I use the materials in this section for several of the classes and workshops I teach. You are of course free to use them independently from any of my courses.
DSAIDE - Dynamical Systems Approaches to Infectious Disease Epidemiology. This is an R package containing multiple Infectious Disease Epidemiology models that the user/student can run through a graphical user interface. The package currently lives on github, you can find it here.
YaRI = Yet another R Introduction - I always wanted to give something a name like that! This is a short introduction to R that I compiled and use for various courses I teach that are based on R. The R-scripts yariexample1.r and yariexample2.r are also needed if you want to work through the whole tutorial. And if you want to mix your own tutorial, here is the source code. (While I don’t insist on it, it would be nice if you shared your remix with me and the rest of the world.)
Note 1: I have solutions to all exercises in YaRI. If you can give me a valid reason why you should be allowed to have these files, email me and I’ll send them. If you are one of my students who has been assigned the YaRI exercises as homework, you’ll have to wait to get the solutions until after the homework deadline :)
Note 2: I wrote the YaRI tutorial several years ago. Since then, a lot of good R tutorials and teaching resources have become available. The 2 I currently recommend you look at first are Datacamp and the Swirl R Package. Datacamp is more polished, feature rich and overall nicer, but requires you to pay a monthly fee to get full access (some content is free). Swirl is completely free. For further links to R (and other) resources, see the compilation of github lists mentioned below.
This set of papers is useful introductory reading material to start learning about infectious disease modeling: IDpapers.zip.