computational-epidemiology

epydemix, the ABC of epidemics

The companion repository to Computational Modeling of Infectious Disease by Chris von Csefalvay

EpiSimulator: A Data-Driven Stochastic Hybrid Model for COVID-19 in Italy.

CE-ABC is a code to simulate the epidemic outbreaks with mechanistic models through a cross-entropy approximate Bayesian framework.

Code for the paper: The importance of non-pharmaceutical interventions during the COVID-19 vaccine rollout

A tool to estimate Instantaneous Reproduction Number

Estimates of COVID-19 R_t in Real-Time.

Python implementation of behavioral-epidemic models for COVID-19

Special repository containing the profile directory of JuliaEpi.

epidWaves is a Matlab/Python package to fit multi-wave statistical models to the complex epidemic data.

Special repository hosting the InPhyT website.

Code, text, figures, etc. for reproducing my dissertation proposal, "Impact of Host and Vaccine Characteristics on Immune Responses following Influenza Vaccination".

An Analysis of Lassa Fever Outbreaks in Nigeria using Machine Learning Models and Shapley Values

Spatial MultiAgent RL for Epidemic Control with Heterogeneous Risk Preferences

Agent-based simulation of epidemic spread in R — stochastic disease-state agents interacting over a social network, with support for policy interventions like stay-at-home orders.

An Agent-Based Model used to Simulate Rodent Control Strategies for the Control of Periodic Outbreaks of Lassa Fever in Nigeria

Code for the paper: Modeling the interplay between disease spread, behaviors, and disease perception with a data-driven approach

Epidemic intelligence platform — compartmental disease models (SIR · SEIR · SEIRD · SEIRDV), live surveillance, and CDC-standard (WIS) validated forecasting, with per-figure uncertainty labelling.

Independent reproduction of a study on how much detail epidemic models need from mobile phone mobility data, extended to test whether administrative borders match how people actually move.

Code and data associated with Billings et al., "High dose inactivated influenza vaccine inconsistently improves heterologous antibody responses in an elderly human cohort", JID 2025.