model_gamma.txt

model{
  # priors:
  alpha[1] <- 0 #area baseline
  for (a in 2:A){alpha[a] ~ dnorm(0, 0.0001)}
  
  for (a in 1:A){beta[1,a] <- 0 } #fleet baseline
  beta[2, 1] <- 0 ; #area baseline
  for (a in 2:A){ beta[2,a] ~ dnorm(0, 0.0001)}

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

  for(f in 1:2){ #loop around fleet
    for(y in 1:Y){ # loop around years
      count[y,f,1:A] ~ dmulti(q[y,f,1:A], M[y,f])
      for(a in 1:A){
        re[y,f,a] ~ dnorm(0, tau)
        q[y,f,a] <- phi[y,f,a]/sum(phi[y,f,])
        log(phi[y,f,a]) <- alpha[a] + beta[f,a] + epsilon[a]*yearc[y] + gamma[f,a]*yearc[y] + re[y,f,a]
      }
    }
  }
}