squire

Last updated on Sep 2, 2022 R, covid
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squire enables users to simulate models of SARS-CoV-2 epidemics. This is done using an age-structured SEIR model that also explicitly considers healthcare capacity and disease severity. The model has been used for epidemic modelling in low- and middle-income countries (LMICs) for the Imperial College COVID-19 Response Team, producing trajectories for the potential global burden of COVID-191.

squire has been used throughout the pandemic to provide projections for every country to the World Health Organization (WHO) as part of the first costing for a global response to COVID-192 and the WHO Essential Supplies Forecasting Tool.

  1. P. G. T. Walker, C. Whittaker, O. J. Watson, M. Baguelin, P. Winskill, A. Hamlet, B. A. Djafaara, Z. Cucunubá, D. Olivera Mesa, W. Green, H. Thompson, S. Nayagam, K. E. C. Ainslie, S. Bhatia, S. Bhatt, A. Boonyasiri, O. Boyd, N. F. Brazeau, L. Cattarino, G. Cuomo-Dannenburg, A. Dighe, C. A. Donnelly, I. Dorigatti, S. L. van Elsland, R. FitzJohn, H. Fu, K. A. M. Gaythorpe, L. Geidelberg, N. Grassly, D. Haw, S. Hayes, W. Hinsley, N. Imai, D. Jorgensen, E. Knock, D. Laydon, S. Mishra, G. Nedjati-Gilani, L. C. Okell, H. J. Unwin, R. Verity, M. Vollmer, C. E. Walters, H. Wang, Y. Wang, X. Xi, D. G. Lalloo, N. M. Ferguson, A. C. Ghani, The impact of COVID-19 and strategies for mitigation and suppression in low- and middle-income countries. Science. 369, 413–422 (2020). (https://www.science.org/doi/10.1126/science.abc0035) ↩︎

  2. T. Tan-Torres Edejer, O. Hanssen, A. Mirelman, P. Verboom, G. Lolong, O. J. Watson, L. L. Boulanger, A. Soucat, Projected health-care resource needs for an effective response to COVID-19 in 73 low-income and middle-income countries: a modelling study. Lancet Glob Health. 8, e1372–e1379 (2020). ↩︎

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OJ Watson
Imperial College Research Fellow

I am an Imperial College Research Fellow supported by an Eric and Wendy Schmidt AI in Science Fellowship, working within Imperial's new AI Initiative: I-X. My primary focus is as an infectious disease modeller, data scientist, epidemiologist and an R developer. My academic work has focussed on modelling the spread of malaria and COVID-19, based at Imperial College London, Brown University and the London School of Hygiene and Tropical Medicine.

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