model22.txt

model {
#
 # Priors
 mean.p ~ dunif(0, 1)        # Detection intercept on prob. scale
 alpha0 <- logit(mean.p)     # same on logit scale
 mean.psi ~ dunif(0, 1)      # Occupancy intercept on prob. scale
 beta0 <- logit(mean.psi)    # same on logit scale
 for(k in 1:3){              # 2 detection covariates + 1 interact
     alpha[k] ~ dnorm(0, 0.01) # Covariates on logit(detection)
 #   alpha[k] ~ dnorm(0, 0.05) # Covariates on logit(detection)
 #   alpha[k] ~ dunif(-10, 10) # Covariates on logit(detection)
 }

 for(k in 1:1){                # 2 occupancy covariates + 1 interact
     beta[k] ~ dnorm(0, 0.01)  # Covariates on logit(occupancy)
 #   beta[k] ~ dnorm(0, 0.05)  # Covariates on logit(occupancy)
 #   beta[k] ~ dunif(-10, 10)  # Covariates on logit(occupancy)
 }

 # Translation of the occupancy parameters in unmarked into those for BUGS:
 # (Intercept)         (beta0 in BUGS)
 # elev                (beta[1])
 # forest              (beta[2])
 # temp                (beta[3])
 # elev:forest         (beta[4])
 # elev:temp           (beta[5])
 # forest:temp         (beta[6])
 # elev:forest:temp    (beta[7])


 # Likelihood
 for (i in 1:M) {
   # True state model for the partially observed true state
   z[i] ~ dbern(psi[i])                      # True occupancy z at site i
   logit(psi[i]) <- beta0 +                  # occupancy (psi) intercept
     beta[1] * elev[i] #+                     # elev
     #beta[2] * forest[i] #+                  # forest
     #beta[3] * elev[i] * forest[i]          # elev:forest
     #beta[4] * elev[i] * temp[i] +          # elev:temp
     #beta[5] * temp[i] +                    # temp
     #beta[6] * forest[i] * temp[i] +        # forest:temp
     #beta[7] * elev[i] * forest[i] * temp[i]   # elev:forest:temp

    for (j in 1:J) {
       # Observation model for the actual observations
       y[i,j] ~ dbern(p.eff[i,j])      # Detection-nondetection at i and j
       p.eff[i,j] <- z[i] * p[i,j]
       logit(p[i,j]) <- alpha0 +             # detection (p) intercept
          alpha[1] * elev[i] +               # effect of elevation on p
          alpha[2] * temp[i,j] +             # effect of temp on p
          alpha[3] * elev[i] * temp[i,j]     # effect of elev:temp on p
    }
 }

 # Derived quantities
 sumZ <- sum(z[])      # Number of occupied sites among those studied
 occ.fs <- sum(z[])/M  # proportion of occupied sites among those studied
 logit.psi <- beta0    # For comparison with unmarked
 logit.p <- alpha0     # For comparison with unmarked
 }