_pkgdown.yml

# navbar:
#   title: "champs"
#   type: inverse
#   left:
#     - text: "Home"
#       href: index.html
#     - text: "Loading Data"
#       href: articles/data.html
#     - text: "Usage"
#       href: articles/usage.html
#     - text: "Reference"
#       href: reference/index.html
#     # - text: "News"
#     #   href: news/index.html
#   right:
#    - icon: fa-github
#      href: https://github.com/ki-tools/champs

articles:
  - title: Articles
    navbar: ~
    contents:
    - data_intro
    - download
    - data_load
    - usage
    - plots_tables
    - calc_deepdive
    - custom_analyses_h_influenzae

# articles:
# - title: Main verbs
#   navbar: ~
#   contents:
#   - data
#   - two-table
#   - rowwise
#   - colwise

reference:
  - title: "Data"
    contents:
      - get_l2_data
      - load_data
      - valid_conditions
      - valid_pathogens
      - valid_sites
      - valid_specimen_types
      - valid_icds
      - valid_age_groups
      - valid_age_subcats
      - mock
      - tac_table
      - infectious_causes

  - title: "Computing Statistics"
    contents:
      - calc_cc_allcases_by_site_age
      - calc_cc_detected_by_site_age
      - calc_detected_allcases_by_site_age
      - calc_detected_by_decode
      - calc_nspecimen_by_pmi
      - calc_pmi_by_age_decode
      - calc_pmi_by_decode_site
      - calc_pmi_by_specimen_site
      - calc_top_tac_pathogens
      - calc_top_dcd_pathogens_by_acq
      - calc_top_tac_pathogens_cc
      - calc_top_etiol_by_age
      - calc_cc_allcases_by_age_acq
      - calc_syndrome_combinations
      - calc_cc_by_age_syndrome

  - title: "Producing Outputs"
    contents:
      - plot_margins_site_age
      - heatmap_site_age
      - plot_top_etiol_by_age
      - plot_syndrome_combinations
      - html_table_site_age