15-poissonBA.R

# Define model effects
sigmaML <- cauchy(0, 1, truncation = c(0, Inf), dim = 3)
a_fem <- normal(0, sigmaML[1], dim = max(female_id))
a_year <- normal(0, sigmaML[2], dim = max(year))
a_group <- normal(0, sigmaML[3], dim = max(group_id))

a <- normal(0, 5)
bA <- normal(0, 3)
bEL <- normal(0, 3)
bES <- normal(0, 3)
bGS <- normal(0, 3)
bP <- normal(0, 3)
bPA <- normal(0, 3)

# Model setup
mu <- a + a_fem[female_id] + a_year[year] + a_group[group_id] +
      Age*bA + Eggs_laid*bEL + Mean_eggsize*bES + Parasite*bP +
      Group_size*bGS + Parasite*Age*bPA

p <- ilogit(mu)
distribution(fro$Successful) <- bernoulli(p)
cuckooModel <- model(a, bA, bEL, bES, bP, bGS, bPA)

# Plot
plot(cuckooModel)

# HMC sampling
draws <- mcmc(cuckooModel, n_samples = 4000,
              warmup = 1000, chains = 4, n_cores = 10)
# Trace plots
mcmc_trace(draws)
# Parameter posterior
mcmc_intervals(draws, prob = .95)