estimateR: an R package to estimate and monitor the effective reproductive number

BMC Bioinformatics

Software

Ana Grosu¹  Adrian Lison¹  Tanja Stadler²  Jérémie Scire²  Jana S. Huisman³  Daniel C. Angst⁴  Sebastian Bonhoeffer⁴  Jinzhou Li⁵  Marloes H. Maathuis⁵ 

[1] Department of Biosystems Science and Engineering, ETH Zurich, Swiss Federal Institute of Technology, Basel, Switzerland;Department of Biosystems Science and Engineering, ETH Zurich, Swiss Federal Institute of Technology, Basel, Switzerland;Swiss Institute of Bioinformatics, Lausanne, Switzerland;Department of Biosystems Science and Engineering, ETH Zurich, Swiss Federal Institute of Technology, Basel, Switzerland;Swiss Institute of Bioinformatics, Lausanne, Switzerland;Department of Environmental Systems Science, ETH Zurich, Swiss Federal Institute of Technology, Zurich, Switzerland;Department of Physics, Massachusetts Institute of Technology, Cambridge, USA;Department of Environmental Systems Science, ETH Zurich, Swiss Federal Institute of Technology, Zurich, Switzerland;Department of Mathematics, ETH Zurich, Swiss Federal Institute of Technology, Zurich, Switzerland;

关键词: R package;    Epidemiology;    Effective reproductive number;    Re;    Rt;    Surveillance;    Monitoring;    Outbreak;    COVID-19;   

DOI  :  10.1186/s12859-023-05428-4

 received in 2022-06-28, accepted in 2023-07-24,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundAccurate estimation of the effective reproductive number (Re\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym}\usepackage{amsfonts}\usepackage{amssymb}\usepackage{amsbsy}\usepackage{mathrsfs}\usepackage{upgreek}\setlength{\oddsidemargin}{-69pt}\begin{document}$$R_e$$\end{document}) of epidemic outbreaks is of central relevance to public health policy and decision making. We present estimateR, an R package for the estimation of the reproductive number through time from delayed observations of infection events. Such delayed observations include confirmed cases, hospitalizations or deaths. The package implements the methodology of Huisman et al. but modularizes the Re\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym}\usepackage{amsfonts}\usepackage{amssymb}\usepackage{amsbsy}\usepackage{mathrsfs}\usepackage{upgreek}\setlength{\oddsidemargin}{-69pt}\begin{document}$$R_e$$\end{document} estimation procedure to allow easy implementation of new alternatives to the currently available methods. Users can tailor their analyses according to their particular use case by choosing among implemented options.ResultsThe estimateR R package allows users to estimate the effective reproductive number of an epidemic outbreak based on observed cases, hospitalization, death or any other type of event documenting past infections, in a fast and timely fashion. We validated the implementation with a simulation study: estimateR yielded estimates comparable to alternative publicly available methods while being around two orders of magnitude faster. We then applied estimateR to empirical case-confirmation incidence data for COVID-19 in nine countries and for dengue fever in Brazil; in parallel, estimateR is already being applied (i) to SARS-CoV-2 measurements in wastewater data and (ii) to study influenza transmission based on wastewater and clinical data in other studies. In summary, this R package provides a fast and flexible implementation to estimate the effective reproductive number for various diseases and datasets.ConclusionsThe estimateR R package is a modular and extendable tool designed for outbreak surveillance and retrospective outbreak investigation. It extends the method developed for COVID-19 by Huisman et al. and makes it available for a variety of pathogens, outbreak scenarios, and observation types. Estimates obtained with estimateR can be interpreted directly or used to inform more complex epidemic models (e.g. for forecasting) on the value of Re\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym}\usepackage{amsfonts}\usepackage{amssymb}\usepackage{amsbsy}\usepackage{mathrsfs}\usepackage{upgreek}\setlength{\oddsidemargin}{-69pt}\begin{document}$$R_e$$\end{document}.

【 授权许可】

CC BY   
© BioMed Central Ltd., part of Springer Nature 2023

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