Estimation of Transmissibility in the Early Stages of a Disease Outbreak

Implements a simple, likelihood-based estimation of the reproduction number (R0) using a branching process with a Poisson likelihood. This model requires knowledge of the serial interval distribution, and dates of symptom onsets. Infectiousness is determined by weighting R0 by the probability mass function of the serial interval on the corresponding day. It is a simplified version of the model introduced by Cori et al. (2013) .


Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.


0.0.5 by Thibaut Jombart, 7 months ago

Report a bug at

Browse source code at

Authors: Thibaut Jombart [aut, cre] , Anne Cori [aut] , Pierre Nouvellet [aut] , Janetta Skarp [aut] , Zhian N. Kamvar [ctb] , Tim Taylor [ctb]

Documentation:   PDF Manual  

MIT + file LICENSE license

Imports stats, distcrete, EpiEstim, epitrix, ggplot2

Suggests testthat, vdiffr, roxygen2, incidence, knitr, rmarkdown, projections, covr

See at CRAN