model{ # prior distributions alpha ~ dnorm(0.37, 1536.292) for(k in 1:K){ b[k] ~ dlogis(0, 1) } lambda[1] ~ dnorm(1.01, 1536.292) lambda[2] ~ dnorm(1.01, 1536.292) ### CALCULATING STABLE STAGE DISTRIBUTION for(i in 1:G){ # looping over all groups # survival probability logit(p[i, 1]) <- b[1] + b[2] * year[i] g[i, 1] <- p[i, 1] # survive to next stage class z[i, 1] <- 0 # remain in current stage class w[i, 1] <- 1 # proportion to stable stage for(s in 2:(S - 1)){ # loop through all stage classes logit(p[i, s]) <- b[1] + b[2] * year[i] g[i, s] <- p[i, s] z[i, s] <- 0 w[i, s] <- g[i, s - 1] / (lambda[year[i] + 1] - z[i, s]) * w[i, s - 1] } logit(p[i, S]) <- b[1] + b[2] * year[i] g[i, S] <- 0 z[i, S] <- p[i, S] w[i, S] <- g[i, S - 1] / (lambda[year[i] + 1] - z[i, S]) * w[i, S - 1] # stable stage distribution C[i, 1:S] <- w[i, 1:S] / sum(w[i, 1:S]) ### EXPECTED COUNT IN EACH STAGE CLASS ey[i, 2] <- p[i, 1] * C[i, 1] ey[i, 3] <- p[i, 2] * C[i, 2] ey[i, 4] <- p[i, 3] * C[i, 3] ey[i, 5] <- p[i, 4] * C[i, 4] ey[i, 6] <- p[i, 5] * C[i, 5] + p[i, 6] * C[i, 6] ey[i, 1] <- alpha * (lambda[year[i] + 1] - sum(ey[i, 2:6])) ### LIKELIHOOD y[i, 1:S] ~ dmulti(ey[i, 1:S], N[i]) ### MODEL CHECKING y_new[i, 1:S] ~ dmulti(ey[i, 1:S], N[i]) for(n in 1:S){ g_obs[i, n] <- y[i, n] * log(y[i, n] / (N[i] * ey[i, n] / sum(ey[i, 1:S]))) g_new[i, n] <- y_new[i, n] * log(y_new[i, n] / (N[i] * ey[i, n] / sum(ey[i, 1:S]))) } } cs_obs <- 2 * sum(g_obs) cs_new <- 2 * sum(g_new) bp <- step(cs_new - cs_obs) }