Yuelin Li
2010-Nov-11 16:48 UTC
[R] R2WinBUGS: Error in bugs(program="openbugs") but not openbugs()
I get an error when I call bugs(..., program="OpenBUGS",
bugs.directory="c:/Program Files/OpenBUGS/OpenBUGS312"),
expecting, as suggested in help(bugs), that it would fit the
model with openbugs() via BRugs.
> help(bugs)
... either winbugs/WinBUGS or openbugs/OpenBUGS, the latter
makes use of function openbugs and requires the CRAN package
BRugs. ...
However, it works fine when I directly call openbugs(). All
other things are exactly the same. It seems that (in my
settings) bugs(program="OpenBUGS") works differently than
openbugs(). Am I doing something wrong with bugs()? Or
there is something wrong with my OpenBUGS installation?
I am using R-2.12.0, R2WinBUGS 2.1-16 (2009-11-06), OpenBUGS
3.1.2 rev 668 (2010-09-28), and BRugs 0.5-3 (2009-11-06) on
a Windows XP machine.
Yuelin.
------- R file ---------
require(R2WinBUGS)
require(BRugs)
# Example in Albert (2007). Bayesian Computation with R. Springer.
# pp. 237-238. Prior = beta(0.5, 0.5), observe Binom(n, p)
# y=7 successes out of a sample of n=50. Estimate p.
y <- 7
n <- 50
alpha <- 1.0
beta <- 1.0
data <- list("y", "n", "alpha",
"beta")
inits <- function() { list(p = runif(1)) }
param <- "p"
# this works
Albert.bugs <- openbugs(data=data, inits=inits, parameters.to.save=param,
model.file = "C:/tryR/WinBUGS/Albert11.txt", n.chains=3, n.iter=500)
print(Albert.bugs, digits.summary = 4)
# this fails
Albert.bugs <- bugs(data=data, inits=inits, parameters.to.save=param,
model.file="C:/tryR/WinBUGS/Albert11.txt", n.chains=3, n.iter=500,
program="OpenBUGS")
------- BUGS file: Albert11.txt ------
model
{
y ~ dbin(p, n)
p ~ dbeta( alpha, beta )
}
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Uwe Ligges
2010-Nov-13 17:05 UTC
[R] R2WinBUGS: Error in bugs(program="openbugs") but not openbugs()
I found the problem which is a scoping issue in BRugs::bugsData() and will fix it for the next release. For now, you can workaround by calling your parameters (in this case particularly beta) with a names that are different from R function names (e.g. call it beta1). Best wishes, Uwe On 11.11.2010 17:48, Yuelin Li wrote:> I get an error when I call bugs(..., program="OpenBUGS", > bugs.directory="c:/Program Files/OpenBUGS/OpenBUGS312"), > expecting, as suggested in help(bugs), that it would fit the > model with openbugs() via BRugs. > > > help(bugs) > ... either winbugs/WinBUGS or openbugs/OpenBUGS, the latter > makes use of function openbugs and requires the CRAN package > BRugs. ... > > However, it works fine when I directly call openbugs().> All> other things are exactly the same. It seems that (in my > settings) bugs(program="OpenBUGS") works differently than > openbugs(). Am I doing something wrong with bugs()? Or > there is something wrong with my OpenBUGS installation? > > I am using R-2.12.0, R2WinBUGS 2.1-16 (2009-11-06), OpenBUGS > 3.1.2 rev 668 (2010-09-28), and BRugs 0.5-3 (2009-11-06) on > a Windows XP machine. > > Yuelin. > > ------- R file --------- > require(R2WinBUGS) > require(BRugs) > # Example in Albert (2007). Bayesian Computation with R. Springer. > # pp. 237-238. Prior = beta(0.5, 0.5), observe Binom(n, p) > # y=7 successes out of a sample of n=50. Estimate p. > y<- 7 > n<- 50 > alpha<- 1.0 > beta<- 1.0 > data<- list("y", "n", "alpha", "beta") > inits<- function() { list(p = runif(1)) } > param<- "p" > # this works > Albert.bugs<- openbugs(data=data, inits=inits, parameters.to.save=param, model.file = "C:/tryR/WinBUGS/Albert11.txt", n.chains=3, n.iter=500) > print(Albert.bugs, digits.summary = 4) > # this fails > Albert.bugs<- bugs(data=data, inits=inits, parameters.to.save=param, model.file="C:/tryR/WinBUGS/Albert11.txt", n.chains=3, n.iter=500, program="OpenBUGS") > > ------- BUGS file: Albert11.txt ------ > model > { > y ~ dbin(p, n) > p ~ dbeta( alpha, beta ) > } > > > > ====================================================================> > Please note that this e-mail and any files transmitted with it may be > privileged, confidential, and protected from disclosure under > applicable law. If the reader of this message is not the intended > recipient, or an employee or agent responsible for delivering this > message to the intended recipient, you are hereby notified that any > reading, dissemination, distribution, copying, or other use of this > communication or any of its attachments is strictly prohibited. If > you have received this communication in error, please notify the > sender immediately by replying to this message and deleting this > message, any attachments, and all copies and backups from your > computer. > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.
Uwe Ligges
2010-Nov-13 17:26 UTC
[R] R2WinBUGS: Error in bugs(program="openbugs") but not openbugs()
On 13.11.2010 18:05, Uwe Ligges wrote:> I found the problem which is a scoping issue in BRugs::bugsData() and > will fix it for the next release. > > For now, you can workaround by calling your parameters (in this case > particularly beta) with a names that are different from R function names > (e.g. call it beta1).Errr, nonsense: much better is to pass the data directly rather than just passing the names. Just replace the line where you define data by: data <- list(y=y, n=n, alpha=alpha, beta=beta) Best, Uwe Ligges> Best wishes, > Uwe > > > > > > > On 11.11.2010 17:48, Yuelin Li wrote: >> I get an error when I call bugs(..., program="OpenBUGS", >> bugs.directory="c:/Program Files/OpenBUGS/OpenBUGS312"), >> expecting, as suggested in help(bugs), that it would fit the >> model with openbugs() via BRugs. >> >> > help(bugs) >> ... either winbugs/WinBUGS or openbugs/OpenBUGS, the latter >> makes use of function openbugs and requires the CRAN package >> BRugs. ... >> >> However, it works fine when I directly call openbugs(). > > > All >> other things are exactly the same. It seems that (in my >> settings) bugs(program="OpenBUGS") works differently than >> openbugs(). Am I doing something wrong with bugs()? Or >> there is something wrong with my OpenBUGS installation? >> >> I am using R-2.12.0, R2WinBUGS 2.1-16 (2009-11-06), OpenBUGS >> 3.1.2 rev 668 (2010-09-28), and BRugs 0.5-3 (2009-11-06) on >> a Windows XP machine. >> >> Yuelin. >> >> ------- R file --------- >> require(R2WinBUGS) >> require(BRugs) >> # Example in Albert (2007). Bayesian Computation with R. Springer. >> # pp. 237-238. Prior = beta(0.5, 0.5), observe Binom(n, p) >> # y=7 successes out of a sample of n=50. Estimate p. >> y<- 7 >> n<- 50 >> alpha<- 1.0 >> beta<- 1.0 >> data<- list("y", "n", "alpha", "beta") >> inits<- function() { list(p = runif(1)) } >> param<- "p" >> # this works >> Albert.bugs<- openbugs(data=data, inits=inits, >> parameters.to.save=param, model.file = "C:/tryR/WinBUGS/Albert11.txt", >> n.chains=3, n.iter=500) >> print(Albert.bugs, digits.summary = 4) >> # this fails >> Albert.bugs<- bugs(data=data, inits=inits, parameters.to.save=param, >> model.file="C:/tryR/WinBUGS/Albert11.txt", n.chains=3, n.iter=500, >> program="OpenBUGS") >> >> ------- BUGS file: Albert11.txt ------ >> model >> { >> y ~ dbin(p, n) >> p ~ dbeta( alpha, beta ) >> } >> >> >> >> ====================================================================>> >> Please note that this e-mail and any files transmitted with it may be >> privileged, confidential, and protected from disclosure under >> applicable law. If the reader of this message is not the intended >> recipient, or an employee or agent responsible for delivering this >> message to the intended recipient, you are hereby notified that any >> reading, dissemination, distribution, copying, or other use of this >> communication or any of its attachments is strictly prohibited. If >> you have received this communication in error, please notify the >> sender immediately by replying to this message and deleting this >> message, any attachments, and all copies and backups from your >> computer. >> >> ______________________________________________ >> R-help at r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide >> http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.