Mathematical Modeling of Infectious Disease Dynamics

Unified COVID-19 Dataset

R Package for individual based epidemiological models

CRAN Task View: Epidemiology

Create Contact Matrices from Population Data

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

An RShiny App for mapping nCoV2019 line list data

A visit-based contact tracing application built to consume healthcare encounter data.

Incidence Estimation Tools

Slides and Practicals for the BIDD modelling short course

PhyloTrace is a GUI platform for bacterial monitoring offering a toolkit of analyses like hashed cgMLST typing and Antimicrobial Resistance Screening.

A dedicated pipeline designed for the inference of COVID19 transmission networks in a population complete with the prediction of unsampled sources of infection using SARS-CoV-2 genomic sequences. Our pipeline is built upon the BEAST2 and TransPhylo software.

This package provides the data used in the Health Metrics and the Spread of Infectious Diseases with R book

Supplementary R package for the book chapter "Forecasting Based on Surveillance Data"

Tools And ggplot Extensions For Infectious Disease Surveillance And Outbreak Investigation

Project for Data Challenge 2491 Module

The pebble game: A simple game that can be used to understand epidemics and vaccination

Estimating the contribution of each step of the HIV cascade to new infections

🌍 R package for the paper on mapping FOI and predicting control impact

An infectious disease surveillance study on estimating the county-level magnitude of infectiousness (eg. time-varied reproductive number) in Georgia from March to July in 2020 by using designed tranmission-based algorithm and maximum likelihood methods to understand spatiotemporal variation of COVID-19 transmission in Georgia.