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Open Access Software

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

Thomas Obadia13, Romana Haneef4 and Pierre-Yves Boëlle123*

Author Affiliations

1 INSERM, U707, Paris, France

2 APHP, Saint-Antoine Hospital, Paris, France

3 UPMC Univ Paris 06, UMR-S, 707, Paris, France

4 EHESP, Paris, France

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BMC Medical Informatics and Decision Making 2012, 12:147  doi:10.1186/1472-6947-12-147

Published: 18 December 2012

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.

Keywords:
Epidemics; Software; Reproduction number; Estimation; R package