Class Schedule

click here for class schedule & ZOOM links

Background Materials

Click on the images below to access each resource.

Download R before class.



Download before class.


Download Sublime before class.


Familiarize yourself with R using this intro tutorial.


Optional background reading.

Day 1

Lecture 1 – part 1 (click for slides)

Lecture 1 – part 2 (click for slides)

Lecture 2 – basic dynamics of SIR models (click for slides)

Suggested reading for Lecture 2:

R session – Intro to Modeling (click here for R code and instructions)

Day 1 lecture recording (click here for video)

Day 2

Lecture 3 – vaccination (click here for slides)

Lecture 4 – heterogeneity (click here for slides)

Lecture 5 – heterogeneity & SES (click here for slides)

R session – Heterogeneity (click here for R code and instructions on GitHub)

Day 2 recording (click here for video)

Day 3

Panel Discussion:

click here to learn about Dr. Lauren Ancel Meyers

click here to learn about Dr. Jacco Wallinga

Lecture 6 – parameter estimation (click here for slides)

Suggested reading for Lecture 6:

Lecture 7 – confronting models with data (click here for slides)

R session – parameter estimation documents:

click here for Estimation PDF

click here for Estimation R Code

click here for Estimation Data Set

click here for answer code

Lecture 8 – Stochasticity and Uncertainty (click here for slides)

Day 3 recording

Certificates of Completion.

Certificates of completion for each module will be available through your registration account shortly after you complete the online Summer Institute evaluations. There will be an evaluation for each module along with an overall institute evaluation that will appear in your dashboard after you complete your last module.

To access evaluations, log in at, click My Account in the upper right, the evaluations will appear on your dashboard. After you have completed your evaluations, a link to download the certificate of completion will appear within 24 hours. Certificates are generated through the registration system and, occasionally, names and module titles lose their formatting. If this is the case, please email and we will get you a corrected copy