### Example for running BUGS through R

setwd("j:/RbugsExample")
library(lme4)
library(Matrix)
library(R2WinBUGS)
library(BRugs)


setwd("j:/RbugsExample")


schools <- read.table ("schools.dat", header=T)
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))}
parameters <- c("theta", "mu.theta", "sigma.theta")
schools.sim <- bugs (data, inits, parameters, "schools.bug", n.chains=3, n.iter=1000) 

schools.sim <- bugs (data, inits, parameters, "schools.bug", n.chains=3, n.iter=1000, debug=T)

print (schools.sim)
plot (schools.sim) 
schools.sim$summary  #info that was printed using print() command

attach.bugs(schools.sim) #The simulated parameter values are now saved in R as:
			       #"theta": a 1500 x 8 matrix, representing 1500 simulations of the vector theta
	 			 #"mu.theta": a vector of length 1500 of simulations of mu.theta
				 #"sigma.theta": a vector of length 1500 of simulations of sigma.theta.


help(bugs)