Epid 501: Modeling Infection Transmission

Instructor: Jong-Hoon Kim
Office:
Office hours: Please email to make an appointment
Email: jonghoon.kim@ivi.int

Quick links:

• Homework problem sets
• Syllabus and reading assignments

Description:

This course will introduce basic theory of infection transmission, particularly the biological and socioligical background and mathematics and develop basic computational skills using mainly R to model infection transmission. The intended audience for this course is those who have backound in biology, sociology, but not necessarily in mathematics or computer programming.

Topics to be covered will include empirical studies of infectious disease outbreaks, models and theory, introduction to R, differential equations, and model fitting.

Requirements

Students should have studied calculus before taking the course, and should in particular be comfortable with the solution of linear differential equations. In addition, a later substantial portion of the course, perhaps six weeks, will deal with computer methods to model infection transmission. Some experience with computer programming, especially R, will be a great help in understanding this part of the course.

Coursework

There will be weekly graded problem sets, consisting of questions on both theory and applications. There will be three midterm exams but no final. The midterms will be in class at the usual time on October 13, November 10, and December 10.

There will be reading assignments for each lecture. The assignments are listed on the schedule below. Students are expected to do the reading for each lecture in a timely manner.

Books

Coursepack (required): Modeling disease transmission, Jong-Hoon Kim, Oxford University Press, Oxford (2010)

In addition to this required coursepack, a list of other useful books is given below. None of them is required, but you may find them useful if you want a second opinion or more detail on certain topics.

General books on modeling disease transmission:

• Roy M. Anderson and Robert M. May, Infectious Diseases of Humans: Dynamics and Control, Oxford University Press (1992). A classic book on modeling disease transmission and disease ecology in general.
• Matt J. Keeling and Pejman Rohani, Modeling Infectious Diseases in Humans and Animals, Princeton University Press (2007). More toward disease transmission modeling. A nice introduction of mathematical modeling of disease transmission
• Fred Brauer and Dawn Bies, Mathematical Models in Population Biology and Epidemiology, Springer (2011). A nice introduction to the mathematics involved in disease transmission modeling.

Books on specific modeling:

• Richard McElreath, Statistical Rethinking: A Bayesian Course with Examples in R and Stan, Chapman and Hall/CRC (2015). This text provides a very nice introduction to the philosophy on modeling and also R in general.

Problem sets:

• Homework 1 - Fundamental concepts in infectious disease transmission
• Homework 2 - Network metrics
• Homework 3 - Computer calculations
• Homework 4 - Random graphs and generating functions
• Homework 5 - Growing networks
• Homework 6 - Community structure
• Homework 7 - Spectral and inference methods
• Homework 8 - Percolation and epidemics

Data:

• In-class social network
• Internet autonomous system data
• Network of political blogs

Syllabus