Skip to content

dsheldon/covid

master
Switch branches/tags
Code

Latest commit

Files

Permalink
Failed to load latest commit information.
Type
Name
Latest commit message
Commit time
 
 
 
 
 
 
 
 
vis
 
 
 
 
 
 
 
 
 
 

Bayesian compartmental models for COVID-19

This repository contains code for Bayesian estimation of compartmental models for COVID-19 using numpyro and jax.

Models

We are experimenting with different Bayesian compartmental models. The basic ingredients are:

This Bayesian SEIRD model is current as of April 27, 2020. Model code here.

Team

The team is based at the College of Information and Computer Sciences and School of Public Health & Health Sciences at UMass. The model contributors are:

Dr. Reich directs the CDC Influenza Forecasting Center of Excellence at UMass.

Installation

Our code depends on recent development versions of numpyro and jax. If you don't have these packages and don't care about tracking their versions, our installation routine will pull and install them as unversioned packages:

git clone https://github.com/dsheldon/covid
cd covid
pip install -e .

Installation Details

If you need to manually install jax and numpyro, here are rough instructions. More details can be found at the project sites.

Install jaxlib (more info here)

pip install --upgrade jaxlib

Install jax (more into here)

git clone https://github.com/google/jax
cd jax
pip install -e .

Install numpyro (more details here)

git clone https://github.com/pyro-ppl/numpyro.git
cd numpyro
pip install -e .[dev]

About

Bayesian modeling of COVID-19

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published