Ed Ionides and Aaron King taught a short course on this topic at the 7th Summer Institute for Statistics and Modeling for Infectious Disease at the University of Washington in Seattle this summer. The materials include:
- an introduction to POMP models,
- essential of stochastic simulation with emphasis on the stochastic Euler algorithm,
- a tutorial on the theory and practice of the particle filter,
- an introduction to iterated filtering, and
- four cases studies illustrating pomp methods:
- understanding polio’s persistence, replicating some of the results in a recent PLoS Biology paper,
- revisiting measles dynamics in England and Wales to see what full-information methods reveal,
- a longitudinal study of sexual behavior changes that illustrates how pomp and
mif2can be used to fit models to panel data, drawn from another recent paper, and - a study showing illustrating model diagnostics and forecasting methods in the context of the recent Ebola outbreak in West Africa, again based on a recent paper.
These materials are available via the pomp website.
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This software has been made possible by support from the U.S. National Science Foundation (Grants #EF-0545276, #EF-0430120), by the “Inference for Mechanistic Models” Working Group supported by the National Center for Ecological Analysis and Synthesis (a Center funded by N.S.F. (Grant #DEB-0553768), the University of California, Santa Barbara, and the State of California), and by the RAPIDD program of the Science & Technology Directorate, Department of Homeland Security and the Fogarty International Center, U.S. National Institutes of Health. |