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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

To use this model, you need to have Rust and Cargo installed. You can find instructions for installing Rust here. To run the main example, use the following command:

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

Synthetic Population

The model requires a synthetic population CSV. A small test file is included at input/people_test.csv. To generate larger populations, first install R dependencies and set up a Census Bureau API key in .env as CENSUS_API_KEY:

make setup-r
make synthetic-population             # default: WY, 1000 people
make synthetic-population STATE=NY N=50000  # custom state and size

Make Targets

Target Description
make run Run the model with default config
make run-1m Generate a 1M WY population and run the model with it
make run-10m Generate a 10M WY population and run the model with it
make synthetic-population Generate a synthetic population (configurable via STATE and N)
make profile Profile the model with samply (configurable, see below)
make setup-r Install required R packages

You can also override the population file directly via CLI with --synth-population:

cargo run --release -- -c input/input.json -o output --synth-population path/to/population.csv

Profiling

make profile runs the model under samply, which opens the Firefox Profiler with a call tree and flame graph. Press Ctrl+C to stop early — samply will still capture the profile. You can also Ctrl+C any make run-* target to kill the simulation early.

make profile                                          # 1M population, no ixa spans
make profile PROFILE_SIZE=10m                         # 10M population
make profile PROFILE_FEATURES=profiling               # with ixa span instrumentation
make profile PROFILE_SIZE=10m PROFILE_FEATURES=profiling  # both

The profiling Cargo feature enables ixa's built-in span timing (open_span/Span::drop). This adds ~25% overhead, so it's off by default for samply runs. The run, run-1m, and run-10m targets enable it for ixa's own profiling output.

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.