We continue using material from the short course Simulation-Based Inference for Epidemiological Dynamics (SBIED). Chapter 15 is Lesson 6 of SBIED. This case study of polio demonstrates time series data analysis via a mechanistic model. It also develops various topics of general interest for inference on POMP models:

Sections VI and VII follow the same route we took for the Consett measles analysis. This workflow is common to many POMP models across diverse applications.


Chapter 15, Sections I Covariates in POMP models and their pomp implementation Lecture video (5 mins)
Chapter 15, Section II A POMP model for historic polio in Wisconsin Lecture video (15 mins)
Chapter 15, Section III A pomp implementation of the polio POMP model Lecture video (9 mins)
Chapter 15, Sections IV Data analysis logistics: tools for a pomp workflow Lecture video (12 mins)
Chapter 15, Section V Persistence of polio Lecture video (7 mins)
Chapter 15, Section VI Likelihood maximization for polio Lecture video (15 mins)
Chapter 15, Section VII A profile likelihood for polio Lecture video (7 mins)
Slides pdf
Notes pdf
R script R
Worked solution to Exercise 6.1 HTML
Worked solution to Exercise 6.2 HTML
Worked solution to Exercise 6.3 HTML
Worked solution to Exercise 6.4 HTML
Worked solution to Exercise 6.5 HTML


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