metawards 0.2.0a0

MetaWards disease metapopulation modelling

MetaWards

References

• "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

Dependancies

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

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
[user@host MetaWards]$ make

This produces an executable named wards.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 MetaWards]$ ../wards.o 42 Testing/ncovparams.csv  4 1

Where the command line arguments are

./wards.o <RANDOM_SEED> <PARAMETER_FILE> <SOME_NUMBER> <SOME_OTHER_NUMBER>

Running an ensemble

To run multiple experiments use the driving shellscript run_repeats.sh