gudaleon/r2multibugs

An R interface to MultiBUGS

R2MultiBUGS

R2MultiBUGS is an R interface to MultiBUGS. MultiBUGS is a parallel implementation of the BUGS modelling framework.

R2MultiBUGS is a port of R2OpenBUGS for MultiBUGS. R2OpenBUGS was

originally written as R2WinBUGS by Andrew Gelman; changes and packaged by Sibylle Sturtz and Uwe Ligges. With considerable contributions by Gregor Gorjanc and Jouni Kerman. Adapted to R2OpenBUGS from R2WinBUGS by Neal Thomas.''

Installation

R2MultiBUGS requires MultiBUGS, which currently works only on Windows. (A Linux port is under preparation.) See the main MultiBUGS website for installation instructions for MultiBUGS.

The current development version of R2MultiBUGS can be installed in R using

# install.packages("devtools")
devtools::install_github("MultiBUGS/R2MultiBUGS")

Alternatively, if you have difficulties with devtools, you can download the latest auto-built Windows binary version of the package, and install in R using

install.packages("R2MultiBUGS_0.9.zip", repos = NULL, type = "win.binary")

Usage

The main functions in R2MultiBUGS are the same as R2OpenBUGS, except you specify the number of workers to be used via the n.workers argument to bugs()

# An example model file is given in:
model.file <- system.file(package='R2MultiBUGS', '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')

## You may need to specify 'MultiBUGS.pgm'
## also you need write access in the working directory:
schools.sim <- bugs(data, inits, parameters, model.file,
    n.chains=3, n.workers = 2, n.iter=5000)
print(schools.sim)
plot(schools.sim)