Code to accompany an age-structured difference equation model on the dynamics of SARS-CoV-2 that incorporates waning immunity. Preprint currently hosted at https://www.medrxiv.org/content/10.1101/2020.07.24.20157982v2 (doi:10.1101/2020.07.24.20157982)
After cloning the repository, run SEIIRRS-analysis.R in RStudio. This script calls the functions in SEIIRRS-functions.R, which runs the age-structured discrete time model. Ensure that required R packages lubridate, testthat & rstudioapi are installed prior to running the code.
Questions about the code can be directed to the corresponding author, Thomas Crellen (thomas.crellen@bdi.ox.ac.uk). The age structured contact matrices for the UK population (in the /data folder) are the property of Dr Petra Klepac (petra.klepac@lshtm.ac.uk).
As these analysis notes are an integral part of the paper and do not have their own DOI, we kindly request that you cite the full paper as follows:
@ARTICLE{Crellen2020, author={Crellen, T and Pi, L and Davis, EL and Pollington, TM and Lucas, TCDL and Ayabina, D and Borlase, A and Toor, J and Prem, K and Medley, GF and Klepac, P and Hollingsworth, TD}, year={2020},
title={{Dynamics of SARS-CoV-2 with waning immunity in the UK population}},
journal={Phil. Trans. R. Soc. B},
doi={10.1098/rstb.2020.0274},
}
This work is licensed under a Creative Commons Attribution 4.0 International License.