[R] Current state of support for BUGS access for Linux users?
gelman at stat.columbia.edu
Wed Jan 18 11:57:43 CET 2006
Hi all. Sorry for any confusion. At one point, close to a year ago I
think, I put in the effort to get the bugs() function in R to work with
OpneBUGS. But at the time, I couldn't get OpenBUGS to do much. After
some effort I got it to work on some simple examples but I couldn't get
it to work on some of my other examples (e.g., a mulitlevel logistic
regression). In the meantime, Uwe and Sibylle set up R2WinBUGS. I
still think that BRugs would be improved by an R front-end (basically,
the bugs() function adapted to BRugs). But I haven't tried to get
OpenBUGS working for awhile so I don't know if it currently fits the
models I'd like to fit. It certainly wouldn't be difficult to extend
the bugs() fuction to do the appropriate BRugs calls.
In a different direction, Jouni Kerman wrote a function to take output
from chains of iterative simulation--not necessarily from Bugs, they
could come from mcmcsamp() or just your own customized Gibbs or
Metropolis program--and convert them into bugs objects, which is nice
because then you can automatically monitor convergence and look at the
inferences using the built-in plot() and print() options in R2WinBUGS.
We'll try to put this in R2WinBUGS soon.
A key part of a bugs object is the way a vector or matrix of parameters
with the same name is structured as a vector or matrix, not simply as
part of a long vector of parameters (this can be clearly seen in the
right half of the plot() output for a hiearchical model fit in Bugs, and
also can be seen if you fit a bugs model and then do attach.bugs() and
look at simulations of parameter vectors or arrays.
Gregor Gorjanc wrote:
>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  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
>>>>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
>>>However Andrew Gelman, has added also support for OpenBUGS so this
>>>might be also a good news for Linux if wine is used. Changelog can be
>>>found at .
Professor, Department of Statistics
Professor, Department of Political Science
gelman at stat.columbia.edu
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