**Location:** Online**Date:** January-March, 2022**Instructors:** John M. Drake (jdrake@uga.edu) & Pej Rohani (rohani@uga.edu)**Data for exercises:** data.zip

## Syllabus

## Project

## Schedule

### Day 1 (January 4, 2022)

- Introductions and course overview
- Lecture: The art of modeling
- Lecture: Modeling pragmatics and practicalities

Assigned reading: Brett et al. 2020. Detecting critical slowing down in high-dimensional epidemiological systems. PLOS Computational Biology 16:e1007679.

### Day 2 (January 11, 2022)

- Lecture: Deterministic compartmental models
- Exercise: Numerical solution of deterministic epidemiological models

Assigned reading: Saad-Roy, C.M. et al. 2020. Immune life history, vaccination, and the dynamics of SARS-CoV-2 over the next 5 years. Science 370:811-818.

### Day 3 (January 18, 2022)

Assigned reading: Drake, J.M. et al. 2021. Five approaches to the suppression of SARS-CoV-2 without intensive social distancing. *Proceedings of the Royal Society, Series B* 288:20203074. Supplement (please read at least the first three pages of the supplement).

### Day 4 (February 1, 2022)

- Lecture: Stochastic compartmental models
- Exercise: Numerical solution of stochastic epidemiological models

### Day 5 (February 8, 2022)

- Lecture: Modeling interventions
- Exercise: Pulsed vaccination

### Day 6 (February 15, 2022)

- Lecture: Model calibration I: ad hoc estimation
- Exercise: Estimation (Solutions)

### Day 7 (February 22, 2022)

- Lecture: Model calibration II: estimation by maximum likelihood
- Exercise: Likelihood estimation

### Day 8 (March 3, 2022)

- Lecture: Uncertainty
- Exercise: Sensitivity analysis

### Day 9 (March 10, 2022)

- Lecture: Contact heterogeneities
- Exercise: Structured models for host heterogeneities

### Day 10 (March 17, 2022)

- Lecture: Forecasting
- Exercise: Forecasting

### Additional resources

### Suggested readings (case studies)

- Anonymous. 1978. Influenza in a boarding school.
*British Medical Journal*1:587. - Blower, S.M., H. B. Gershengorn, R.M. 2000. A tale of two futures: HIV and antiretroviral therapy in San Francisco.
*Science*287:650-654. - Grais, R.F., M.J. Ferrari, C. Dubray, O.N. Bjornstad, B.T. Grenfell, A. Djibo, F. Fermon, P.J. Guerin. 2006. Estimating transmission intensity for a measles epidemic in Niamey, Niger: Lessons for intervention.
*Transactions of the Royal Society of Tropical Medicine and Hygiene*100:867-873. - Legrand, J., R.F. Grais, P.Y. Boelle, A.J. Valleron, & A. Flahault. 2007. Understanding the dynamics of Ebola epidemics.
*Epidemiology & Infection*135:610-621. - McCabe, R. et al. 2021. Communicating uncertainty in epidemic models.
*Epidemics*37:100520. - Park, A.W., J.M. Daly, N.S. Lewis, D.J. Smith, J.L.N. Wood, B.T. Grenfell. 2009. Quantifying the impact of immune escape on transmission dynamics of influenza.
*Science*326:726-728. - Pitzer, V.E. et al. 2012. Direct and indirect effects of rotavirus vaccination: Comparing predictions from transmission dynamic models.
*PLOS One*7(8): e42320. - Read, J., Lessler, J., Riley, S., Wang, S., Tan, L.J., Kwok, K.O., et al. 2014. Social mixing patterns in rural and urban areas of southern China.
*Proceedings of the Royal Society B: Biological Sciences*281:20140268. - Rohani, P., Zhong, X., & King, A. A. 2010. Contact network structure explains the changing epidemiology of pertussis.
*Science*330:982–985. - Schenzle, D. 1984. An age-structured model of pre- and post-vaccination measles transmissiont.
*IMA Journal of Mathematics Applied in Medicine and Biology*1:169–191.

### Suggested readings (modeling)

- Keeling, M.J. & P. Rohani. 2007.
*Modeling infectious diseases in humans and animals*. Princeton University Press. - Vynnyky, E., & R. White. 2010.
*An introduction to infectious disease modelling*. Oxford University Press. - Heesterbeek, J. A. P., & Roberts, M. G. 2007. The type-reproduction number T in models for infectious disease control.
*Mathematical Biosciences*206(1):3–10. - Diekmann, O., Heesterbeek, J. A. P., & Roberts, M. G. 2009. The construction of next-generation matrices for compartmental epidemic models.
*Journal of the Royal Society Interface*7:873–885. - Heffernan, J.M., R.J. Smith & L. Wahl. 2005. Perspectives on the basic reproductive ratio.
*Journal of the Royal Society Interface*2:281-293. - van den Driessche, P. & J. Watmough. 2002. Reproduction numbers and sub-threshold endemic equilibria for compartmental models of disease transmission.
*Mathematical Biosciences*180:29-48.

### Suggested readings (R programming)

- Crawley, M.J. 2007.
*The R book*. Wiley. - Matloff, N. 2011.
*The Art of R Programming*. No Starch Press. - Venables, W.N., & B.D Ripley. 2002.
*Modern Applied Statistics with S*. 4th edition. Springer. - Jones, O., R. Maillardet, & A. Robinson. 2014.
*Introduction to scientific programming and simulation with R*. Second edition. Chapman & Hall. - Wickham, H. & G. Grolemund. 2016.
*R for Data Science*. O’Reilly.