kingaa / clim-dis

Materials for ICTP Workshop on Mathematical Models of Climate Variability, Environmental Change and Infectious Diseases

ICTP Climate and Disease Workshop

Course Notes

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These are notes for workshop activities led by Aaron King as part of the ICTP Workshop on Mathematical Models of Climate Variability, Environmental Change and Infectious Diseases. They draw in large part on the notes from a SISMID course and from a course taught as part of the ICTP Spring College.

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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.

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Readings

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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Links

• Course notes
• R Tutorial
• pomp homepage

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