_pkgdown.yml

url: https://framverse.github.io/framrsquared/
template:
  bootstrap: 5
reference:
  - title: "Connecting to FRAM database"
    desc: >
      Functions to connect a disconnect to a FRAM database
    contents:
      - connect_fram_db
      - disconnect_fram_db
  - title: "Importing FRAM tables"
    desc: >
      Functions to import a FRAM database table into R
    contents:
      - starts_with("fetch_table")
  - title: "FRAM filtering"
    desc: >
      Functions to filter FRAM tables by fishery
    contents:
      - starts_with("filter_")
  - title: "Comparing FRAM runs"
    desc: >
      Functions that compare two FRAM runs within the same database
    contents:
      - starts_with("compare_")
  - title: "FRAM Screen Reports"
    desc: >
      Functions that replicate FRAM UI screen reports
    contents:
      - starts_with("msf_")
      - population_statistics
      - fishery_mortality
      - stock_mortality
  - title: "Stock impact visualizations"
    desc: >
      Functions that visualize impacts of stocks in fisheries
    contents:
      - starts_with("plot_")
      - make_impacts_per_catch_heatmap
  - title: "Initializing R FRAM Projects"
    desc: >
      Creates a standardized workspace for fram related R projects
    contents:
      - initialize_project
      - fetch_quarto_templates
  - title: "Database altering functions"
    desc: >
      Functions that alter FRAM database tables, use with caution
    contents:
      - starts_with("copy_")
      - starts_with("change_")
      - remove_run
  - title: "Week calculations"
    desc: >
      Functions calculate a week number
    contents:
      - ends_with("_week")
  - title: "Validations"
    desc: >
      Functions that validate FRAM data
    contents:
      - contains("validate_")
  - title: "Terminal Runs"
    desc: >
      Functions that unpack the TRuns table in the FRAM database
    contents:
      - contains("truns_")
  - title: "Post-season FRAM"
    desc: >
      Functions that focus on post-season runs and backwards FRAM
    contents:
      - bkfram_checks_coho
      - post_season_abundance
  - title: "Describing the FRAM Database"
    desc: >
        Functions that describe the current FRAM database
    contents:
      - starts_with("fram_")
      - get_run_ids
      - find_tables_by_column_
      - provide_table_names
      - run_info
  - title: "Data checking"
    desc: >
        Functions that provide checks for the current data
    contents:
      - contains("check")
  - title: "Misc."
    desc: >
        Miscellaneous functions
    contents:
      - add_flag_text
      - aeq_mortality
      - coho_mark_rates
      - input_summary_
      - mortality_scalers
      - msp_mortality
      - NR_flag_translate
      - scalers_flag_translate
      - stock_id_comp
      - welcome