Using python 3.9.18 on windows
python -m venv venv
.venv/Scripts/activate
pip install -r requirements.txt
running monkeypox_optuna.py will calibrate
usage: python monkeypox_optuna.py [-h] [--vaccine_file VACCINE_FILE]
--cases_file CASES_FILE
[--population POPULATION]
[--ntrials NTRIALS]
optional arguments:
-h, --help show this help message and exit
--vaccine_file VACCINE_FILE
File with vaccine dose and date pairs. Should be CSV
with columns: date,vx_doses
--cases_file CASES_FILE
File with daily case counts over time. Should be CSV
with columns: diagnosis_date,count Simulation and
calibration will occur only for the dates in this file
--population POPULATION
Susceptible population
--ntrials NTRIALS Number of trials to calibrate
usage: python scenario_monkeypox.py [-h] [--vaccine_file VACCINE_FILE]
[--vaccine_effectiveness VACCINE_EFFECTIVENESS]
[--social_distance_start_date SOCIAL_DISTANCE_START_DATE]
[--social_distance_effect SOCIAL_DISTANCE_EFFECT]
[--incubation_period INCUBATION_PERIOD]
[--infectious_period INFECTIOUS_PERIOD]
[--r0 R0] [--population POPULATION]
[--initial_exposed INITIAL_EXPOSED]
[--date_start DATE_START]
[--date_end DATE_END]
optional arguments:
-h, --help show this help message and exit
--vaccine_file VACCINE_FILE
File with vaccine dose and date pairs. Should be CSV
with columns: date,vx_doses
--vaccine_effectiveness VACCINE_EFFECTIVENESS
effectiveness of a single vaccine does [0,1]
--social_distance_start_date SOCIAL_DISTANCE_START_DATE
Start date at which attack rate starts to slow.
Format: YYYY-MM-DD
--social_distance_effect SOCIAL_DISTANCE_EFFECT
Multiplier to attack rate due to social distancing
--incubation_period INCUBATION_PERIOD
Duration of incubation period in days.
--infectious_period INFECTIOUS_PERIOD
Duration of infectious period.
--r0 R0
--population POPULATION
Susceptible population
--initial_exposed INITIAL_EXPOSED
Number exposed at t=0
--date_start DATE_START
Start date of simulation. Format YYYY-MM-DD
--date_end DATE_END End date of simulation. Format YYYY-MM-DD