To distinguish between resources that are used in the course, and others that are related but not directly used, I decided to have two resource pages. The Course Resources page lists materials we’ll be using in the course. This page tries to provide a fairly comprehensive list of resources related to the course topic.
Apart from the books, most other materials described below are (should be) freely available online. Some of the resources I list are dynamic and ever changing. That means occasionally links might not work, sites go offline, chapters in online books get re-arranged, etc. If any link does not work and you can’t access the materials for some reason, let me know.
Obviously, there is no way my list is exhaustive. Let me know if you find other relevant and good sources.
Approximately sorted in order of difficulty (my opinion)
Some of these books are useful for learning general modeling concepts. They do not exclusively focus on infectious diseases.
Currently just a copy & paste list from my former class slides. Needs to be updated/curated.
Throughout this course, I link to videos from a few online courses that cover similar topics to this course. While the videos are embedded and you do not need to sign up for those online courses, if you are interested, you could. Signing up for those courses should be free. Coursera might want to talk you into getting a certificate (and paying), but you can skip that and get the whole course content for free (last time I checked, let me know if that has changed.)
Note that the HKU course started out as a course called “Epidemics” on the EdX platform. Now there is the above course on the Coursera platform. In addition, there is a sequence of courses, Epidemics I-IV on the EdX platform. The Coursera and EdX offerings seem similar, I don’t know if/how they differ.
For this class, I will embed all relevant materials. You therefore don’t need to further check out those courses if you don’t want to. However, if you are interested, I encourage you to give them a try. They have great content and cover some topics which we won’t cover in this course. Neither of these courses takes an explicit model-based perspective, but many topics are discussed with such a framework in mind (and several of the instructors for each course are infectious disease modelers).
Dynamical Systems Approach to Infectious Disease Epidemiology (DSAIDE). The R package that goes with this course.
idmodelr by Sam Abbott. Many basic compartmental (SIR type) models, a little bit of coding is required. He also has a list of related resources, which - not surprisingly - has a lot of overlap with the information on this page.
shinySIR by Sinead Morris. Exploration of several SIR-type models through Shiny. It doesn’t have the detailed documentation of DSAIDE, but it includes some models not in DSAIDE.
The R Epidemics Consortium maintains several R packages related to infectious disease modeling. Most of the content is oriented toward researchers/practitioners, but there is also some teaching/learning material.
Epimodel is a website for the R package(s) of the same name that allow fairly user-friendly building and exploring of ID Epi models. The strength of Epimodel and related packages (the Statnet suite of R packages) is in network based models.
The pomp R package to fit stochastic dynamic models (and more) to time-series data. This is a powerful package and the package contains a good bit of tutorials and information. It is overall fairly advanced material.
NRICH project on infectious disease dynamics. A nice collection of resources and activities related to infectious disease epidemiology from a mathematical and modeling angle. The target age group are teenagers, but the material is likely suitable for older ages too. This is mainly meant for teachers to implement, but can also be useful for self-learning.
The Epirecipes site contains a cookbook of many standard infectious disease models with code in several different programming languages (including R).