This course is given in the spring semester of 2021.
See information sheet for details.
This course is taught in a “flipped” format. What that means is that you will learn the course material from recorded lectures or other resources, and answer the assignment questions at times convenient to you. Every week we will meet for an active session in which the assignment solutions will be presented and discussed by the students.
Generally speaking, course materials are available to the public, but attendance in the active sessions is restricted to registered students. If you are a Technion student and are not yet sure you’d like to register you are welcome to join the first active meeting, given that you have completed assignment I and are enrolled as a free listener. Students from other universities may follow intrauniversity procedures to enroll.
Week  Lecture  Lecture notes  Additional reference  Assignment  Active class meeting 
Introduction and fundamental concepts  
1a  Introduction by Guest lecturer: Amit Huppert 
Slides  – The first week of the Coursera course Developing the SIR Model partially overlaps with this week’s material. Note that you can access the course material in `audit’ mode.
– The beginning of Chapter 2 in Brauer’s book discusses compartmental models and the SIS model, but please do note that beta is defined a bit differently than in my lecture. 
Assignments are restricted to registered students. The worksheet is available here. 
Active class meeting #1 Zoom meeting
Active meetings are restricted to registered students. If you are not yet sure you’d like to register you are welcome to join the first meeting, given that you have completed the assignment and are enrolled as a free listener. 
1b  First examples – the SIS mode  Notes  
1c  First code in R  Code  – Installing an R environment  
2a  Model extension – SIDS  Notes  – Chapter 2 in the book by Keeling and Rohani provides an excellent reference for lectures 2a and 2b.
– The first week of the Coursera course Developing the SIR Model partially overlaps with this week’s material. Note that you can access the course material in `audit’ mode. – Here is a link to the Insightmaker demonstration presented in the lecture 
Assignment 2  Active class meeting #2
Active meetings are restricted to registered students. 
2b  Notes  
2c  The basic reproduction number and the next generation matrix  Notes  – Chapter 5.2 in Brauer’s book.


Systematic derivation of the SIR model  
3a  Intro: The KermackMcKendric paper 
– The paper from 1927 is available here (or here for registered students)  Details are published in the course website  
3b  The basic stochastic ageofinfection model  Notes  – The lecture is based on section 2 in Guy Katriel’s paper available here (or here for registered students)  
3c  A stochastic simulation in R  R code #1 R code #2 

3d  A deterministic version of the model  Notes  – The lecture is based on section 3 in Guy Katriel’s paper available here (or here for registered students)  
3e  Model approximations and reduction to the SIR model  Notes  – The lecture is based on section 4 in Guy Katriel’s paper available here (or here for registered students)  
Analysis of ODE epidemic models  
4a  Outline of an epidemic as described by the SIR model  Notes  – Chapter 2 in the book by Keeling and Rohani provides a basis for lectures 4a and 4b.
– Chapters 3 and 7 in the book by Martcheva provides a good overview of the analysis of autonomous dynamical systems – If you are new to dynamical systems, you may want to refer to Strogatz’s wellknown book on this subject 

Details are published in the course website 
4b  Analysis of an SIR model with natural birth/death  Notes  
4c  Analysis of an SEI model for tuberculosis (TB)  Notes  – Chapter 7.5 in the book by Martcheva


5  Oscillations in Epidemic models  Notes  – Chapter 3.6 in the book by Martcheva
– For Background on limit cycles, see, e.g., chapter 7 in Strogatz’s wellknown book on this subject. 
Details are published in the course website  
6  Epidemic final size  Notes  – This paper presents the derivation of final size equations in a rather general case, together with examples.
– Guy Katriel’s paper available here (or here for registered students) presents the derivation of final size equations for discretetime ageofinfection models. – An R code for solving the nonlinear algebraic final size equation is available here. 

Subpopulations  
7  Subpopulations  Notes  – Here is an excellent short description of the subject. It also includes reference to an R code for the system presented in the lecture. 