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#################################################
## Run OpenBUGS through R2OpenBUGS on Mac OS X ##
#################################################
# Johannes Karreth
# jkarreth@albany.edu
# The code below uses the help file for bugs()
# Adjust file paths to your system
library(R2OpenBUGS)
model.file <- system.file(package="R2WinBUGS", "model", "schools.txt")
# Some example data (see ?schools for details):
data(schools)
J <- nrow(schools)
y <- schools$estimate
sigma.y <- schools$sd
data <- list(J=J, y=y, sigma.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")
schools.sim <- bugs(data = data,
inits = inits,
parameters = parameters,
model.file = model.file,
n.chains=3,
n.burnin = 2500,
n.iter=5000,
debug = FALSE,
OpenBUGS.pgm = "/Applications/Wineskin/OpenBUGS.app/Contents/Resources/drive_c/Program Files/OpenBUGS/OpenBUGS323/OpenBUGS.exe",
working.directory = "/Users/johanneskarreth/R/Bayes/R2OpenBUGS", # Note: spaces in this path will create errors!
useWINE = TRUE,
bugs.seed = 12)
print(schools.sim)
plot(schools.sim)
# For a function to create a barebones summary table, use
# https://github.com/jkarreth/JKmisc/blob/master/mcmctab.R
# install.packages("devtools")
devtools::source_url("https://raw.githubusercontent.com/jkarreth/JKmisc/master/mcmctab.R")
mcmctab(schools.sim)
# Access posterior draws for postestimation
# Rows are draws, columns are parameters
schools.out <- schools.sim$sims.matrix