allows p < 1 (Panel 9.2).

`panel9pt2.fn` <-
function(ni=1100,nb=100,nt=2,nc=3){
# this script fits the model given in Panel 9.2 to the crossbill data from
# the Swiss bird survey.  The model allows p < 1.  

library("R2WinBUGS")

sink("model.txt")
cat("
model {

psi~dunif(0,1)
for(i in 1:(nyear-1)){
  gamma[i]~dunif(0,1)
  phi[i]~dunif(0,1)
  p[i]~dunif(0,1)
}
p[nyear]~dunif(0,1)

for(i in 1:nsite){
  z[i,1]~dbern(psi)
  for(t in 2:nyear){
     muZ[i,t]<- z[i,t-1]*phi[t-1] + (1-z[i,t-1])*gamma[t-1]
     z[i,t]~dbern(muZ[i,t])
 }
}

for (t in 1:nyear){
 for(i in 1:nsite){
 for(j in 1:nrep){
   Py[i,j,t]<- z[i,t]*p[t]
   y[i,j,t] ~ dbern(Py[i,j,t])
}
}
}

psivec[1]<-psi
psi.fs[1]<-sum(z[1:nsite,1])/nsite  
for(t in 2:nyear){
  psivec[t]<-psivec[t-1]*phi[t-1] + (1-psivec[t-1])*gamma[t-1]
  psi.fs[t]<-sum(z[1:nsite,t])/nsite  
turnover[t-1]<- ((1 - psivec[t-1]) * gamma[t-1])/( (1 - psivec[t-1]) * gamma[t-1] + phi[t-1]*psivec[t-1])
}

}
",fill=TRUE)
sink()

data<-crossbill.data
y<-data$data
y[y>1]<-1
Zst<-data$Zmat
nsite<-dim(y)[1]
nrep<-3
nyear<-4

pst<-c(.5,.5,.5,.5)
data <- list ( "y","nsite","nrep","nyear")


inits <- function()
  list (p=pst,z=Zst)

parameters <- c("p","gamma","phi")
out <- bugs (data, inits, parameters, "model.txt", n.thin=nt,n.chains=nc, n.burnin=nb,n.iter=ni,debug=TRUE)

return(out)



}