Model-based Inference


Prof. Aaron A. King, Ph.D.
Departments of Ecology & Evolutionary Biology and Mathematics
University of Michigan

Preparing for the workshop

  1. Complete the R tutorial before the beginning of the course.
  2. If you wish to use your own computer, install R and RStudio on it before the first day of the course. Instructions for doing so are here.


The following papers serve as background for some of the central issues:

  • S. N. Wood (2010) Statistical inference for noisy nonlinear ecological dynamic systems. Nature466: 1102–1104. DOI: 10.1038/nature09319.
  • A. A. King, E. L. Ionides, M. Pascual, and M. J. Bouma (2008) Inapparent infections and cholera dynamics. Nature454: 877–880. DOI: 10.1038/nature07084
  • S. Shrestha, A. A. King, and P. Rohani (2011) Statistical Inference for Multi-Pathogen Systems. PLoS Comput. Biol.7: e1002135. DOI: 10.1371/journal.pcbi.1002135

A good reference for modeling in infectious disease epidemiology is:

  • Keeling, M. & Rohani, P. Modeling infectious diseases in humans and animals. Princeton University Press, 2008.

The pomp package is described and illustrated in

  • A. A. King, D. Nguyen, and E. L. Ionides (2016) Statistical Inference for Partially Observed Markov Processes via the R Package pomp. J. Stat. Soft.69: 1–43. DOI: 10.18637/jss.v069.i12




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