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https://github.com/cdcgov/pyrenew-flu-light
An Epidemia influenza forecasting model re-instantiated in PyRenew.
https://github.com/cdcgov/pyrenew-flu-light
forecasting-model infectious-disease-modeling inference modeling statistics
Last synced: 15 days ago
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An Epidemia influenza forecasting model re-instantiated in PyRenew.
- Host: GitHub
- URL: https://github.com/cdcgov/pyrenew-flu-light
- Owner: CDCgov
- License: apache-2.0
- Created: 2024-08-20T14:17:26.000Z (5 months ago)
- Default Branch: main
- Last Pushed: 2024-12-09T15:38:34.000Z (about 1 month ago)
- Last Synced: 2024-12-09T16:42:05.840Z (about 1 month ago)
- Topics: forecasting-model, infectious-disease-modeling, inference, modeling, statistics
- Language: Python
- Homepage:
- Size: 13.4 MB
- Stars: 1
- Watchers: 11
- Forks: 0
- Open Issues: 10
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Codeowners: .github/CODEOWNERS
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README
# 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](https://imperialcollegelondon.github.io/epidemia/), with the name `cfaepim`) that has been re-instantiated via [PyRenew](https://github.com/CDCgov/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](https://python-poetry.org/docs/) 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.
- [x] An Apache 2.0 license
- [x] An issue template (taken from PyRenew).
- [x] A `pre-commit` schema.
- [x] A `.gitignore` file (taken from PyRenew).
- [x] Formal contribution language (hybrid, from `cdcent`)
## CDCGov & Disclaimers, Notices, And Code Of Conduct
Please refer to [CDC's Template Repository](https://github.com/CDCgov/template) for more information about open source contributing in CDCGov repositories, [public domain notices and disclaimers](https://github.com/CDCgov/template/blob/master/DISCLAIMER.md), and the [code of conduct](https://github.com/CDCgov/template/blob/master/code-of-conduct.md).
## General Disclaimer
This repository was created for use by CDC programs to collaborate on public health related projects in support of the [CDC mission](https://www.cdc.gov/about/organization/mission.htm). 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](https://creativecommons.org/publicdomain/zero/1.0/). 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](https://github.com/CDCgov/template/blob/master/DISCLAIMER.md)
and [Code of Conduct](https://github.com/CDCgov/template/blob/master/code-of-conduct.md). For more information about CDC's privacy policy, please visit [http://www.cdc.gov/other/privacy.html](https://www.cdc.gov/other/privacy.html).
## Contributing Standard Notice
Anyone is encouraged to contribute to the repository by [forking](https://help.github.com/articles/fork-a-repo) and submitting a pull request. (If you are new to GitHub, you might start with a [basic tutorial](https://help.github.com/articles/set-up-git).) 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](http://www.apache.org/licenses/LICENSE-2.0.html) 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](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](http://www.cdc.gov).