Function reference • bbsBayes

BBS Data

Functions for downloading and managing BBS data

fetch_bbs_data(): Fetch Breeding Bird Survey dataset

have_bbs_data(): Check whether BBS data exists locally

load_bbs_data(): Load Breeding Bird Survey data

Processing data

Functions for processing BBS data according to the type of models to be run

stratify(): Stratify and filter Breeding Bird Survey data

prepare_data(): Filter for data quality

prepare_spatial(): Define neighbouring strata for spatial analyses

prepare_model(): Prepare model parameters

Stan models

Functions for running Stan models via cmdstanr, as well as for saving and evaluating convergence

run_model(): Run Bayesian model

save_model_run(): Save output of run_model()

copy_model_file(): Copy model file

get_convergence(): Convergence metrics

get_model_vars(): Get model variables

get_summary(): Return the cmdstanr summary

Indices and trends

Functions for generating indices and trends from models

generate_indices(): Regional annual indices of abundance

generate_trends(): Generate regional trends

Plots

Functions for plotting indices and trends

plot_map(): Generate a map of trends by strata

plot_indices(): Generate plots of index trajectories by stratum

plot_geofacet(): Create geofacet plot of population trajectories by province/state

Helper functions

search_species(): Search for species

load_map(): Load a map of of the geographic strata.

assign_prov_state(): Categorize polygon by Province/State if applicable

remove_cache(): Remove bbsBayes cache

Included data

bbs_data_sample: Sample BBS data

bbs_strata: List of included strata

bbs_models: Stan models included in bbsBayes

pacific_wren_model: Example model output

species_forms: Species forms

Deprecated/Defunct functions

generate_cont_indices() generate_regional_indices() generate_strata_indices() generate_cont_trend() generate_regional_trends() generate_strata_trends() get_final_values() get_mcmc_list() extract_index_data() get_prepared_data() get_strata_area() get_composite_regions() plot_cont_indices() prepare_jags_data() p_waic() waic(): bbsBayes defunct functions

generate_map() geofacet_plot(): bbsBayes deprecated functions