2022
DOI: 10.1111/rssa.12971
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Efficient Bayesian inference of Instantaneous Reproduction Numbers at Fine Spatial Scales, with an Application to Mapping and Nowcasting the Covid-19 Epidemic in British Local Authorities

Abstract: information about population flows to model potential transmissions across local areas. A simple approach to posterior simulation quickly becomes computationally infeasible, which is problematic if the system is required to provide timely predictions. We describe how to make posterior simulation for the model efficient, so that we are able to provide daily updates on epidemic developments.The results can be found at our web site https://localcovid.info, which is updated daily to display estimated instantaneous… Show more

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Cited by 10 publications
(8 citation statements)
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References 15 publications
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“…Oxford CSML Model Dashboard on [56] Hierarchical semi-mechanistic Bayesian model fitted to cases, similar to Epidemia and as described in [33], but with a spatio-temporal component R is derived using the renewal Equation ( 2…”
Section: Future and Lessons Learntmentioning
confidence: 99%
“…Oxford CSML Model Dashboard on [56] Hierarchical semi-mechanistic Bayesian model fitted to cases, similar to Epidemia and as described in [33], but with a spatio-temporal component R is derived using the renewal Equation ( 2…”
Section: Future and Lessons Learntmentioning
confidence: 99%
“…They both adopt a renewal equation framework for the epidemic modelling and a Bayesian estimation framework, differing in how they treat the spatial dynamics of transmission. Mishra et al (2022) do not explicitly model spatial dependence between areas, whereas Teh et al (2022) adopt a spatiotemporal hierarchical formulation and resort to some approximations to address the resulting computational issues. The final session returned to the topic of the R-number with a detailed discussion by Pellis et al (2022) of its properties and of the statistical issues faced for its estimation as the underlying model is progressively complexified.…”
Section: S4 |mentioning
confidence: 99%
“…Simulation results, however, will necessarily depend on which model is used to generate data, and it is unclear to what degree they translate to the real world. It has been argued that R t estimates can be evaluated based on derived short-term forecasts (Teh et al, 2022); this, however, is challenging as e.g., errors in the estimated R t and the assumed generation time distribution may cancel out so that even bad R t estimates can yield acceptable forecasts. In this work, we take a complementary approach to simulation and forecasting studies by describing discrepancies between real-world R t estimates and relating them to underlying analytical choices.…”
Section: Introductionmentioning
confidence: 99%