MOSAIC-pkg/_pkgdown.yml at main · InstituteforDiseaseModeling/MOSAIC-pkg · GitHub

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url: https://institutefordiseasemodeling.github.io/MOSAIC-pkg/
template:
  bootstrap: 5
  bootswatch: flatly
  bslib:
    primary: "#0054A6"
    link-color: "#0054A6"

navbar:
  structure:
    left:  [intro, reference, articles, news]
    right: [search, github]
  components:
    articles:
      text: Articles
      menu:
      - text: Installation
        href: articles/Installation.html
      - text: Running LASER
        href: articles/Running-LASER.html
      - text: Running MOSAIC
        href: articles/Running-MOSAIC.html
      - text: Deployment
        href: articles/Deployment.html

articles:
- title: "Getting Started"
  desc: "Installation and basic usage"
  contents:
  - Installation
  - Running-LASER
  - Running-MOSAIC
  - Deployment

reference:
  - title: "Core Workflow"
    desc: Main functions for running MOSAIC simulations
    contents:
    - run_LASER
    - run_MOSAIC
    - make_LASER_config
    - sample_parameters
    - check_dependencies
    - install_dependencies
    - set_root_directory
    - get_paths

  - title: "Configuration & Control"
    desc: Functions for configuring MOSAIC execution settings
    contents:
    - mosaic_control_defaults
    - mosaic_io_presets

  - title: "Model Execution"
    desc: Functions starting with run_, make_, or create_
    contents:
    - matches("^run_")
    - matches("^make_")
    - matches("^create_")

  - title: "Parameter Estimation"
    desc: Estimation and fitting functions
    contents:
    - matches("^est_")
    - matches("^fit_")
    - matches("^sample_")

  - title: "Calculations"
    desc: Calculation functions
    contents:
    - matches("^calc_")

  - title: "Data Processing"
    desc: Processing and downloading data
    contents:
    - matches("^process_")
    - matches("^download_")
    - matches("^combine_")

  - title: "Visualization"
    desc: Plotting functions
    contents:
    - matches("^plot_")

  - title: "Utility Functions"
    desc: Helper and utility functions
    contents:
    - matches("^get_")
    - matches("^check_")
    - matches("^convert_")
    - matches("^read_")
    - matches("^write_")
    - matches("^use_")
    - matches("^attach_")
    - matches("^detach_")
    - matches("^lock_")
    - matches("logit")
    - log_msg

  - title: "Distribution Functions"
    desc: Gompertz distribution functions
    contents:
    - dgompertz
    - pgompertz
    - qgompertz
    - rgompertz

  - title: "Package Data"
    desc: Built-in datasets
    contents:
    - matches("^config_")
    - priors_default
    - estimated_parameters
    - epidemic_peaks
    - matches("^iso_codes")

  - title: "Internal & Other Functions"
    desc: Other exported functions and internal helpers
    contents:
    - lacks_concepts("internal")

authors:
  John R Giles:
    href: https://github.com/gilesjohnr
  Christopher W Lorton:
    href: https://github.com/ChristopherWLorton
  Tony Ting: {}
  Dejan Lukacevic: {}
  Meikang Wu: {}