Pathogen.jl: Infectious Disease Transmission Network Modelling with Julia
Abstract
We introduce Pathogen.jl for simulation and inference of transmission network individual level models (TN-ILMs) of infectious disease spread in continuous time. TN-ILMs can be used to jointly infer transmission networks, event times, and model parameters within a Bayesian framework via Markov chain Monte Carlo (MCMC). We detail our specific strategies for conducting MCMC for TN-ILMs, and our implementation of these strategies in the Julia package, Pathogen.jl, which leverages key features of the Julia language. We provide an example using Pathogen.jl to simulate an epidemic following a susceptible-infectious-removed (SIR) TN-ILM, and then perform inference using observations that were generated from that epidemic. We also demonstrate the functionality of Pathogen.jl with an application of TN-ILMs to data from a measles outbreak that occurred in Hagelloch, Germany in 1861(Pfeilsticker 1863; Oesterle 1992).
Cite
@article{arxiv.2002.05850,
title = {Pathogen.jl: Infectious Disease Transmission Network Modelling with Julia},
author = {Justin Angevaare and Zeny Feng and Rob Deardon},
journal= {arXiv preprint arXiv:2002.05850},
year = {2021}
}