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EpiEstim is a tool to estimate the time-varying instantaneous reproduction number during epidemics.


The following vignettes provide worked examples, FAQs and details about how EpiEstim can be used alongside some other R packages in an outbreak analysis workflow.

vignette("short_demo", package="EpiEstim")
vignette("full_EpiEstim_vignette", package="EpiEstim")

To estimate the transmission advantage of pathogen variants or strains in real-time, please see the pre-print by Bhatia et al ( and the vignette below:

vignette("MV_EpiEstim_vignette", package="EpiEstim")   

To find out more about alternative software that may be more suitable for your specific data or analysis, please see below:

vignette("alternative_software", package="EpiEstim")

Citing our paper

Anne Cori, Neil M. Ferguson, Christophe Fraser, Simon Cauchemez, A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics, American Journal of Epidemiology, Volume 178, Issue 9, 1 November 2013, Pages 1505–1512.

@article{Cori2013, author={Cori, A and Ferguson, NM and Fraser, C and Cauchemez, S}, year={2013}, title={{A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics}}, journal={Am. J. Epidemiol.}, doi={10.1093/aje/kwt133}, }

Citing this code resource

We kindly request that you cite this codebase as follows (BibTeX format):

@misc{Cori2021, author={Cori, A and Kamvar, ZN and Stockwin, J and Jombart, T and Dahlqwist, E and FitzJohn, R and Thompson, R}, year={2021}, title={{EpiEstim v2.2-3: A tool to estimate time varying instantaneous reproduction number during epidemics}}, publisher={GitHub}, journal={GitHub repository}, howpublished = {\url{}}, commit={c18949d93fe4dcc384cbcae7567a788622efc781}, }

annecori/EpiEstim documentation built on April 6, 2022, 9:12 p.m.