This code can be used to generate the figures from the paper:

Public efforts to reduce disease transmission implied from a spatial game

available on arxiv at this url.

All the code is located in the code folder.

Model - BSIRS

The model (section 2 of the paper) is contained in bsirs_model.py, the interaction matrix is contained in exposure_matrix.py. To generate all the outputs (calibrated parameters) of the model, use simulation_results.ipynb. This uses execute_system.py to evolve the system. The obtained varables (average infection-cutting rate u, infection number etc.) are saved inside static>saved_params.

Figures

The figures that are available in the paper are generated inside Jupyter Notebooks (notebooks folder) then they are saved into static>saved_figures folder.

Data (csv and shp)

The NHS Covid-19 data and all other data used in this work is contained in the folder static>utla_data. These are either csv files or shape files (shp). In particular, the processed NHS data is contained in the file static/utla_data/shp/covid-cases_EN_recent.shp; these contains the number of active Covid-19 cases in each UTLA in England between 01-07-2020 - 02-16-2021. This was obtained by processing the UTLA data of Covid-19 cases from https://coronavirus.data.gov.uk/.

To generate active cases directly from https://coronavirus.data.gov.uk/ please see the notebook generate_active_cases.ipynb. gm