bugs.R was base for R2WinBUGS, I conclude that BRugs was not involved here. Since then Gelman was active with his pages and things changed/improved. I do not know what he has done to handle also OpenBUGS. Perhaps Gelman and R2WinBUGS maintainers could tell us and I hope that upstream (by Gelman) changes will find way into R2WinBUGS package.>> >>>Re R packages: >>>- R2WinBUGS is compatible with WinBUGS-1.4.x only, its newest version >>>can speak with WinBUGS under wine thanks to user contributions. But it >>>still depends on WinBUGS-1.4.x, hence Windows only (considering wine as >>>Windows). >> >>However Andrew Gelman, has added also support[1] for OpenBUGS so this >>might be also a good news for Linux if wine is used. Changelog can be >>found at [2]. >> >>[1]http://www.stat.columbia.edu/~gelman/bugsR/ >>[2]http://www.stat.columbia.edu/~gelman/bugsR/bugs.R-- 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.