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Geographically weighted generalized Farrington algorithm for rapid outbreak detection over short data accumulation periods
Author(s) -
Yoneoka Daisuke,
Kawashima Takayuki,
Makiyama Koji,
Tanoue Yuta,
Nomura Shuhei,
Eguchi Akifumi
Publication year - 2021
Publication title -
statistics in medicine
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.996
H-Index - 183
eISSN - 1097-0258
pISSN - 0277-6715
DOI - 10.1002/sim.9182
Subject(s) - computer science , outbreak , algorithm , count data , data mining , statistics , mathematics , medicine , virology , poisson distribution
The demand for rapid surveillance and early detection of local outbreaks has been growing recently. The rapid surveillance can select timely and appropriate interventions toward controlling the spread of emerging infectious diseases, such as the coronavirus disease 2019 (COVID‐19). The Farrington algorithm was originally proposed by Farrington et al (1996), extended by Noufaily et al (2012), and is commonly used to estimate excess death. However, one of the major challenges in implementing this algorithm is the lack of historical information required to train it, especially for emerging diseases. Without sufficient training data the estimation/prediction accuracy of this algorithm can suffer leading to poor outbreak detection. We propose a new statistical algorithm—the geographically weighted generalized Farrington (GWGF) algorithm—by incorporating both geographically varying and geographically invariant covariates, as well as geographical information to analyze time series count data sampled from a spatially correlated process for estimating excess death. The algorithm is a type of local quasi‐likelihood‐based regression with geographical weights and is designed to achieve a stable detection of outbreaks even when the number of time points is small. We validate the outbreak detection performance by using extensive numerical experiments and real‐data analysis in Japan during COVID‐19 pandemic. We show that the GWGF algorithm succeeds in improving recall without reducing the level of precision compared with the conventional Farrington algorithm.