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MetaWards

References

  • "The role of routine versus random movements on the spread of disease in Great Britain" Leon Danon, Thomas A. House, Matt J. Keeling, Epidemics, 2009, Volume 1, Issue 4, December 2009, Pages 250-258 DOI: 10.1016/j.epidem.2009.11.002

  • "Individual identity and movement networks for disease metapopulations" Matt J. Keeling, Leon Danon, Matthew C. Vernon, Thomas A. House Proceedings of the National Academy of Sciences May 2010, 107 (19) 8866-8870; DOI: 10.1073/pnas.1000416107

  • "A spatial model of CoVID-19 transmission in England and Wales: early spread and peak timing" Leon Danon, Ellen Brooks-Pollock, Mick Bailey, Matt J Keeling medRxiv 2020.02.12.20022566; doi: 10.1101/2020.02.12.20022566

Summary

This repository has the code used for the papers and preprints in the References section

Dependencies

The code depends on the GSL - the GNU Scientific Library, install with your operating system's package manager or load the appropriate module if you are on an HPC system.

Building

C/C++ CI

Clone the repository

[user@host ~]$ git clone https://github.com/ldanon/MetaWards.git

Change in to the repository and run make

[user@host ~]$ cd MetaWards/Model
[user@host Model]$ make

This produces an executable named MetaWards.o

Running

MetaWards currently expects the data files to be found in a hard coded path under your home Directory ~/GitHub/MetaWards/2011Data/. If you don't have the cloned repository there you can create a symlink.

Running a single experiment

[user@host MetaWards]$ mkdir expt
[user@host MetaWards]$ cd expt
[user@host expt]$ ../MetaWards.o 42 Testing/ncovparams.csv  4 1 Testing/ExtraSeedsGeneralised.dat

Running an ensemble

To run multiple experiments use the driving shellscript run_repeats.sh

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