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As for Chapter 11, we use material from the short course Simulation-Based Inference for Epidemiological Dynamics (SBIED). We develop a concrete example of the general POMP modeling framework, and we see the theory and practice of implementing a simulator for the model.

The Susceptible-Infected-Recovered (SIR) model used for this chapter is a central concept for epidemiology. For the purposes of STATS/DATASCI 531, we view it as one example of a mechanistic model, which exemplifies a more general process of model development and data analysis. One epidemiological idea used without definition in the lecture is R0, defined to be the expected number of secondary infections arising from one infected individual in a fully susceptible population. The SIR model supposes that previously infected individuals cannot become reinfected, so those in compartment R are protected from infection.

The SIR model in epidemiology is closely related to predator-prey models in ecology. Similar models can be used to describe spread of ideas (including rumors or mis-information) on social networks.

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Annotated slides pdf
Notes pdf
R script R
Worked solutions to the Exercises html
Recording, Chapter 12, Part 1 Compartment models (17 mins)
Recording, Chapter 12, Part 2 Euler’s method for simulating Markov processes (24 mins)
Recording, Chapter 12, Part 3 Compartment models in the pomp package (47 mins)
Recording, Chapter 12, Part 4 Discussion of exercises (10 mins)


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