rbugs: Run BUGS from R in a BATCH

In rbugs: Fusing R and OpenBugs and Beyond

Description

Generate files (data, init, script) that are necessary to run BUGS, call BUGS through the OS, and collect the MCMC output.

Usage

rbugs(data, inits, paramSet, model,
      n.chains = 1, n.iter = 2000, n.burnin = floor(n.iter/2),
      n.thin = max(1, floor(n.chains * (n.iter - n.burnin)/1000)),
      dic = FALSE,
      debug = FALSE,
      bugs = system("which OpenBUGS", TRUE),
      bugsWorkingDir,
      OpenBugs = TRUE,
      cleanBugsWorkingDir = FALSE,
      genFilesOnly = FALSE,
      verbose = FALSE, seed = NULL)

Arguments

data	a list of data object to be used by BUGS
inits	a list of list of initial values, or a function which returns a list of initial values
paramSet	a vector of the names of the parameters to be monitored
model	the file name of the model description
n.chains	the number of chains to be monitored
n.iter	the number of iteration of each chain
n.burnin	the length of the burn-in
n.thin	thinning rate
dic	if TRUE, dic will be monitored
debug	a logical value indicating whether or not closing the BUGS window
bugs	the full name (including the path) of the BUGS executable
bugsWorkingDir	a directory to store all the intermediate files
OpenBugs	if TRUE, OpenBugs is used

cleanBugsWorkingDir	if TRUE, the generated files will be removed from the bugsWorkingDir
genFilesOnly	If TRUE, the script, data, inits, and model files will be generated but not run.
verbose	if TRUE, print the log file from BUGS
seed	an interger of random number seed

Value

A list with the inforamtion of the MCMC sample and each one of the nChains .

Author(s)

Jun Yan [e-mail] and Marcos Prates [e-mail]

Examples

 ##see examples in \code{\link{pumps}} and \code{\link{schools}}

rbugs documentation built on Jan. 15, 2019, 5:04 p.m.