Skip to Main content Skip to Navigation
Journal articles

The R0 package: a toolbox to estimate reproduction numbers for epidemic outbreaks

Abstract : Background: Several generic methods have been proposed to estimate transmission parameters during an outbreak, especially the reproduction number. However, as of today, no dedicated software exists that implements these methods and allow comparisons. Results: A review of generic methods used to estimate transmissibility parameters during outbreaks was carried out. Most methods used the epidemic curve and the generation time distribution. Two categories of methods were available: those estimating the initial reproduction number, and those estimating a time dependent reproduction number. We implemented five methods as an R library, developed sensitivity analysis tools for each method and provided numerical illustrations of their use. A comparison of the performance of the different methods on simulated datasets is reported. Conclusions: This software package allows a standardized and extensible approach to the estimation of the reproduction number and generation interval distribution from epidemic curves.
Document type :
Journal articles
Complete list of metadatas

Cited literature [28 references]  Display  Hide  Download
Contributor : Thomas Obadia <>
Submitted on : Tuesday, May 19, 2020 - 12:38:10 PM
Last modification on : Thursday, August 20, 2020 - 3:05:23 AM


Publication funded by an institution


Distributed under a Creative Commons Attribution 4.0 International License




Thomas Obadia, Romana Haneef, Pierre-Yves Boëlle. The R0 package: a toolbox to estimate reproduction numbers for epidemic outbreaks. BMC Medical Informatics and Decision Making, BioMed Central, 2012, 12, pp.147. ⟨10.1186/1472-6947-12-147⟩. ⟨pasteur-02612613⟩