Fitting mechanistic epidemic models to data: A comparison of simple Markov chain Monte Carlo approaches. (July 2018)

• Record Type: Journal Article
• Authors: Li, Michael; Dushoff, Jonathan; Bolker, Benjamin M
• Other Names: Dattner Itai guest-editor.; Huppert Amit guest-editor.
• Is Part Of: Statistical methods in medical research. Volume 27:Number 7(2018)
• Page Start: 1956
• Page End: 1967
• Publication Date: 2018-07
• Subjects: Markov chain Monte Carlo -- Hamiltonian Monte Carlo -- discrete-time susceptible-infectious-removed model -- dispersion -- moment-matching; Medicine -- Research -- Statistical methods -- Periodicals; Research -- Periodicals; Review Literature -- Periodicals; Statistics -- methods -- Periodicals; Médecine -- Recherche -- Méthodes statistiques -- Périodiques; 610.727
• DOI: 10.1177/0962280217747054
• Languages: English
• ISSNs: 0962-2802

Abstract

Simple mechanistic epidemic models are widely used for forecasting and parameter estimation of infectious diseases based on noisy case reporting data. Despite the widespread application of models to emerging infectious diseases, we know little about the comparative performance of standard computational-statistical frameworks in these contexts. Here we build a simple stochastic, discrete-time, discrete-state epidemic model with both process and observation error and use it to characterize the effectiveness of different flavours of Bayesian Markov chain Monte Carlo (MCMC) techniques. We use fits to simulated data, where parameters (and future behaviour) are known, to explore the limitations of different platforms and quantify parameter estimation accuracy, forecasting accuracy, and computational efficiency across combinations of modeling decisions (e.g. discrete vs. continuous latent states, levels of stochasticity) and computational platforms (JAGS, NIMBLE, Stan).