Geographically weighted generalized Farrington algorithm for rapid outbreak detection over short data accumulation periods

Daisuke Yoneoka*, Takayuki Kawashima, Koji Makiyama, Yuta Tanoue, Shuhei Nomura, Akifumi Eguchi

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)6277-6294
Number of pages18
JournalStatistics in Medicine
Issue number28
Publication statusPublished - 2021 Dec 10
Externally publishedYes


  • emerging infectious disease
  • geographically weighted quasi-Poisson regression
  • outbreak detection
  • statistical surveillance

ASJC Scopus subject areas

  • Epidemiology
  • Statistics and Probability


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