A fast and flexible Bayesian tool for estimation of the time-varying reproduction number.

Local area reproduction numbers and S-gene target failure.

Comparing crowd sourced and model derived forecasts of Covid-19 for Germany and Poland

Joint forecasting of case counts and sequence (or SGTF) data across countries reporting data to GISAID

Code associated with A population-level SEIR model for COVID-19 scenarios (updated) by James P. Gleeson, Thomas Brendan Murphy, Joseph D. O'Brien, and David J. P. O'Sullivan.

epidemia package

Various implementations of the classical SIR model in Julia

Tools to enable flexible and efficient hierarchical nowcasting of epidemiological time-series using a semi-mechanistic Bayesian model with support for a range of reporting and generative processes.

SEIR transmission model of COVID-19. Documentation at:

Public Health Surveillance

Adaptive multiple importance sampling (AMIS) for infectious diseases

Data for MRC/J-IDEA COVID-19 Report 36: Modelling ICU capacity under different epidemiological scenarios of the COVID-19 pandemic in three western European countries.

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

🤝🤧 Systematic review of contact surveys relevant to transmission of respiratory pathogens 🤧🤝

code and data for "Trade-offs between individual and ensemble forecasts of an emerging infectious diseases"

Supplementary code for paper "Bayesian workflow for disease transmission model".

Code and data for the manuscript "Optimal, near-optimal, and robust epidemic control"

Contains the code for reproducing the results and figures from the paper "Model-based Bayesian inference of disease outbreaks with invertible neural networks"

Estimate epidemiological quantities from repeated cross-sectional prevalence measurements

Tools to specify and simulate individual based models, using applied category theory

Video lectures, slides and code for "The Mathematics and Statistics of Infectious Disease Outbreaks" course at Stockholm University

Repo for the course Statistical Methods in Infectious Disease Epidemiology at UZH

This project enables users to generate random and biased testing distributions.

Points of Significance: Modeling infectious epidemics

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

MetaWards disease metapopulation analysis and modelling software. Professional geographical SIR model with a flexible plugin architecture to support complex scenario modelling