Simulation-based inference methods for partially observed Markov model via the R package is2

Abstract

Partially observed Markov process (POMP) models are powerful tools for time series modeling and analysis. Inherited the flexible framework of R package pomp, the is2 package extends some useful Monte Carlo statistical methodologies to improve on convergence rates. A variety of efficient statistical methods for POMP models have been developed including fixed lag smoothing, second-order iterated smoothing, momentum iterated filtering, average iterated filtering, accelerate iterated filtering and particle iterated filtering. In this paper, we show the utility of these methodologies based on two toy problems. We also demonstrate the potential of some methods in a more complex model, employing a nonlinear epidemiological model with a discrete population, seasonality, and extra-demographic stochasticity. We discuss the extension beyond POMP models and the development of additional methods within the framework provided by is2.

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