IXA-EPI-COVID

This project presents a general transmission model implemented in ixa, the Center for Forecasting and Outbreak Analytics' agent-based modeling framework. Our goal is to develop a model that can appropriately represent all stages of a respiratory disease outbreak, including case importation, a detailed transmission model accounting for time-varying infectiousness and immunity, and the assessment of non-pharmaceutical interventions. This model is a next generation update of ixa-epi-isolation.

Project Admin

Community Mitigation and Economic Impacts team of the CDC Center for Forecasting and Outbreak Analytics. Team lead: Guido Camargo España (CDC/IOD/ORR/CFA)

Getting Started

This repo uses uv for dependency management, be sure that uv is installed on your machine. To run any python script, you will need to initialize the uv environment first:

make uv-sync
```bash

To use this model, you need to have Rust and Cargo installed. You can find instructions for installing Rust [here](https://www.rust-lang.org/tools/install).
To run the main example, use the following command:

```bash
cargo run -- -c input/input.json -o output

To use the importation.geographies tools, you will require a Census Bureau API key, and need to supply it in the CENSUS_API_KEY field of the .env file. You can request and authenticate an API key here.

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.

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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.

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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.