bugs function takes data and starting values as
input. It automatically writes a OpenBUGS script, calls the model, and
saves the simulations for easy access in R.bugs(data, inits, parameters.to.save, n.iter, model.file="model.txt", n.chains=3, n.burnin=floor(n.iter / 2), n.thin=1, saveExec=FALSE,restart=FALSE, debug=FALSE, DIC=TRUE, digits=5, codaPkg=FALSE, OpenBUGS.pgm=NULL, working.directory=NULL, clearWD=FALSE, useWINE=FALSE, WINE=NULL, newWINE=TRUE, WINEPATH=NULL, bugs.seed=1, summary.only=FALSE, save.history=(.Platform$OS.type == "windows" | useWINE==TRUE), over.relax = FALSE)model.file) of the data for the OpenBUGS model,
or a vector or list of the names of the data objects used by
the model. If data is a one element character vector (such as "data.txt"),
it is assumed that data have already been written to the working directory into that file,
e.g. by the function bugs.data.n.chains elements; each element of the
list is itself a list of starting values for the OpenBUGS model,
or a function creating (possibly random) initial values.
Alternatively, if inits=NULL, initial values are generated
by OpenBUGS. If inits is a character vector with n.chains elements,
it is assumed that inits have already been written to the working directory into those files,
e.g. by the function bugs.inits.working.directory.
The old convention allowing model.file to be named ‘.bug’ has been eliminated
because the new OpenBUGS feature that allows the program image
to be saved and later restarted uses the .bug extension for the saved
images.
Alternatively, model.file can be an R function that contains a BUGS model that is written to a
temporary model file (see tempfile) using write.model.n.iter/2, that is,
discarding the first half of the simulations.n.thin = 1. The thinning is implemented in the OpenBUGS update phase, so
thinned samples are never stored, and they are not counted in n.burnin or
n.iter. Setting n.thin=2, doubles the number of iterations OpenBUGS
performs, but does not change n.iter or n.burnin. Thinning implemented
in this manner is not captured in summaries created by packages such as coda.basename (model.file) and extension .bug in the working
directory, which must be specified. The .bug files can be large, so
users should monitor them carefully and remove them when not needed.
n.burnin=0,additional iterations are performed and all iterations since
the previous burnin are used (including those from past executions). If
n.burnin>0, a new burnin is performed, and the previous iterations are
discarded, but execution continues from the status at the end of the previous
execution. When restart=TRUE, only n.burnin, n.iter,
and saveExec inputs
should be changed from the call creating the .bug file, otherwise
failed or erratic results may be produced. Note the default has n.burnin>0.
FALSE (default), OpenBUGS is closed automatically
when the script has finished running, otherwise OpenBUGS remains open
for further investigation. The debug option is not available for linux execution.TRUE (default), compute deviance, pD,
and DIC. The results are extracted directly
from the OpenBUGS log, which uses the rule pD =
Dbar - Dhat. If extraction fails or
if there are less iterations than required for the
adaptive phase, the rule pD=var(deviance) / 2
is computed in R. See bugs.log for more
information on extracting results from the log file.formatCFALSE (default) a bugs object
is returned, if TRUE file names of OpenBUGS output are
returned for easy access by the coda package through function
read.bugs.
A bugs object can be converted to an mcmc.list object as
used by the coda package with the method as.mcmc.list
(for which a method is provided by R2OpenBUGS).NULL (unset) and the environment variable
OpenBUGS_PATH is set the latter will be used as the default.
If NULL (unset), the environment variable
OpenBUGS_PATH is unset and the global option
R2OpenBUGS.pgm is not NULL the latter will be
used as the default.
If none of the former are set and OS is Windows, the
most recent OpenBUGS version
registered in the Windows registry will be used as the default.
For other operating systems, the location is guessed by Sys.which("OpenBUGS").
NULL, a temporary working directory via
tempdir is used.TRUE, this argument is only respected if
codaPkg=FALSE.FALSE. If WINE is used, the arguments OpenBUGS.pgm and working.directory must be given in form of Linux paths
rather than Windows paths (if not NULL).which and locate)
to get the information automatically if not given.which and locate)
to get the information automatically if not given.TRUE, only a parameter summary for very quick analyses is given,
temporary created files are not removed in that case.TRUE (the default), trace plots are generated at the end.TRUE, over-relaxed form of MCMC is used if available from OpenBUGS.codaPkg=TRUE the returned values are the names
of coda output files written by OpenBUGS containing
the Markov Chain Monte Carlo output in the CODA format.
This is useful for direct access with read.bugs.If codaPkg=FALSE, the following values are returned:
(n.iter-n.burnin) / n.thin)n.chains * n.keep)n.keep*n.chains simulations in
sims.matrix and sims.list (but NOT sims.array) have been randomly
permuted)n.chains*n.keep rows and one column for each element of
each saved parameter (for convenience, the n.keep*n.chains
simulations in sims.matrix and sims.list (but NOT sims.array) have
been randomly permuted)parameters.to.save and
“deviance”indexes.shortroot.shortmean(deviance) + pDwrite.model).
bugs function and run it (see
Example section).
debug=TRUE.
BUGS version support:
Operation system support:
useWINE=TRUE
If useWINE=TRUE is used, all paths (such as
working.directory and model.file, must be given in
native (Unix) style, but OpenBUGS.pgm can be given in
Windows path style (e.g. “c:/Program Files/OpenBUGS/”) or
native (Unix) style
(e.g. “/path/to/wine/folder/dosdevices/c:/Program
Files/OpenBUGS/OpenBUGS321/OpenBUGS.exe”).
Sturtz, S., Ligges, U., Gelman, A. (2005): R2WinBUGS: A Package for Running WinBUGS from R. Journal of Statistical Software 12(3), 1-16.
print.bugs, plot.bugs, as well as
coda and BRugs packages# An example model file is given in:
model.file <- system.file(package="R2OpenBUGS", "model", "schools.txt")
# Let's take a look:
file.show(model.file)
# Some example data (see ?schools for details):
data(schools)
schools
J <- nrow(schools)
y <- schools$estimate
sigma.y <- schools$sd
data <- list ("J", "y", "sigma.y")
inits <- function(){
list(theta=rnorm(J, 0, 100), mu.theta=rnorm(1, 0, 100),
sigma.theta=runif(1, 0, 100))
}
## or alternatively something like:
# inits <- list(
# list(theta=rnorm(J, 0, 90), mu.theta=rnorm(1, 0, 90),
# sigma.theta=runif(1, 0, 90)),
# list(theta=rnorm(J, 0, 100), mu.theta=rnorm(1, 0, 100),
# sigma.theta=runif(1, 0, 100))
# list(theta=rnorm(J, 0, 110), mu.theta=rnorm(1, 0, 110),
# sigma.theta=runif(1, 0, 110)))
parameters <- c("theta", "mu.theta", "sigma.theta")
## Not run:
# ## You may need to specify "OpenBUGS.pgm"
# ## also you need write access in the working directory:
# schools.sim <- bugs(data, inits, parameters, model.file,
# n.chains=3, n.iter=5000)
# print(schools.sim)
# plot(schools.sim)
# ## End(Not run)
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