AYNA_CJS_simple.jags

    model {
    
    # -------------------------------------------------
    # Parameters:
    # phi: survival probability, grouped by age category
    # p: recapture probability when breeding
    # -------------------------------------------------


    ## Priors and constraints

      ### RECAPTURE PROBABILITY
      mean.p ~ dunif(0, 1)                          # Prior for mean recapture
      logit.p <- log(mean.p / (1-mean.p))           # Logit transformation

      for (t in 1:n.occasions){
          logit(p[t]) <- logit.p  + capt.raneff[t]
          capt.raneff[t] ~ dnorm(0, tau.capt)
      }
      
      ### SURVIVAL PROBABILITY
      for (i in 1:nind){
        for (t in f[i]:(n.occasions-1)){
          logit(phi[i,t]) <- mu[AGEMAT[i,t]] + surv.raneff[t]
        } #t
      } #i
    
    
    ## AGE-SPECIFIC SURVIVAL 
    for (age in 1:2){
      beta[age] ~ dunif(0, 1)                         # Priors for age-specific survival
      mu[age] <- log(beta[age] / (1-beta[age]))       # Logit transformation
    }

    ## RANDOM TIME EFFECT ON SURVIVAL 
    for (t in 1:(n.occasions-1)){
      surv.raneff[t] ~ dnorm(0, tau.surv)
    }
    
    ### PRIORS FOR RANDOM EFFECTS
    sigma.surv ~ dunif(0, 10)                     # Prior for standard deviation of survival
    tau.surv <- pow(sigma.surv, -2)
    
    sigma.capt ~ dunif(0, 10)                     # Prior for standard deviation of capture
    tau.capt <- pow(sigma.capt, -2)

    


    # Likelihood 
    for (i in 1:nind){
      # Define latent state at first capture
      z[i,f[i]] <- 1
        for (t in (f[i]+1):n.occasions){
          # State process
          z[i,t] ~ dbern(mu1[i,t])
          mu1[i,t] <- phi[i,t-1] * z[i,t-1]

          # Observation process
          y[i,t] ~ dbern(mu2[i,t])
          mu2[i,t] <- p[t] * z[i,t]
        } #t
      } #i

    # DERIVED SURVIVAL PROBABILITIES PER YEAR 
    for (t in 1:(n.occasions-1)){
      for (age in 1:2){
        logit(ann.surv[age,t]) <- mu[age] + surv.raneff[t]
      }
    }


    }