get_final_values: Get final values of JAGS model

In BrandonEdwards/bbsBayes: Hierarchical Bayesian Analysis of North American BBS Data

Get final values of JAGS model

Description

get_final_values returns the final values of all parameters of the model created by run_model as a list. This function would mostly be used in conjunction with run_model to provide initial values.

Usage

get_final_values(model = NULL)

Arguments

model

Model object returned by run_model

Value

List of final values of monitored parameters.

Examples

# 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)

# Get the final values
final_values <- get_final_values(model = jags_mod)

# Then, we can use these final values as input for another model run
jags_mod2 <- run_model(jags_data = jags_data,
                       n_adapt = 0,
                       n_burnin = 0,
                       n_iter = 50,
                       n_thin = 1,
                       inits = final_values)

BrandonEdwards/bbsBayes documentation built on March 3, 2023, 9:55 a.m.