get_mcmc_list {bbsBayes} | R Documentation |
get_mcmc_list
will return both the mcmc.list
object
and the sims.list
object from jagsUI. mcmc.list
is a list of the MCMC samples generated by the rjags library,
and sims.list
is a vectorized version of mcmc.list
produced by the jagsUI library.
get_mcmc_list(jags_mod = NULL)
jags_mod |
JAGS object returned by |
List containing:
mcmc_list |
MCMC samples produced by rjags |
sims_list |
Vectorized posterior samples produced by jagsUI |
# Toy example with Pacific Wren sample data # First, stratify the sample data strat_data <- stratify(by = "bbs_cws", sample_data = TRUE) # Prepare the stratified data for use in a JAGS model. jags_data <- prepare_jags_data(strat_data = strat_data, species_to_run = "Pacific Wren", model = "firstdiff", min_year = 2009, max_year = 2018) # Now run a JAGS model. For the sake of speed, we've adjusted # some arguments so that the JAGS model will not run any # adaptation steps (n_adapt = 0), no burnin steps (n_burnin = 0), # only 50 iterations per chain (n_iter = 50), and will not # thin the chain (n_thin = 1). This will produce several convergence # warnings, but we can ignore them for the sake of this toy example. jags_mod <- run_model(jags_data = jags_data, n_adapt = 0, n_burnin = 0, n_iter = 10, n_thin = 1) # Now, obtain the MCMC list mcmc_list <- get_mcmc_list(jags_mod = jags_mod)