3MC Course on Epidemiological Modelling

You will find here material for the 3MC Course on Epidemiological Modelling that is to be held in South Africa in April 2022. Most of the material is arranged in 5 main subdirectories. Note that you can also access a web version of this site by following this link. In that version, the slides will open properly in a browser.

• CODE contains the R code that will be used during the School as well as some additional code that might prove useful.
• DATA contains a few datasets that will be used. These datasets will also be available online directly, but for the convenience of participants, they are collected here.
• FIGS contains some figures. These are mostly used internally in the slides and should not be useful.
• OUTPUT will contain any output generated by the code (figures, tables, etc.).
• SLIDES_MD contains all written material for the course, including slides and any other material. To compile the slides, you could for instance use the command npx @marp-team/marp-cli@latest --html 2022_04_3MC_EpiModelling*.md from within this directory.

Preparing for the school

All of my code is in R. If I have time, I will try to produce Python versions of some of it, but there is no guarantee that this will happen. You should therefore install R, which can be downloaded here. Although not strictly necessary, downloading RStudio is also a good idea. This can be done from this website. Once you have installed R (and perhaps RStudio), run the file CODE/install_required_libraries.R either from RStudio or from the command line so that the libraries we will be using are installed on your machine. See details in the file itself.