Complex model calibration through emulation, a worked example for a stochastic epidemic model

Authors: Dunne, Michael;

Mohammadi, Hossein;

Challenor, Peter;

Borgo, Rita;

Porphyre, Thibaud;

Vernon, Ian;

Firat, Elif E.;

Turkay, Cagatay ;

Torsney-Weir, Thomas;

Goldstein, Michael;

Reeve, Richard ;

Fang, Hui;

Swallow, Ben

Source: Epidemics

Full text

: http://dx.doi.org/10.1016/j.epidem.2022.100574

Abstract

Uncertainty quantification is a formal paradigm of statistical estimation that aims to account for all uncertainties inherent in the modelling process of real-world complex systems. The methods are directly applicable to stochastic models in epidemiology, however they have thus far not been widely used in this context. In this paper, we provide a tutorial on uncertainty quantification of stochastic epidemic models, aiming to facilitate the use of the uncertainty quantification paradigm for practitioners with other complex stochastic simulators of applied systems. We provide a formal workflow including the important decisions and considerations that need to be taken, and illustrate the methods over a simple stochastic epidemic model of UK SARS-CoV-2 transmission and patient outcome. We also present new approaches to visualisation of outputs from sensitivity analyses and uncertainty quantification more generally in high input and/or output dimensions.

Rights

http://creativecommons.org/licenses/by-nc-nd/4.0/

Cite as

Dunne, M., Mohammadi, H., Challenor, P., Borgo, R., Porphyre, T., Vernon, I., Firat, E., Turkay, C., Torsney-Weir, T., Goldstein, M., Reeve, R., Fang, H. & Swallow, B. 2022, 'Complex model calibration through emulation, a worked example for a stochastic epidemic model', Epidemics, 39, article no: 100574. http://dx.doi.org/10.1016/j.epidem.2022.100574

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DOI: http://dx.doi.org/10.1016/j.epidem.2022.100574

Repository URI: http://eprints.gla.ac.uk/271989/