pyrenew-flu-light is an influenza forecasting model (originally written in R, using the package Epidemia, with the name cfaepim) that has been re-instantiated via PyRenew.
NOTE: Presently, this pyrenew-flu-light cannot be installed and used with current NHSN data.
PFL (pyrenew-flu-light) can be used in two modes: "active" and "historical". The "active" mode uses respiratory incidence data sourced from available API frameworks whereas the "historical" mode relies on saved dataset snapshots (currently, these snapshots are from the 2023-24 NHSN data, and were generated by cfaepim code).
Before running PFL, installing poetry and creating a virtual environment will very likely be necessary. This can be first done via pipx install poetry (see Poetry website for more information) and then, to create the environment, poetry install followed by poetry shell in the PFL folder (only done after cloning: git clone https://github.com/CDCgov/pyrenew-flu-light).
After poetry shell has been run, then to use the "historical" mode (once within the folder pyrenew_flu_light), the run.py file creates an experiment. Each experiment generates forecasts based on selected jurisdictions and a configuration file. The configuration files for the "historical" mode are derived from the configuration files used in cfaepim; the reader will most often never need to worry about configuration files in the "historical" mode. To run:
poetry run python run.py --reporting_date 2024-01-20 --regions NY,AL,CA --historical --forecast --exp_name experiment_01
poetry run python run.py --reporting_date 2024-03-30 --regions not:NY,AL,CA --historical --forecast --exp_name experiment_02
- A pull request template
- A website.
- An Apache 2.0 license
- An issue template (taken from PyRenew).
- A
pre-commitschema. - A
.gitignorefile (taken from PyRenew). - Formal contribution language (hybrid, from
cdcent)
Please refer to CDC's Template Repository for more information about open source contributing in CDCGov repositories, public domain notices and disclaimers, and the code of conduct.
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