Likelihood-based inference for disease outbreak data can be very challenging due to the inherent dependence of the data and the fact that they are usually incomplete. In this paper we review recent Approximate Bayesian Computation (ABC) methods for the analysis of such data by fitting to them stochastic epidemic models without having to calculate the likelihood of the observed data. We consider both non-temporal and temporal-data and illustrate the methods with a number of examples featuring different models and datasets. In addition, we present extensions to existing algorithms which are easy to implement and provide an improvement to the existing methodology. Finally, R code to implement the algorithms presented in the paper is available on https://github.com/kypraios/epiABC.
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http://dx.doi.org/10.1016/j.mbs.2016.07.001 | DOI Listing |
Proc Biol Sci
January 2025
Mathematical Institute, University of Oxford, Oxford, UK.
Towards the end of an infectious disease outbreak, when a period has elapsed without new case notifications, a key question for public health policymakers is whether the outbreak can be declared over. This requires the benefits of a declaration (e.g.
View Article and Find Full Text PDFFront Vet Sci
January 2025
Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada.
Introduction: Antimicrobial resistance (AMR) is a growing threat to the efficacy of antimicrobials in humans and animals, including those used to control bovine respiratory disease (BRD) in high-risk calves entering western Canadian feedlots. Successful mitigation strategies require an improved understanding of the epidemiology of AMR. Specifically, the relative contributions of antimicrobial use (AMU) and contagious transmission to AMR emergence in animal populations are unknown.
View Article and Find Full Text PDFPLoS One
January 2025
Department of Mathematics, Konkuk University, Seoul, Republic of Korea.
Mathematical and statistical methods are invaluable in epidemiological investigations, enhancing our understanding of disease transmission dynamics and informing effective control measures. In this study, we presented a method to estimate transmissibility using patient-level data, with application to the 2015 MERS outbreak at Pyeongtaek St. Mary's Hospital, the Republic of Korea.
View Article and Find Full Text PDFInt J Cancer
January 2025
Department of Radiotherapy, Harbin Medical University Cancer Hospital, Harbin, China.
In mainland China, cancer registration relies on household-registered populations, overlooking migrant populations. Estimating cervical cancer incidence among permanent residents, including migrants, offers a more accurate representation of the true burden. The data from 487 cancer registries across China in 2016 were analyzed using a Bayesian spatial regression model with the integrated nested Laplace approximation-stochastic partial differential equation method.
View Article and Find Full Text PDFPLoS One
January 2025
Department of Health Informatics, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan.
School closures are a safe and important strategy for preventing infectious diseases in schools. However, the effects of school closures have not been fully demonstrated, and prolonged school closures have a negative impact on students and communities. This study evaluated class-specific school closure strategies to prevent the spread of seasonal influenza and determine the optimal timing and duration.
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