The PyRenew-HEW project aims to create short-term forecasts of respiratory disease burden using the PyRenew library and several data sources:
- Hospital Admissions from the National Healthcare Safety Network
- Emergency Department Visits from the National Syndromic Surveillance Program
- Wastewater virus concentration from the National Wastewater Surveillance System
This is a work in progress, and not all data sources are currently integrated into the model.
This repository contains code for the PyRenew-HEW model itself, as well as pipelines for running the model in production, and utilities for working with model outputs.
The project uses GitHub Actions for automatically building container images based on the project's Containerfile and Containerfile.dependencies files. The images are currently hosted on Azure Container Registry and are built and pushed via the containers.yaml GitHub Actions workflow.
Images can also be built locally. The Makefile contains several targets for building and pushing images. Although the Makefile uses Docker as the default engine, the ENGINE environment variable can be set to podman to use Podman instead, for example:
ENGINE=podman make dep_container_build
# Equivalent to:
# podman build . -t pyrenew-hew-dependencies -f Containerfile.dependenciesContainer images pushed to the Azure Container Registry are automatically tagged as either latest (if the commit is on the main branch) or with the branch name (if the commit is on a different branch). After a branch is deleted, the image tag is remove from the registry via the delete-container-tag.yaml GitHub Actions workflow.
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.
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.
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.
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.
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.
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.