Flu And Coronavirus Simulator (FACS)

FACS is an agent-based modelling code that models the spread of flu and coronaviruses in local regions. Up to now, we have used it to model the spread of Covid-19 in a range of London boroughs.

The code can be repurposed to model other regions, and its current (sequential) implementation should be able to run up to 500,000 households within a reasonable time frame. It also supports vaccination programmes, track and trace and mutated versions of the virus.

What sets FACS apart from many other codes is that we have a partially automated location extraction approach from OpenStreetMaps data (the scripts reside at https://www.github.com/djgroen/covid19-preprocess), that we resolve a wide range of different location types (e.g., supermarkets, offices, parks, schools, leisure locations and hospitals) and that we have a specific algorithm for modeling infections within these locations, taking into account the physical size of each location.

We are currently finalizing a first journal paper about FACS, and will link to it from this page once it has become available.

Quick installation notes

To install FACS, simply clone the GitHub repository, and ensure the dependencies are met.

git clone https://github.com/djgroen/facs.git

These dependencies are:

  • PyYaml
  • numpy
  • pandas

How to run the code

To run a simple simulation of a basic test dataset, type: python3 run.py -g –location=test –output_dir=.

Here, the -g flag indicates that output will be written to out.csv, instead of an output file with a more specific name.

To run a simulation of the Borough of Brent, type: python3 run.py –location=brent –measures_yml=measures –output_dir=.

Note that in this case, we explicitly specify the measures YML file that we wish to use. This is done in the format: covid_data/<measures_yml>.yml

So in this case FACS will use the file covid_data/measures.yml.

Outputs are written as CSV files in the output_dir. E.g. for the test run you will get: covid_out_infections.csv test-extend-lockdown-62.csv

There is a hardcoded lockdown in run.py which is representative for the UK. This can be disabled by selecting the transition scenario “no-measures”.

We also included a simple plotting script. This could be called e.g. as follows: python3 PlotSEIR.py out.csv test (this has not been tested in a while, as we usually use FabCovid19 for plotting these days)

Citing FACS

Our journal paper on FACS has now been accepted, and can be found here: https://bura.brunel.ac.uk/handle/2438/20914

The BibTex code is here:

@article{mahmood2020facs,
  title={FACS: A geospatial agent-based simulator for analyzing COVID-19 spread and public health measures on local regions},
  author={Mahmood, Imran and Arabnejad, Hamid and Suleimenova, Diana and Sassoon, Isabel and Marshan, Alaa and Serrano, Alan and Louvieris, Panos and Anagnostou, Anastasia and Taylor, S and Bell, David and others},
  year={2020},
  journal={Journal of Simulation (in press)}
  publisher={Taylor \& Francis}
}

Contents:

Indices and tables