Outcomes module

The SEIR module computes the infections dynamics on the defined statial setup. The main output of this module is the daily new infection per spatial node.

The Outcomes modules computes any outcomes (such as incident and current hospitalisation, ICU, death) based on the SIER simulation. Indeed, the Outcomes module should be run after an SEIR simulation is performed.

Config

` #outcomes:

method: delayframe # Only fast is supported atm. Makes fast delay_table computations. Later agent-based method ?

paths:

param_from_file: TRUE

param_place_file: <path.csv> # OPTIONAL: File with param per csv. For each param in this file

scenarios: # Outcomes scenarios to run

- low_death_rate

- mid_death_rate

settings: # Setting for each scenario

low_death_rate:

new_comp1: # New compartement name

source: incidence # Source of the new compartement: either an previously defined compartement or "incidence" for diffI of the SEIR

probability: # Branching probability from source

delay: # Delay from incidence of source to incidence of new_compartement

duration: # OPTIONAL ! Duration in new_comp. If provided, the model add to it's output "new_comp1_curr" with current amount in new_comp1

new_comp2: # Example for a second compatiment

source: new_comp1

probability:

delay:

duration:

death_tot: # Possibility to combine compartements for death.

sum: ['death_hosp', 'death_ICU', 'death_incid']

mid_death_rate:

...

## Input Data

* {param_place_file} is a csv with columns place, parameter, value. Parameter is constructed as, e.g for comp1:

probability: Pnew_comp1|source

delay: Dnew_comp1

duration: Lnew_comp1

## Output Data

* {output_path}/model_output/{spatial_setup::setup_name}_[scenario]/[simulation ID].hosp.parquet

`

Equivalent config for outcomes and hospitalization

The outcomes module is meant as a replacement of the hospitalization module. The config below produce the same result between hospitalization and outcomes.

hospitalization:
  paths:
    output_path: hospitalization
    run_age_adjust: TRUE
  parameters:
    time_hosp: [log(7), 0.3]
    time_disch: [log(11.5), log(1.22)]
    time_ICU: [log(3), 0.3]
    time_ICUdur: [log(8), 0.2]
    time_ventdur: [log(7), 0.2]
    time_vent: [log(1), 0.4]
    time_onset_death: [2.84, 0.52]
    p_death: [.0025, .005, .01]
    p_death_names: ["low","med","high"]
    p_hosp_inf: [0.025, 0.05, 0.1]

outcomes:
  method: delayframe        
  param_from_file: True
  param_place_file: COVIDScenarioPipeline/Outcomes/data/usa-geoid-params-output.parquet
  categories: ['10-20', '20-30']
  scenarios:
    - low
    - med
    - high
  #  - high_death_rate
  settings:
    high_death_rate:
      hospitalization:
        source: incidI
        probability:
          value:
            distribution: uniform
            low: .1
            high: .1
        delay:
          value:
            distribution: fixed
            value: 7
        duration:
          value:
            distribution: fixed
            value: 7
          name: hosp_curr
      deaths:
        source: hospitalization
        probability:
          value:
            distribution: fixed
            value: .01
        delay:
          value:
            distribution: fixed
            value: 7
    low:
      incidH:
        source: incidI
        probability:
          value:
            distribution: uniform
            low: .1
            high: .3
        delay:
          value:
            distribution: fixed
            value: 7
        duration:
          value:
            distribution: fixed
            value: 12
          name: hosp_curr
      incidICU:
        source: incidH
        probability:
          value:
            distribution: fixed
            value: 0.354506482   # Average of file
        delay:
          value:
            distribution: fixed
            value: 3
        duration:
          value:
            distribution: fixed
            value: 8
          name: icu_curr
      incidVent:
        source: incidICU
        probability:
          value:
            distribution: fixed
            value: 0.43866538
        delay:
          value:
            distribution: fixed
            value: 1
        duration:
          value:
            distribution: fixed
            value: 7
          name: vent_curr
      incidD:
        source: incidI
        probability:
          value:
            distribution: fixed
            value: 0.0025
        delay:
          value:
            distribution: fixed
            value: 20
    med:
      incidH:
        source: incidI
        probability:
          value:
            distribution: uniform
            low: .1
            high: .3
        delay:
          value:
            distribution: fixed
            value: 7
        duration:
          value:
            distribution: fixed
            value: 12
          name: hosp_curr
      incidICU:
        source: incidH
        probability:
          value:
            distribution: fixed
            value: 0.354506482   # Average of file
        delay:
          value:
            distribution: fixed
            value: 3
        duration:
          value:
            distribution: fixed
            value: 8
          name: icu_curr
      incidVent:
        source: incidICU
        probability:
          value:
            distribution: fixed
            value: 0.43866538
        delay:
          value:
            distribution: fixed
            value: 1
        duration:
          value:
            distribution: fixed
            value: 7
          name: vent_curr
      incidD:
        source: incidI
        probability:
          value:
            distribution: fixed
            value: 0.005
        delay:
          value:
            distribution: fixed
            value: 20
    high:
      incidH:
        source: incidI
        probability:
          value:
            distribution: uniform
            low: .1
            high: .3
        delay:
          value:
            distribution: fixed
            value: 7
        duration:
          value:
            distribution: fixed
            value: 12
          name: hosp_curr
      incidICU:
        source: incidH
        probability:
          value:
            distribution: fixed
            value: 0.354506482   # Average of file
        delay:
          value:
            distribution: fixed
            value: 3
        duration:
          value:
            distribution: fixed
            value: 8
          name: icu_curr
      incidVent:
        source: incidICU
        probability:
          value:
            distribution: fixed
            value: 0.43866538
        delay:
          value:
            distribution: fixed
            value: 1
        duration:
          value:
            distribution: fixed
            value: 7
          name: vent_curr
      incidD:
        source: incidI
        probability:
          value:
            distribution: fixed
            value: 0.01
        delay:
          value:
            distribution: fixed
            value: 20
      incidC:
        source: incidI
        probability:
          value:
            distribution: fixed
            value: 0.01
        delay:
          value:
            distribution: fixed
            value: 20