Hi all,
I use the excellent packages rjags and cacheSweave, and unfortunately
seem to have found an incompatibility between them. Below are a
minimal .Rnw file and corresponding JAGS model file which illustrate
the problem:
*** JAGS model file; name=j.bug ***
model {
mu ~ dnorm(0,1.0E-5)
sigma ~ dunif(0,100)
for(i in 1:length(y)) {
y[i] ~ dnorm(mu,sigma)
}
}
***
*** .Rnw file; name=testCacheSweave-jags.Rnw ***
\documentclass[12pt]{article}
\usepackage{Sweave}
\begin{document}
<<loadLib>>=
library(rjags)
@
<<testJags,cache=T>>=
y <- rnorm(100)
m <- jags.model("j.bug")
update(m,100)
res <- coda.samples(m,c("mu","sigma"),n.iter=1000)
@
<<plotResults,fig=T>>=
plot(res)
@
\end{document}
***
When I run Sweave with cacheSweaveDriver, I get the following error
(note that this happens on the first invocation, not just on repeat
invocations):
> Sweave("testCacheSweave-jags.Rnw",driver=cacheSweaveDriver)
Writing to file testCacheSweave-jags.tex
Processing code chunks ...
1 : echo term verbatim (label=loadLib)
2 : echo term verbatim (label=testJags)
Error: chunk 2 (label=testJags)
Error in jags.model("j.bug") : RUNTIME ERROR:
Unable to evaluate upper index of counter i
Reading through the cacheSweave documentation, it remains unclear to
me why this error would occur. Would anyone be able to clarify, and/
or suggest a possible workaround? It's an unfortunate conflict
because running JAGS models is one of the most computation-intensive
operations that I have in my .Rnw document.
Best & many thanks in advance.
Roger
--
Roger Levy Email: rl...@ling.ucsd.edu
Assistant Professor Phone: 858-534-7219
Department of Linguistics Fax: 858-534-4789
UC San Diego Web: http://ling.ucsd.edu/~rlevy
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