get_mcmc_list {bbsBayes}R Documentation

Obtain MCMC list from jagsUI object


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 object returned by run_model


List containing:


MCMC samples produced by rjags


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)

[Package bbsBayes version 2.5.2 Index]