##ZIP model
##read in data
##N is number of buildings
##T is time points
##covariates should be self-explanatory
d<-list(N=N, T=T,
	observed=observed,
	expected=expected,
	x1=datb$PercentTree,
	x2=datb$PercentGrass,
	x3=as.vector(scale(datb$WindowArea))	
)

##Model in WinBUGS
baymodel<-function(){
for(i in 1:N) {
	for( t in 1:T){
		observed[i,t] ~ dpois(mu[i,t])
		log(theta[i,t]) <- log(expected[i,t])+beta1*x1[i]+beta2*x2[i]+beta3*x3[i]+delta[t]
		mu[i,t] <- (1-W[i,t])*theta[i,t]+0.00001
		W[i,t]~dbern(p[i])
	}
	logit(p[i])<-gamma[i]
	gamma[i]<-beta1g*x1[i]+beta2g*x2[i]+beta3g*x3[i]
	}
##poisson parameters
beta1~dnorm(0,1.0E-2)
beta2~dnorm(0,1.0E-2)
beta3~dnorm(0,1.0E-2)

#binomial paramters
beta1g~dnorm(0,1.0E-2)
beta2g~dnorm(0,1.0E-2)
beta3g~dnorm(0,1.0E-2)

mu.delta~dnorm(0,1)
tau.delta<-0.001#dgamma(0.02,0.02)
pred.delta[1]<-mu.delta
delta[1]~dnorm(pred.delta[1],tau.delta)

for(t in 2:T){
pred.delta[t]<-delta[t-1]
delta[t]~dnorm(pred.delta[t],tau.delta)
}
}

##where to save and write file
modelfile <- "Y:/Documents/Bird_Facade_Data/model.txt"
write.model(baymodel, modelfile)

##initial values for MCMC
init1 <- list(beta1=0,beta2=0,beta3=0,delta=rep(0,T),#p=rep(0.5,N))#,
	 beta1g=0,beta2g=0,beta3g=0)
inits<-list(init1)

##WinBUGS directory
wdir <- "Y:/Documents/Bird_Facade_Data/Dir"
if(!file.exists(wdir)){dir.create(wdir)}
BugsDir <- "\\\\psf/Home/Applications/winbugs14_unrestricted/WinBUGS14"

##run MCMC
bugs1 <- bugs(data = d, inits = inits,
   working.directory = wdir,
   parameters.to.save = c("theta","beta1","beta2","beta3","delta","p","beta1g","beta2g","beta3g"),
   n.chains = 1, n.iter = 30000, n.burnin = 15000, n.thin = 5,
   model.file = modelfile,
   bugs.directory = BugsDir,debug=F)