config_sample_2pop_outcomes.yml

name: sample_2pop
setup_name: minimal
start_date: 2020-02-01
end_date: 2020-05-31
nslots: 1

subpop_setup:
  geodata: model_input/geodata_sample_2pop.csv
  mobility: model_input/mobility_sample_2pop.csv

initial_conditions:
  method: SetInitialConditions
  initial_conditions_file: model_input/ic_2pop.csv
  allow_missing_subpops: TRUE
  allow_missing_compartments: TRUE

compartments:
  infection_stage: ["S", "E", "I", "R"]

seir:
  integration:
    method: rk4
    dt: 1
  parameters:
    sigma:
      value: 1 / 4
    gamma:
      value: 1 / 5
    Ro:
      value: 2.5
  transitions:
    - source: ["S"]
      destination: ["E"]
      rate: ["Ro * gamma"]
      proportional_to: [["S"],["I"]]
      proportion_exponent: ["1","1"]
    - source: ["E"]
      destination: ["I"]
      rate: ["sigma"]
      proportional_to: ["E"]
      proportion_exponent: ["1"]
    - source: ["I"]
      destination: ["R"]
      rate: ["gamma"]
      proportional_to: ["I"]
      proportion_exponent: ["1"]

outcomes:
  method: delayframe
  outcomes:
    incidHosp: #incidence of hospitalizations
      source:
        incidence:
          infection_stage: "I"
      probability:
        value: 0.05
      delay:
        value: 7
      duration:
        value: 10
        name: currHosp # will track number of current hospitalizations (ie prevalence)
    incidDeath: #incidence of deaths
      source: incidHosp
      probability:
        value: 0.2
      delay:
        value: 14