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pyrenew-flu-light

⚠️ This is a work in progress.

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.

Usage

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

...Contained Within This Repository

  • A pull request template
  • A website.
  • An Apache 2.0 license
  • An issue template (taken from PyRenew).
  • A pre-commit schema.
  • A .gitignore file (taken from PyRenew).
  • Formal contribution language (hybrid, from cdcent)

CDCGov & Disclaimers, Notices, And Code Of Conduct

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.

General Disclaimer

This repository was created for use by CDC programs to collaborate on public health related projects in support of the CDC mission. GitHub is not hosted by the CDC, but is a third party website used by CDC and its partners to share information and collaborate on software. CDC use of GitHub does not imply an endorsement of any one particular service, product, or enterprise.

Public Domain Standard Notice

This repository constitutes a work of the United States Government and is not subject to domestic copyright protection under 17 USC § 105. This repository is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the CC0 1.0 Universal public domain dedication. All contributions to this repository will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest.

License Standard Notice

This repository is licensed under ASL v2 or later.

This source code in this repository is free: you can redistribute it and/or modify it under the terms of the Apache Software License version 2, or (at your option) any later version.

This source code in this repository is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache Software License for more details.

You should have received a copy of the Apache Software License along with this program. If not, see http://www.apache.org/licenses/LICENSE-2.0.html

The source code forked from other open source projects will inherit its license.

Privacy Standard Notice

This repository contains only non-sensitive, publicly available data and information. All material and community participation is covered by the Disclaimer and Code of Conduct. For more information about CDC's privacy policy, please visit http://www.cdc.gov/other/privacy.html.

Contributing Standard Notice

Anyone is encouraged to contribute to the repository by forking and submitting a pull request. (If you are new to GitHub, you might start with a basic tutorial.) By contributing to this project, you grant a world-wide, royalty-free, perpetual, irrevocable, non-exclusive, transferable license to all users under the terms of the Apache Software License v2 or later.

All comments, messages, pull requests, and other submissions received through CDC including this GitHub page may be subject to applicable federal law, including but not limited to the Federal Records Act, and may be archived. Learn more at http://www.cdc.gov/other/privacy.html.

Records Management Standard Notice

This repository is not a source of government records but is a copy to increase collaboration and collaborative potential. All government records will be published through the CDC web site.