athogen.jl: Infectious Disease Transmission Network Modeling with Julia
Dublin Core
Title
athogen.jl: Infectious Disease Transmission Network Modeling with Julia
Subject
epidemic, individual level models, transmission networks, Bayesian, Julia.
Description
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).
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).
Creator
Justin Angevaare
Source
https://www.jstatsoft.org/article/view/v104i04
Publisher
University of Guelph
Date
September 2022
Contributor
Fajar bagus W
Format
PDF
Language
English
Type
Text
Files
Collection
Citation
Justin Angevaare, “athogen.jl: Infectious Disease Transmission Network Modeling with Julia,” Repository Horizon University Indonesia, accessed April 5, 2025, https://repository.horizon.ac.id/items/show/8274.