#######################
##
##  O-Ring Analysis
##
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 # "t" from book, later =5000
burn_in <- 1000

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

ORing_data <- 
read.csv(url("http://stat.unm.edu/~fletcher/LLM/DATA/O-ring_data.csv"))

n <- dim(ORing_data)[1]
y <- ORing_data$Failure
temp <- ORing_data$Temperature

# Delete case 18 in book
# which is case/flight 21 in Fletch's file
#y[21]=NA


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


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

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

parameters <- list( "beta" )

ORing.sim <- bugs( data, inits, parameters,
                   model.file=model_a_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)
ORing.sim$summary
beta <- t(ORing.sim$sims.list$beta)
# save 2 x t matrix of posterior beta iterates for later use
save(beta,file="post-samp.Rda")
# save case 18 deleted beta
# save(beta,file="post-samp-18.Rda")
# save thinned samples of beta
# save(beta,file="post-samp-thin.Rda")