Re: [R] BRugs crash, question
Bob O'Hara rni.boh at gmail.com writes:
On 4 April 2012 05:35, Jack Tanner ihok at hotmail.com wrote:
samplesBgr(beta) # crash
samplesBgr(beta, plot=FALSE) # also crash
Have you plotted your histories? I haven't used samplesBgr() much, so I
don't know how stable it is (although I do know it's slow).
Yes, plotting histories, densities works fine. Above, beta was an array of
parameters; plotBgr of a singleton parameter also crashes.
samplesStats() calls internal OpenBUGS functions (not R functions), so
that would mean saving the whole BUGS run (like externalise in OpenBUGS
itself. From you code fit$Stats should give you the same as
sampleStats('*'): if you want more use BRugsFit(..., coda=T) and work with
the coda object it produces (check the documentation for BRugsFit and coda).
I thought about that, but that's not good either. fit$Stats doesn't have
parameter names attached. Is there a way to figure out where in
fit$Stats[,mean], say, beta ends and theta begins? They seem to be in
arbitrary order, as below.
The downside to BrugsFit(..., coda=TRUE) is that you don't get DIC (even if you
also pass DIC=TRUE).
str(fit)
List of 3
$ Stats:'data.frame': 194 obs. of 8 variables:
..$ mean : num [1:194] 0.536 0.552 0.037 0.33 0.327 ...
..$ sd : num [1:194] 0.4505 0.214 0.1398 0.0789 0.3183 ...
..$ MC_error : num [1:194] 0.02775 0.011 0.00696 0.00346 0.02071 ...
..$ val2.5pc : num [1:194] -0.341 0.16 -0.215 0.179 -0.291 ...
..$ median : num [1:194] 0.5238 0.5409 0.0331 0.3279 0.3227 ...
..$ val97.5pc: num [1:194] 1.429 1.043 0.327 0.488 0.974 ...
..$ start: int [1:194] 1001 1001 1001 1001 1001 1001 1001 1001 1001 1001
...
..$ sample : int [1:194] 750 750 750 750 750 750 750 750 750 750 ...
$ DIC :'data.frame': 3 obs. of 4 variables:
..$ Dbar: num [1:3] 8.94 1661 1670
..$ Dhat: num [1:3] 17.2 1556 1573
..$ DIC : num [1:3] 0.686 1766 1767
..$ pD : num [1:3] -8.26 105.3 97.01
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[R] BRugs crash, question
(Using BRugs 0.7-5, R 2.14.2 32-bit on 64-bit Windows 7, OpenBUGS 3.2.1)
1. BRugs crashes R for me as follows. Sorry about the lack of detail; please let
me know if / how to supply a more useful bug report on this issue.
fit - BRugsFit(...)
# BRugs and OpenBUGS runs fine, the parameter estimates are reasonable
# across 3 chains
samplesBgr(beta) # crash
samplesBgr(beta, plot=FALSE) # also crash
2. I'd like to run a bunch of models via BRugs, saving the state after each one,
like so:
for (m in models) {
fit - BRugsFit(paste(m$modelname, .bug), ...)
save(fit, paste(m$modelname, .RData))
}
After I load the saved fitted objects in a new R process, BRugs functions like
samplesStats() no longer work. Is it possible to somehow load the saved objects
and use samplesStats and other BRugs functions?
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] BRugs crash, question
On 4 April 2012 05:35, Jack Tanner i...@hotmail.com wrote:
(Using BRugs 0.7-5, R 2.14.2 32-bit on 64-bit Windows 7, OpenBUGS 3.2.1)
1. BRugs crashes R for me as follows. Sorry about the lack of detail;
please let
me know if / how to supply a more useful bug report on this issue.
fit - BRugsFit(...)
# BRugs and OpenBUGS runs fine, the parameter estimates are reasonable
# across 3 chains
samplesBgr(beta) # crash
samplesBgr(beta, plot=FALSE) # also crash
Have you plotted your histories? I haven't used samplesBgr() much, so I
don't know how stable it is (although I do know it's slow).
2. I'd like to run a bunch of models via BRugs, saving the state after
each one,
like so:
for (m in models) {
fit - BRugsFit(paste(m$modelname, .bug), ...)
save(fit, paste(m$modelname, .RData))
}
After I load the saved fitted objects in a new R process, BRugs functions
like
samplesStats() no longer work. Is it possible to somehow load the saved
objects
and use samplesStats and other BRugs functions?
samplesStats() calls internal OpenBUGS functions (not R functions), so
that would mean saving the whole BUGS run (like externalise in OpenBUGS
itself. From you code fit$Stats should give you the same as
sampleStats('*'): if you want more use BRugsFit(..., coda=T) and work with
the coda object it produces (check the documentation for BRugsFit and coda).
Bob
--
Bob O'Hara
Biodiversity and Climate Research Centre
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D-60325 Frankfurt am Main,
Germany
Tel: +49 69 798 40216
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WWW: http://www.bik-f.de/root/index.php?page_id=219
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