Input Files

Each simulation is controlled by one JSON file. The main sections are:

Section	Purpose
`data`	Paths to population, contact, mobility, and risk-ratio files.
`disease_model`	Disease model identity and model parameters.
`travel_model`	Travel model identity and travel parameters.
`initial_infected`	Seed infections by county and age group.
`non_pharma_interventions`	Optional transmission reductions by day, place, and age.
`antiviral_model`	Optional antiviral stockpile strategy.
`vaccine_model`	Optional vaccine stockpile strategy.

Required Data Files

The data directory for a state or region should contain:

INPUT_*.json: simulation properties file.
contact_matrix_*_Mistry2021_all.csv: age-by-age daily contacts.
county_pop_by_age_*.csv: county population by age group.
*_high-risk-ratios-*.csv: age-specific high-risk proportions.
*_mobility-matrix.csv: county-by-county mobility matrix.

The order of age groups must match between the population file, contact matrix, vaccine parameters, antiviral parameters, and any age-specific disease parameters.

Initial Infections

Initial infections are placed into the low-risk unvaccinated exposed compartment for the requested age group.

"initial_infected": [
  {
    "county": "48113",
    "infected": "10",
    "age_group": "2"
  }
]

If more people are requested than are susceptible in that group, the simulator only exposes the available susceptible population.