**Program:** 5th Annual Summer Institute in Statistical Modeling of Infectious Diseases

**Location:** University of Washington

**Date:** July 8-10, 2013

**Instructors:** Pejman Rohani (rohani@umich.edu) & John M. Drake (jdrake@uga.edu)

Objectives

Monday Morning |
Monday Afternoon |
Tuesday Morning |
Tuesday Afternoon |
Wednesday Morning |
---|---|---|---|---|

Lecture notes |
Lecture notes |
Lecture notes | Lecture notes | Lecture notes |

Files for computer lab | Files for computer lab | Files for computer lab Stochastic models |
Files for computer lab | Files for computer lab Sensitivity analysis - Sensitivity analysis through latin hypercube sampling (Handout)
- Sensitivity analysis through latin hypercube sampling (Code)
- Sensitivity analysis through latin hypercube sampling (Slides)
- Sensitivity analysis through latin hypercube sampling (Solutions)
Seasonality |

Further exercises:

- Estimating model parameters through maximum likelihood (Data)
- The distribution of outbreak sizes: Immune escape and transmission of equine influenza

Suggested reading (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.
- 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.

Suggested reading (modeling infectious diseases):

- 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.

Suggested reading (programming in R):

- 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. 2009. Introduction to scientific programming and simulation with R. Chapman & Hall.