inst/jags/Nmix_cmr.R

In crushing05/Nmix.doublecount:

sink("inst/jags/Nmix_cmr.jags")
cat("
    model {
    ##################
    ### Priors
    ##################

      lambda ~ dunif(0, 100)         # Abundance rate
      theta ~ dunif(0, 100)          # Detection rate
      phi ~ dunif(0, 1)              # Probability(marked)

    ##################
    ### Likelihoods
    ##################

    ## Count data
      for (s in 1:S) {
        ## Total abundance
        N[s] ~ dpois(lambda)            # Abundance, site s
        Nm[s] ~ dbinom(phi, N[s])       # Number of marked individuals, site s
        Nu[s] <- N[s] - Nm[s]           # Number of unmarked individuals, site s


        ## Counts
        for (k in 1:K) {
          n[s, k] ~ dpois(theta * Nu[s])         
        }#k
      }#s
    

    ## Capture-recapture data
      for(i in 1:TotNm){
        for(k in 1:K){
          y[i, k] ~ dpois(theta)    
        }#k
      }#i


    ###########################
    ### Derived parameters
    ###########################
    
    ## Total abundance

      Ntot <- sum(N[1:S])

    ## 'Detection' probability

      p <- 1 - exp(-theta)


    }#model
    ",fill = TRUE)
sink()