Important Note: Some of these materials have been updated for use with version 2.8. As of version 2, pomp syntax has changed substantially. These changes are documented on the pomp website.
Some of the materials have been superseded entirely. In these cases, links are provided to the updated material.
Prof. Aaron A. King,
Ph.D. Departments of Ecology & Evolutionary Biology and Mathematics
University of Michigan
Preparing for the workshop
- Complete the R tutorial before the beginning of the course.
- 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. Nature, 466: 1102–1104. DOI: 10.1038/nature09319.
- A. A. King, E. L. Ionides, M. Pascual, and M. J. Bouma (2008) Inapparent infections and cholera dynamics. Nature, 454: 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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