Adds script scripts/20210615_partition_model.py that implements a minimum viable partitioning model.
Basic argparse CLI that takes paths to
Configuration YAML file
Travel CSV file
Contacts CSV file
Usage
$ PYTHONPATH='.' poetry run python scripts/20210615_partition_model.py --help
usage: 20210615_partition_model.py [-h] [-v] [--config-fp CONFIG_FP] [--travel-fp TRAVEL_FP] [--contacts-fp CONTACTS_FP] [--census-counts-csv CENSUS_COUNTS_CSV]
[--beta BETA] [--initial-ia INITIAL_IA] [--start-date START_DATE] [--end-date END_DATE]
optional arguments:
-h, --help show this help message and exit
-v, --verbose
--config-fp CONFIG_FP
path to YAML configuration file
--travel-fp TRAVEL_FP
path to travel.csv file
--contacts-fp CONTACTS_FP
path to contacts.csv file
--census-counts-csv CENSUS_COUNTS_CSV
path to file containing populations of ZCTAs
--beta BETA global transmission parameter
--initial-ia INITIAL_IA
initial size of the Ia compartment (low risk only)
--start-date START_DATE
starting date for the simulation, in string format of pandas.date_range
--end-date END_DATE end date for the simulation, in string format of pandas.date_range
scripts/20210615_partition_model.py
that implements a minimum viable partitioning model.Usage