Mathematical Modeling of Infectious Disease Dynamics

Unified COVID-19 Dataset

R Package for Analyzing John Snow's 1854 Cholera Map

Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in https://doi.org/10.18637/jss.v104.i03.

Public Available Code and Data to Reproduce Analyses in "Air pollution and COVID-19 mortality in the United States: Strengths and limitations of an ecological regression analysis."

Bayesian spatial analysis

A modular Bayesian framework for real-time infectious disease surveillance. Provides tools for nowcasting, reproduction number estimation, delay estimation, and forecasting from data subject to reporting delays, right-truncation, missing data, and incomplete ascertainment

An R package with over 50 highly cited, read-to-use, up-to-date COVID-19 pandemic data resources

Report templates and helper functions for applied epidemiology

COVID-19 Pandemic Data R Package

A framework for data-driven stochastic disease spread simulations

R package with classes and helper functions for working with epidemiological parameters and access to a library of epidemiological parameters for infectious diseases

Source code for the EpiEstim app.

R Package for individual based epidemiological models

R package for epigraphdb

Analysis and visualization of Taiwan’s COVID-19 data

Network Models of HIV Transmission Dynamics among MSM and Heterosexuals

R interface to the CDC National Public Health Tracking Network API

CRAN Task View: Epidemiology

Estimates the Force-of-Infection of a given pathogen from population based sero-prevalence studies