Agent Based Model framework utilised for National Cabinet

Compiling and running

This code relies on C++14. A makefile is included for compilation using gnu make.

To run the code, you will need to create a JSON parameters file. NationalVaccineModel/parameters/dev/ has an example of the file and includes all relevant inputs.

Once compiled, the code can be run with ./Run parameters/dev/parameters-dev.json, or with whatever JSON file you have created. Line-listed outputs for infected cases will appear in the output_directory, with 1 file per simulation.

Combining outputs

The R script combine_outputs.R will take the output files and combine them into a single output file for further processing. It takes one argument, the parameter file JSON, and will calculate everything else required. The combined output will appear in the higher level folder.

Generating HPC parallel jobs

The R script create_batch_parameters.R will generate parameter JSONs, and slurm job scripts for submitting to the SLURM HPC queueing system. It takes two arguments: the path to the 'master' JSON file and the desired number of iterations. The slurm scripts will appear in the current working directory.