model_alpha0_pred.txt

model{
  # priors:
  alpha[1] <- 0 #area baseline
  for (a in 2:A){alpha[a] ~ dnorm(0, 0.0001)}
  
  tau ~ dgamma(0.001, 0.001) # prior for mixed effect precision
  sd <- sqrt(1/tau)

  for(y in 1:Y){ # loop around years
    count[y,1,1:A] ~ dmulti(q[y,1:A], M[y,1])
    for(a in 1:A){
      re[y,a] ~ dnorm(0, tau)
      q[y,a] <- phi[y,a]/sum(phi[y,])
      log(phi[y,a]) <- alpha[a] + re[y,a]
    }
  }
  pred_count[1, 1:A] ~ dmulti(q_pred[1:A], pred_M[1])
  for(a in 1:A){
    re_pred[a] ~ dnorm(0, tau)
    q_pred[a] <- phi_pred[a]/sum(phi_pred[])
    log(phi_pred[a]) <- alpha[a] + re_pred[a]
  }
}