Scarponi, Danny; Iskauskas, Andrew; Clark, Rebecca A; Vernon, Ian; McKinley, Trevelyan J; Goldstein, Michael; Mukandavire, Christinah; Deol, Arminder; Weerasuriya, Chathika; Bakker, Roel; +2 more... White, Richard G; McCreesh, Nicky; (2023) Demonstrating multi-country calibration of a tuberculosis model using new history matching and emulation package - hmer. Epidemics, 43. 100678-. ISSN 1755-4365 DOI: https://doi.org/10.1016/j.epidem.2023.100678
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Abstract
Infectious disease models are widely used by epidemiologists to improve the understanding of transmission dynamics and disease natural history, and to predict the possible effects of interventions. As the complexity of such models increases, however, it becomes increasingly challenging to robustly calibrate them to empirical data. History matching with emulation is a calibration method that has been successfully applied to such models, but has not been widely used in epidemiology partly due to the lack of available software. To address this issue, we developed a new, user-friendly R package hmer to simply and efficiently perform history matching with emulation. In this paper, we demonstrate the first use of hmer for calibrating a complex deterministic model for the country-level implementation of tuberculosis vaccines to 115 low- and middle-income countries. The model was fit to 9-13 target measures, by varying 19-22 input parameters. Overall, 105 countries were successfully calibrated. Among the remaining countries, hmer visualisation tools, combined with derivative emulation methods, provided strong evidence that the models were misspecified and could not be calibrated to the target ranges. This work shows that hmer can be used to simply and rapidly calibrate a complex model to data from over 100 countries, making it a useful addition to the epidemiologist's calibration tool-kit.
Item Type | Article |
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Faculty and Department | Faculty of Epidemiology and Population Health > Dept of Infectious Disease Epidemiology & Dynamics (2023-) |
Research Centre |
TB Modelling Group Vaccine Centre TB Centre Centre for the Mathematical Modelling of Infectious Diseases |
PubMed ID | 36913805 |
Elements ID | 200028 |
Official URL | http://dx.doi.org/10.1016/j.epidem.2023.100678 |
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