rm(list = ls())
library(R2OpenBUGS)


BUGS_path <-
"c:\\Program Files (x86)\\OpenBUGS\\OpenBUGS323\\OpenBUGS.exe"
setwd("c:\\E-drive\\Books\\LOGLIN3\\BAYES\\")
working_dir <- "c:\\E-drive\\Books\\LOGLIN3\\BAYES\\"
model_a_filename <- "O-ring_model_a.txt"
model_b_filename <- "O-ring_model_b.txt"


iterates <- 10000
burn_in <- 1000

########################
##  O-ring data

ORing_data <- read.csv("O-ring_data.csv", header=T)

n <- dim(ORing_data)[1]
y <- ORing_data$Failure
# To rerun the analysis without obs. 18
# uncomment the line following the next
# case 18 in book is case 21 in Fletch's data
# y[21]=NA
temp <- ORing_data$Temperature
centered_temp <- scale(temp, scale=F)
c.temp <- centered_temp[,1]
temp
c.temp

### Fletch used BIDA not LOGLIN3 Priors
#   so I have changed them
#a <- c( 1.6, 1 )
#b <- c( 1, 1.6 )
# LOGLIN3 priors
a <- c( 1, .577 )
b <- c( .577, 1 )


data <- list( "n", "y", "c.temp", "a", "b" )

inits <- function() {
  list( ptilde = c( 0.5, 0.5 ) )
}

parameters <- list( "beta" )


ORing.c.sim <- bugs( data, inits, parameters,
                   model.file=model_b_filename,
                   n.chains=1, n.iter=iterates+burn_in,
                   n.thin=1, n.burnin=burn_in,
                   OpenBUGS.pgm=BUGS_path,
                   working.directory=working_dir,
                   debug=F)
# save 2 x t matrix of posterior iterates
beta.c <- t(ORing.c.sim$sims.list$beta)
save(beta.c,file="post-c-samp.Rda")
#save(beta.c,file="post-c-samp-18.Rda")