dfgdata <- read.table("DFGforR.csv", header=TRUE, sep=";")
case <- dfgdata$case
day <- dfgdata$day
occasion <- dfgdata$occasion
good <- dfgdata$good + 1
well <- dfgdata$well + 1
K <- 3
L <- 2
alpha <- c(1,1,1,1,1)
data <- list ("case", "day", "occasion","good","well","K","L","alpha")
inits <- function() {
list(
  beta0well = structure(.Data = c(0,-3,-3,-3,0,-3,-3,-3,0), .Dim=c(3,3)),
  beta0good = structure(.Data = c(0,-3,-3,-3,0,-3,-3,-3,0), .Dim=c(3,3)),
  beta1well = c(0, .5), 
  beta1good = c(0, .5),
  pstateinit = structure(.Data = c(.3,.3,.4,.4,.3,.3) , .Dim=c(2,3)), 
  pstatetran = structure(.Data = c(.8,.1,.1,.1,.8,.1,.1,.1,.8,.8,.1,.1,.1,.8,.1,.1,.1,.8), .Dim=c(2,3,3)),
  pclassinit = c(.5, .5), 
  pclasstran = structure(.Data = c(.9,.1,.1,.9), .Dim=c(2,2))
)
}
dfg.sim <- bugs(data, inits, 
  parameters=c("pwell","pgood","pstateinit", "pstatetran","pclassinit", "pclasstran"), 
  model.file="DFGbugsmodellogit.txt",
  n.chains=1, n.iter=1000, n.burnin=500, n.thin=1,
  bugs.directory="c:/WinBUGS14/",debug=TRUE)
dfg.sim