https://github.com/cdcgov/pyrenew
Python package for multi-signal Bayesian renewal modeling with JAX and NumPyro.
https://github.com/cdcgov/pyrenew
epidemiology infectious-disease-models package renewal-process
Last synced: about 1 month ago
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Python package for multi-signal Bayesian renewal modeling with JAX and NumPyro.
- Host: GitHub
- URL: https://github.com/cdcgov/pyrenew
- Owner: CDCgov
- License: apache-2.0
- Created: 2024-02-15T13:55:19.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-04-14T20:02:14.000Z (about 2 months ago)
- Last Synced: 2025-04-14T20:22:48.941Z (about 2 months ago)
- Topics: epidemiology, infectious-disease-models, package, renewal-process
- Language: Python
- Homepage: https://cdcgov.github.io/PyRenew/
- Size: 10.3 MB
- Stars: 16
- Watchers: 14
- Forks: 5
- Open Issues: 52
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Codeowners: .github/CODEOWNERS
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README
# PyRenew: A Package for Bayesian Renewal Modeling with JAX and NumPyro.
⚠️ This is a work in progress ⚠️
`pyrenew` is a flexible tool for simulation and statistical inference of epidemiological models, emphasizing renewal models. Built on top of the [numpyro](https://num.pyro.ai/) Python library, `pyrenew` provides core components for model building, including pre-defined models for processing various types of observational processes. To start, visit the tutorials section on the project's website [here](https://cdcgov.github.io/PyRenew/tutorials/index.html).
The following diagram illustrates the composition of the `HospitalAdmissionsModel` class. Notably, all components are modular and can be replaced with custom implementations.
```mermaid
flowchart LR
%% Elements
rt_proc["Random Walk Rt\nProcess (latent)"];
latent_inf["Latent Infections"]
latent_ihr["Infection to Hosp.\nrate (latent)"]
neg_binom["Observation process\n(hospitalizations)"]
latent_hosp["Latent Hospitalizations"];
i0["Initial infections\n(latent)"];
gen_int["Generation\ninterval (fixed)"];
hosp_int["Hospitalization\ninterval (fixed)"];
%% Models
basic_model(("Infections\nModel"));
admin_model(("Hospital Admissions\nModel"));
%% Latent infections
rt_proc --> latent_inf;
i0 --> latent_inf;
gen_int --> latent_inf;
latent_inf --> basic_model
%% Hospitalizations
hosp_int --> latent_hosp
neg_binom --> admin_model;
latent_ihr --> latent_hosp;
basic_model --> admin_model;
latent_hosp --> admin_model;
```
## Installation
Install via pip with
```bash
pip install git+https://github.com/CDCgov/PyRenew@main
```
## Models Implemented With PyRenew
- [CDCgov/pyrenew-covid-wastewater](https://github.com/CDCgov/pyrenew-covid-wastewater): _Models and infrastructure for forecasting COVID-19 hospitalizations using wastewater data with PyRenew._
- [CDCgov/pyrenew-flu-light](https://github.com/CDCgov/pyrenew-flu-light/): _An instantiation in PyRenew of an influenza forecasting model used in the 2023-24 respiratory season._
## Resources
* [The MSR Website](https://cdcgov.github.io/PyRenew/tutorials/index.html) provides general documentation and tutorials on using MSR.
* [The Model Equations Sheet](https://github.com/CDCgov/PyRenew/blob/main/equations.md) describe the mathematics of the renewal processes and models MSR supports.
* Additional reading on renewal processes in epidemiology
* [_Semi-mechanistic Bayesian modelling of COVID-19 with renewal processes_](https://academic.oup.com/jrsssa/article-pdf/186/4/601/54770289/qnad030.pdf)
* [_Unifying incidence and prevalence under a time-varying general branching process_](https://link.springer.com/content/pdf/10.1007/s00285-023-01958-w.pdf)
## 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
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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
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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).
## Additional Standard Notices
Please refer to [CDC's Template Repository](https://github.com/CDCgov/template)
for more information about [contributing to this repository](https://github.com/CDCgov/template/blob/master/CONTRIBUTING.md),
[public domain notices and disclaimers](https://github.com/CDCgov/template/blob/master/DISCLAIMER.md),
and [code of conduct](https://github.com/CDCgov/template/blob/master/code-of-conduct.md).