Comparison of Filtering Methods for the Modeling and Retrospective Forecasting of Influenza Epidemics
Comparison of Filtering Methods for the Modeling and Retrospective Forecasting of Influenza Epidemics Wan Yang1*, Alicia Karspeck2, Jeffrey Shaman1 1 Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, New York, United States of America, 2 Climate and Global Dynamics Division, National Center for Atmospheric Research, Boulder, Colorado, United States of America Abstract A variety of filtering methods enable the recursive estimation of system state variables and inference of model parameters. These methods have found application in a range of disciplines and settings, including engineering design and forecasting, and, over the last two decades, have been applied to infectious disease epidemiology. For any system of interest, the ideal filter depends on the nonlinearity and complexity of the model to which it is applied, the quality and abundance of observations being entrained, and the ultimate application (e.g. forecast, parameter estimation, etc.). Here, we compare the performance of six state-of-the-art filter methods when used to model and forecast influenza activity. Three particle filters— a basic particle filter (PF) with resampling and regularization, maximum likelihood estimation via iterated filtering (MIF), and particle Markov chain Monte Carlo (pMCMC)—and three ensemble filters—the ensemble Kalman filter (EnKF), the ensemble adjustment Kalman filter (EAKF), and the rank histogram filter (RHF)—were used in conjunction with a humidity-forced susceptible-infectious-recovered-susceptible (SIRS) model and weekly estimates of influenza incidence. The modeling frameworks, first validated with synthetic influenza epidemic data, were then applied to fit and retrospectively forecast the historical incidence time series of seven influenza epidemics during 2003–2012, for 115 cities in the United States.
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