_pkgdown.yml

destination: docs

navbar:
  title: "malariasimulation"
  structure:
    left: [vignettes, functions, news]
    right: [icon]
  components:
    vignettes:
      text: "Vignettes"
      menu:
      - text: "Model Introduction"
        href: articles/Model.html
      - text: "Demography"
        href: articles/Demography.html
      - text: "Treatment"
        href: articles/Treatment.html
      - text: "MDA and Chemoprevention"
        href: articles/MDA.html
      - text: "Vaccines"
        href: articles/Vaccines.html
      - text: "Vector Control: Bednets"
        href: articles/VectorControl_Bednets.html
      - text: "Vector Control: Indoor Residual Spraying"
        href: articles/VectorControl_IRS.html
      - text: "Mosquito Species"
        href: articles/SetSpecies.html
      - text: "Carrying Capacity"
        href: articles/Carrying-capacity.html
      - text: "Matching PfPR2-10 to EIR"
        href: articles/EIRprevmatch.html
      - text: "Metapopulation Modelling"
        href: articles/Metapopulation.html
      - text: "Stochastic Variation"
        href: articles/Variation.html
      - text: "Parameter Variation"
        href: articles/Parameter_variation.html
    functions:
      text: "Functions"
      href: reference/index.html
    icon:
      icon: fa-github
      href: https://github.com/mrc-ide/malariasimulation

reference:
- title: "Run functions"
  contents:
    - run_simulation
    - run_metapop_simulation
    - run_simulation_with_repetitions
    - run_resumable_simulation
- title: "Parameter functions"
  contents:
    - get_parameters
    - get_correlation_parameters
    - set_parameter_draw
    - set_equilibrium
    - set_epi_outputs
- title: "Demography functions"
  contents:
    - set_demography
- title: "Mosquito species functions and parameters"
  contents:
    - set_species
    - set_carrying_capacity
    - calculate_carrying_capacity
    - get_init_carrying_capacity
    - arab_params
    - fun_params
    - gamb_params
    - steph_params
- title: "Intervention functions"
- subtitle: "Drug treatments"
  contents:
    - set_drugs
    - set_clinical_treatment
    - AL_params
    - DHA_PQP_params
    - SP_AQ_params
    - set_antimalarial_resistance
    - get_antimalarial_resistance_parameters
- subtitle: "MDA and chemoprevention"
  contents:
    - set_mda
    - set_pmc
    - set_smc
    - peak_season_offset
- subtitle: "Vaccines"
  contents:
    - set_mass_pev
    - set_pev_epi
    - set_tbv
    - rtss_profile
    - rtss_booster_profile
    - r21_profile
    - r21_booster_profile
- subtitle: "Vector control"
  contents:
    - set_bednets
    - set_spraying
- title: "Non-user functions"
  contents:
    - CorrelationParameters
    - create_pev_profile
    - create_progress_process
    - find_birthrates
    - parameter_draws
    - parameterise_mosquito_equilibrium
    - parameterise_total_M