The first two folders pertain to the two main components of this paper and the third folder contains the data for figures.
- Geographic Analysis including human mobility model and relative risk framework:
./HumanMobility_RR/ - Fitness Model quantifying the relative fitness over time of serotypes individually, grouped by whether they are vaccine type or non-vaccine type, and penicillin susceptibility:
./Fitness/ - Figures and source code for all figures.
./Figures/
Unfortunately these each require different versions of R. The best workaround is to create two separate conda environments each with the R versions you want in them in which you can open individual RStudios or just run from the command line