_site.yml

name: big_data_biogeography
output_dir: docs
navbar:
  title: Big Data Biogeography
  type: inverse
  left:
  - text: Home
    icon: fa-home 
    href: index.html
  - text: Course schedule
    href: schedule.html
  - text: Monday
    menu:
      - text: Setup
        href: mo_setup.html
      - text: Explore GBIF
        href: mo_explore_gbif.html
      - text: Explore the Paleobiology database
        href: mo_explore_paleobioDB.html
      - text: explore the IUCN database
        href: mo_explore_iucn.html
  - text: Tuesday
    menu:
    - text: 1. Obtaining geographic occurrence records from GBIF
      href: tue_download_GBIF_data.html
    - text: 2. Cleaning geographic data
      href: tue_cleaning_geographic_data.html
    - text: 3. Exploring sampling bias
      href: tue_accesibility_bias.html
    - text: 4. Species ranges & richness maps
      href: tue_species_richness.html
    - text: 5. Taxon-specific bioregionalization
      href: tue_taxon_specific_bioregions.html
    - text: 6. Species to biome classification
      href: tue_biome_classification.html
    - text: 7. Obtaining environmental data
      href: tue_obtaining_environmental_data.html
    - text: Optional - Automated conservation assessment and IUCN assessments
      href: tue_automated_conservation_assessment.html
    - text: Optional - Obtaining fossil data from PaleoDB
      href: tue_obtaining_data_from_paleoDB.html
    - text: Optional - Cleaning fossil data
      href: tue_fossil_cleaning.html
  - text: Wednesday
    menu:
    - text: 1. Preparing the input for phylogenetic analyses
      href: wed_data_preparation.html  
    - text: 2. Reconstructing ancestral areas (DEC)
      href: wed_ancestral_areas_DEC.html
    - text: 3. Estimating the number of shifts (DEC BSM)
      href: wed_DEC_bsm.html
    - text: 4. Diversification rate estimation (GeoSSE)
      href: wed_diversification_rates_geosse.html
  - text: Thursday
    menu:
    - text: 1. Ancestral ranges as continuous traits
      href: thu_BITE_script.html
  - text: Friday
    menu:
    - text: Student presentations
      href: fr_presentations.html

  right:
  - text: GitHub
    href: https://github.com/idiv-biodiversity/2019_big_data_biogeography
  
output:
  html_document:
    lib_dir: site_libs
    self_contained: no