Re: [R] Current state of support for BUGS access for Linux users?

From: Andrew Gelman <gelman_at_stat.columbia.edu>
Date: Wed 18 Jan 2006 - 21:57:43 EST

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 [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
>>>

-- 
Andrew Gelman
Professor, Department of Statistics
Professor, Department of Political Science
gelman@stat.columbia.edu
www.stat.columbia.edu/~gelman

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Received on Wed Jan 18 22:05:17 2006

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