SISMID 2013: Mathematical Modeling of Infectious Disease

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

R0 and parameter estimation

Files for computer lab

Files for computer lab
Sensitivity analysis

Seasonality

Further exercises:

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.