_pkgdown.yml

url: https://bbsbayes.github.io/bbsBayes2/
template:
  bootstrap: 5
navbar:
  structure:
    left:
    - intro
    - reference
    - articles
    - news
    right:
    - search
    - github
articles:
- title: Usage
  contents:
  - articles/bbsBayes2
  - articles/stratification
  - articles/models
  - articles/advanced
reference:
- title: BBS Data
  desc: Functions for downloading and managing BBS data
  contents:
  - ends_with("bbs_data")
  - remove_cache
- title: Processing data
  desc: |
    Functions for processing BBS data according to the type of models to be run
  contents:
  - stratify
  - prepare_data
  - prepare_spatial
  - prepare_model
- title: Stan models
  desc: |
    Functions for running Stan models via cmdstanr, as well as for saving and evaluating convergence
  contents:
  - run_model
  - save_model_run
  - copy_model_file
  - get_convergence
  - get_model_vars
  - get_summary
  - have_cmdstan
- title: Indices and trends
  desc: Functions for generating indices and trends from models
  contents:
  - generate_indices
  - generate_trends
- title: Plots
  desc: Functions for plotting indices and trends
  contents:
  - plot_map
  - plot_indices
  - plot_geofacet
- title: Helper functions
  contents:
  - search_species
  - load_map
  - assign_prov_state
- title: Included data
  contents:
  - bbs_data_sample
  - bbs_strata
  - bbs_models
  - pacific_wren_model
  - species_forms
  - species_notes
  - equal_area_crs
- title: Deprecated/Defunct functions
  contents:
  - bbsBayes2-defunct
  - bbsBayes2-deprecated