Repository for the MT3002 summer 2020 course on "The Mathematics and Statistics of Infectious Disease Outbreaks" given at the Department of Mathematics, Stockholm University, Sweden, by Tom Britton and Michael Höhle.

Undergraduate knowledge of mathematics (e.g. differential equations, optimization) and statistics (e.g. random variables, distributions, maximum likelihood inference) as well as some programming skills in a language with a data science component (python, R, Julia, matlab, ...).

Audience for the 2020 course were B.Sc. students in the natural science (statistics, mathematics, engineering, physics, ...), but we hope the material is also of interest for others, e.g., Ph.D. students in the field of epidemic modelling, infectious disease epidemiologists with a like for the quantitative side of matters, and for those who just want to improve their armchair epidemiology skills.

The video lectures are publicly available from a corresponding channel at the video server of Stockholm University (don't forget to unmute the video). For a better distributed access, the lectures are also available from a YouTube playlist.

Lectures were given in flipped classroom mode during July (L1-L7) and August (L8-L12) of 2020. The recordings below served as preparation for an live Zoom meeting (not recorded), where we discussed the content of the lectures.

• Introduction to the Course [Tom Britton | Michael Höhle]
• L01: Mathematical Modelling [Part 1 | Part 2]
• L02: Simulation and Fitting of Epidemic Models [Part 1 | Part 2 | Part 3]
• L03: Timing and observations + Endemic models [Part 1 | Part 2]
• L04: Estimating Reproduction Numbers [Part 1 | Part 2]
• L05: Effective Reproduction Number [Part 1 | Part 2]
• L06: Latencies and Delays [Part 1 | Part 2]
• L07: Vaccination, other Preventive Measures and Uncertainties [Part 1 | Part 2]
• L08: Modeling using Networks and other Heterogeneities [Part 1 | Part 2]
• L09: Univariate Outbreak Detection [Part 1 | Part 2]
• L10: Multivariate Outbreak Detection [Part 1 | Part 2]
• L11: COVID-19 (I): Reproduction Number and Herd Immunity [Part 1 | Part 2]
• L12: COVID-19 (II): Digital Contact Tracing [Part 1 | Part 2]

PDFs of the individual lectures is available here.

R code to produce the graphs and tables of the lecture slides is available for many of the lectures from the same folders as the lecture slides.

Exercises for the written exam are scattered throughout the lecture slides. The two homework assignments mentioned in the lecture can be found in the Projects folder.

The content of the slides etc is available under a Creative Commons 3.0 Attribute-ShareAlike. The code is available under a GNU GPL v3.0 license. The video lectures are copyright (c) Tom Britton and Michael Höhle, respectively.

We would very much appreciate your feedback to the lectures and its material. Either as GitHub issues, pull requests or by comments on the respective videos.