_pkgdown.yml

url: https://bailey-lab.github.io/coiaf

template:
  bootstrap: 5
  bootswatch: flatly
  bslib:
    base_font: { google: "Lato" } # usually serif fonts
    heading_font: { google: "Fira Sans" } # usually sans-serif fonts
    code_font: { google: "Fira Code" } # usually monospace fonts
    pkgdown-nav-height: 73.5px

navbar:
  structure:
    left: [reference, articles, news]
    right: [search, github]
  components:
    news:
      text: News
      menu:
        - text: "Change log"
          href: news/index.html

development:
  mode: auto

authors:
  Aris Paschalidis:
    href: "https://www.arispas.com"
  OJ Watson:
    href: https://www.imperial.ac.uk/people/o.watson15

reference:
  - title: Complexity of Infection
    desc: >
      Determine the complexity of infection (COI) of a sample
    contents:
      - optimize_coi
      - likelihood
      - compute_coi
      - compute_coi_regression
      - optimize_coi_regression
      - theoretical_coi
      - bootstrap_ci
  - title: Real Data
    desc: >
      Process and run real data
    contents:
      - process_real
      - example_real_data
  - title: Simulation
    desc: >
      Simulate data and run algorithm
    contents:
      - sim_biallelic
      - process_sim
      - disc_sensitivity
      - cont_sensitivity
  - title: Visualize
    contents:
      - plot-simulation
      - error_plot
      - sensitivity_plot
      - world_map
      - theme_coiaf

articles:
  - title: Use with real data
    navbar: ~
    contents:
      - example_real_data

  - title: Sensitivity analysis
    navbar: Sensitivity analysis
    contents:
      - starts_with("sensitivity_analysis")

  - title: Internals
    desc: Internal workings of algorithms
    contents:
      - simulator_details