Hierarchical Bayesian Analysis of North American BBS Data


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Documentation for package ‘bbsBayes’ version 2.3.7.2020

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bird_sample Sample point count data per species (Pacific Wren only)
fetch_bbs_data Fetch Breeding Bird Survey dataset
generate_indices Generate regional annual indices of abundance continent and strata and optionally for countries, states/provinces, or BCRs from analyses run on the stratifications that support these composite regions
generate_map Generate a map of trends by strata.
generate_trends Generate regional trends continent and strata and optionally for countries, states/provinces, or BCRs from analyses run on the stratifications that support these composite regions
geofacet_plot Generate a geofacet plot of population trajectories by province/state
get_composite_regions Get the area of each strata
get_final_values Get final values of JAGS model
get_mcmc_list Obtain MCMC list from jagsUI object
get_prepared_data Get the prepared species dataset used for JAGS
get_strata_area Get the area of each strata
load_bbs_data Load Breeding Bird Survey dataset into R Session
load_map Load a map of of the geographic strata.
load_sample_data Load Sample Breeding Bird Survey dataset into R Session
lppd Calculate log posterior predictive density
model_to_file Save model to text file
plot_indices Generate plots of index trajectories by stratum
prepare_data Wrangle data to use for modelling input
route_sample Sample route data per year run (Pacific Wren only)
run_model Run JAGS model for prepared species data
r_hat Generate Gelman-Rubin's R-Hat statistic
species_sample Sample North American bird species list (Pacific Wren only)
stratify Stratify raw Breeding Bird Survey data