Parameterizing Spatial Models of Infectious Disease Transmission that Incorporate Infection Time Uncertainty Using Sampling-Based Likelihood Approximations

• Published in: PloS one 2016-01, Vol.11 (1), p.e0146253-e0146253
• Main Authors: Malik, Rajat, Deardon, Rob, Kwong, Grace P S
• Format: Article
• Language: English
• Subjects: Algorithms; Approximation; Bayesian analysis; Care and treatment; Communicable diseases; Communicable Diseases - transmission; Computer Simulation; Data augmentation; Datasets; Disease spread; Disease transmission; Epidemics; Foot & mouth disease; Health risks; Humans; Immunization; Infections; Infectious diseases; Influenza; Markov analysis; Markov chains; Mathematical models; Mathematics; Models, Theoretical; Monte Carlo Method; Monte Carlo methods; Pressure; Probability; Random sampling; Risk factors; Sampling; Sampling methods; Time Factors; Uncertainty
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0146253

A class of discrete-time models of infectious disease spread, referred to as individual-level models (ILMs), are typically fitted in a Bayesian Markov chain Monte Carlo (MCMC) framework. These models quantify probabilistic outcomes regarding the risk of infection of susceptible individuals due to various susceptibility and transmissibility factors, including their spatial distance from infectious individuals. The infectious pressure from infected individuals exerted on susceptible individuals is intrinsic to these ILMs. Unfortunately, quantifying this infectious pressure for data sets containing many individuals can be computationally burdensome, leading to a time-consuming likelihood calculation and, thus, computationally prohibitive MCMC-based analysis. This problem worsens when using data augmentation to allow for uncertainty in infection times. In this paper, we develop sampling methods that can be used to calculate a fast, approximate likelihood when fitting such disease models. A simple random sampling approach is initially considered followed by various spatially-stratified schemes. We test and compare the performance of our methods with both simulated data and data from the 2001 foot-and-mouth disease (FMD) epidemic in the U.K. Our results indicate that substantial computation savings can be obtained--albeit, of course, with some information loss--suggesting that such techniques may be of use in the analysis of very large epidemic data sets.