openbugs: Wrapper to run OpenBUGS
In R2WinBUGS: Running 'WinBUGS' and 'OpenBUGS' from 'R' / 'S-PLUS'

Description Usage Arguments Value Note Author(s) See Also Examples

The openbugs function takes data and starting values as input. It automatically calls the package BRugs and runs something similar to BRugsFit. Not available in S-PLUS.

openbugs(data, inits, parameters.to.save,
    model.file = "model.txt", n.chains = 3, n.iter = 2000,
    n.burnin = floor(n.iter/2),
    n.thin = max(1, floor(n.chains * (n.iter - n.burnin) / n.sims)),
    n.sims = 1000,  DIC = TRUE, 
    bugs.directory = "c:/Program Files/OpenBUGS/",
    working.directory = NULL, digits = 5, over.relax = FALSE, seed=NULL)

`data`	either a named list (names corresponding to variable names in the `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`.
`inits`	a list with `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` are missing or `inits = NULL`, initial values are generated by OpenBUGS.
`parameters.to.save`	character vector of the names of the parameters to save which should be monitored
`model.file`	file containing the model written in OpenBUGS code. The extension can be either ‘.bug’ or ‘.txt’. If ‘.bug’, a copy of the file with extension ‘.txt’ will be created in the `bugs()` call and removed afterwards. Note that similarly named ‘.txt’ files will be overwritten.
`n.chains`	number of Markov chains (default: 3)
`n.iter`	number of total iterations per chain (including burn in; default: 2000)
`n.burnin`	length of burn in, i.e. number of iterations to discard at the beginning. Default is `n.iter/2`, that is, discarding the first half of the simulations.
`n.thin`	thinning rate. Must be a positive integer. Set `n.thin` > 1 to save memory and computation time if `n.iter` is large. Default is `max(1, floor(n.chains * (n.iter-n.burnin) / 1000))` which will only thin if there are at least 2000 simulations.
`n.sims`	The approximate number of simulations to keep after thinning.
`DIC`	logical; if `TRUE` (default), compute deviance, pD, and DIC. This is done in BRugs directly.
`digits`	number of significant digits used for OpenBUGS input, see `formatC`
`bugs.directory`	directory that contains the OpenBUGS executable - currently unused
`working.directory`	sets working directory during execution of this function; WinBUGS in- and output will be stored in this directory; if `NULL`, a temporary working directory via `tempdir` is used.
`over.relax`	If `TRUE`, over-relaxed form of MCMC is used if available from OpenBUGS.
`seed`	random seed (default is no seed)

A bugs object.

By default, BRugs (and hence openbugs()) is quite verbose. This can be controlled for the whole BRugs package by the option ‘BRugsVerbose’ (see options) which is set to TRUE by default.

Andrew Gelman, gelman@stat.columbia.edu; modifications and packaged by Sibylle Sturtz, sturtz@statistik.tu-dortmund.de, and Uwe Ligges.

bugs and the BRugs package

# An example model file is given in:
model.file <- system.file(package = "R2WinBUGS", "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: 
## both write access in the working directory and package BRugs required:
schools.sim <- bugs(data, inits, parameters, model.file,
    n.chains = 3, n.iter = 5000,
    program = "openbugs", working.directory = NULL)
print(schools.sim)
plot(schools.sim)

## End(Not run)