Modelling of pandemics using EpiModel We use the data from the german RKI
The features supported are:
- Exploration of RGG's as the infection spreads
- Multi-core support
- History recording
- Graph diagnostics such as average degree and average distance over time
- Persistent storage of result objects
- Rich printing of returned objects
- Geographical sampling of initial infections by the use of population density data
- Heatmap of simulation, even through time
First of all install the required R packages. This can be done by running install.R, which installs the required packages. On Windows this should pull other binary dependencies, but for UNIX like systems, one should install at least: gcc, gcc-fortran and gdal to build them on demand.
The main code for RGG's is contained in the scripts/RGG folder. To run a scenario, head over to the scripts/scenarios-directory. Here one can run a simulation by using an RGG. See an example for the paremeters that can be set. In addition, the software supports multi-core machines by way of forking. This greatly improves simulations. However, this is only available on UNIX like systems, as Windows does not offer such a kernel call. For 8 concurrent processes at 1 million nodes it is advised to have 16 GB of RAM.
- RKI data: RKI dataset
- Population density tiles: European Commission
- Territories in vector format: Natural Earth