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RAINIER

RAINIER is a statistical approach for fitting SEIR epidemic models to case and mortality data. We use the approach to create models of COVID-19 transmission in King County, WA.

For detailed information, see the report on King County associated with this code.

In this repository, we demonstrate how the approach can be applied to a synthetically generated, King County-like dataset.

Requirements

We did the analysis using Python 3.6.10. The following Python packages are also required:

  • numpy (1.14.5)
  • scipy (1.1.0)
  • pandas (0.25.0)
  • matplotlib (3.1.0)
  • tqdm (4.26.0)

Recommended Install Instructions

  1. Clone a copy of the repository.

  2. (Optional) Create and activate a virtual environment.

  3. Navigate to the root of the repository and install with:
    python setup.py develop
    

This will install all the required Python package dependencies.

Running RAINIER

  1. From the report_april26 directory, run
  2. > python <Report_Script_Name>.py (e.g. RAINIER.py)

Licenses

See the LICENSE file for more information.

Disclaimer

The code in this repository was developed by IDM to support our research in disease transmission and managing epidemics. We’ve made it publicly available under the Creative Commons Attribution-Noncommercial-ShareAlike 4.0 License to provide others with a better understanding of our research and an opportunity to build upon it for their own work. We make no representations that the code works as intended or that we will provide support, address issues that are found, or accept pull requests. You are welcome to create your own fork and modify the code to suit your own modeling needs as contemplated under the Creative Commons Attribution-Noncommercial-ShareAlike 4.0 License.

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RAINIER applied to COVID-19 data in King County, WA from the Washington Disease Reporting System

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