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 is available on CRAN , the most up-to-date and complete information can be found on its Github page. I also wrote a paper that describes the package in some detail. You can read it here – and then cite it if you end up using bits of the code in a research project 🙂

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. I used to not share them freely (for obvious reasons), but because of note #2 you can now find them on my github site where the other files are.

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.

I maintain a compilation of lists with further resources, pertaining to learning R, Data Analysis, and other topics on Github.

This set of papers is useful introductory reading material to start learning about infectious disease modeling: IDpapers.zip.