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Outcomes module
Joseph Lemaitre edited this page Jul 30, 2020
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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.
#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: <random distribution> # Branching probability from source
# delay: <random distribution> # Delay from incidence of source to incidence of new_compartement
# duration: <random distribution> # 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: <random distribution>
# delay: <random distribution>
# duration: <random distribution>
# death_tot: # Possibility to combine compartements for death.
# sum: ['death_hosp', 'death_ICU', 'death_incid']
#
# mid_death_rate:
# ...
#
# ## Input Data
#
# * <b>{param_place_file}</b> 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
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