Process_mobility-Gowalla.ipynb is the notebook which processes the infect_stat_res.txt (generated by SpreadSim) to generate cluster_checkin_events and cluster_inf_events for the Hawkes process-based model.
This is currently set to work with pandas, but can be modified to work with larger dataset using parquet. Depending upon the dataset at hand, one may need to change the column names appropriately. This also creates cluster-specific files OD_matrix_<>.npy and cluster_centers_<>.npy
Once the files are generated, our model can be run using the matlab script run_hawkes_gowalla.m by setting the appropriate paths.
This part is adapted from git repo https://github.com/chiangwe/HawkPR
Main files to run: run_hawkes_gowalla.m This generates the risk.csv file which can be used for visualization by subsequent steps.
Create_maps_Gowalla.ipynb can be used for prototyping and generating the plots. Create_risk_inf_plots.ipynb is used to create infection plots.