jcblemai

emcee

The Python ensemble sampling toolkit for affine-invariant MCMC

dynamax

State Space Models library in JAX

PyPaperBot

PyPaperBot is a Python tool for downloading scientific papers using Google Scholar, Crossref, and SciHub.

EpiNow2

Estimate Realtime Case Counts and Time-varying Epidemiological Parameters

COVIDScenarioPipeline

Public shared code for doing scenario forecasting and creating reports for various governmental entities.

delphi-epidata

An open API for epidemiological data.

jayrobwilliams.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

MicroCanonicalHMC

MCHMC: sampler from an arbitrary differentiable distribution

Interpretability

Resources for Machine Learning Explainability

collaboratory-epiparameter-community

COVID19NPISecondWave

WNV-forecast-project-2023

Data and forecast submission repository for the 2023 CDC West Nile virus Forecasting Challenge

OpenCOVID

Source code for OpenCOVID, an individual-based model of SARS-CoV-2 transmission and COVID-19 disease dynamics.

flu-forecast-hub

Influenza forecasting hub

flepiMoP

The Flexible Epidemic Modeling Pipeline

interval-scoring

This repository contains python implementations of scoring rules for forecasts provided in a prediction interval format.

influpaint

Influpaint : Inpainting denoising diffusion probabilistic models for infectious disease (such as influenza) forecasting

functionalbayes

A Functional Programming Approach to Composable Bayesian Workflow

EpiForecastStatMech

Exploring methods for merging mechanistic and models to forecast epidemics.

HETTMO

cholera_seasonality_ssa

presentations

norovirus-nowcast

Code repository for norovirus nowcasting paper winter 2023/24

EpiInvert

flusight_hub_archive

Hubversion of FluSight 1 (2015-2019)

epidemicity-paper

Evaluate the reproduction number and epidemicity index for the SEPIAR model.

flepimop_sample

grande-saline-cholera-serosurvey

Public Repository for Reanalysis of Cholera Serosurvey from Grand Saline Haiti

infectious_disease_predictability

Code and data for On the Predictability of Infectious Disease Outbreaks by SV Scarpino & G Petri

.github