_site.yml

name: big_data_biogeography
output_dir: docs
navbar:
  title: Big Data Biogeography
  type: inverse
  left:
  - text: Home
    icon: fa-home 
    href: Readme.html
  - text: Course schedule
    href: 01_schedule.html
  - text: Student project
    href: 02_student_project.html
  - text: Day 1
    menu:
      - text: Overview
        href: mo_overview.html
      - text: Setup
        href: mo_setup.html
      - text: Download from GBIF
        href: mo_download_gbif.html
      - text: Download from Paleobiology database
        href: mo_download_paleobioDB.html
      - text: Download from IUCN database
        href: mo_download_iucn.html
  - text: Day 2
    menu:
    - text: Overview
      href: tue_overview.html
    - text: 1. Cleaning geographic records from public databases
      href: tue_clean_geographic_data.html
    - text: 2. Cleaning fossil data (optional)
      href: tue_clean_fossils.html
    - text: 3. Quantifying sampling bias
      href: tue_sampling_bias.html
    - text: 4. Probabilistic cleaning with bRacatus
      href: tue_probabilistic_cleaning.html
    - text: 5. Species richness and range size
      href: tue_species_ranges_and_richness.html
    - text: Further reading
      href: tue_further_reading
  - text: Day 3
    menu:
    - text: Overview
      href: wed_overview.html
    - text: 1. Taxon-specific bioregionalization
      href: wed_taxonspecific_bioregionalization.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: Further reading
      href: wed_further_reading
  - text: Day 4
    menu:
    - text: Overview
      href: thu_overview.html
    - text: 1. Automated conservation assessments IUCN Criterion B
      href: thu_aa_criterion_B.html
    - text: 2. Automated assessments using Neural Networks
      href: thu_aa_neural_network.html
    - text: Further reading
      href: thu_further_reading
  - text: Day 5
    menu:
    - text: Overview
      href: fr_overview.html
    - text: Student presentations
      href: fr_presentations.html

  right:
  - text: GitHub
    href: https://github.com/azizka/big_data_biogeography
  
output:
  html_document:
    lib_dir: site_libs
    self_contained: no