EpiEstim

EpiEstim is a tool to estimate the time-varying instantaneous reproduction number during epidemics. To install the latest version, use:

devtools::install_github("mrc-ide/EpiEstim", build_vignettes = TRUE)

Vignettes

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 apply EpiEstim to temporally aggregated incidence data (e.g. weekly), please see:

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

To estimate the transmission advantage of pathogen variants or strains in real-time, please see the pre-print by Bhatia et al (https://www.medrxiv.org/content/10.1101/2021.11.26.21266899v1) 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")

Cite our papers

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},
}

Thompson RN, Stockwin JE, van Gaalen RD, Polonsky JA, Kamvar ZN, Demarsh PA, et al. Improved inference of time-varying reproduction numbers during infectious disease outbreaks, Epidemics, Volume 29, 1 December 2019, 100356.

Nash RK, Nouvellet P, Cori A. Real-time estimation of the epidemic reproduction number: Scoping review of the applications and challenges, PLOS Digital Health, Volume 1, Issue 6, 27 June 2022, e0000052.

Bhatia S, Wardle J, Nash RK, Nouvellet P, Cori A. A generic method and software to estimate the transmission advantage of pathogen variants in real-time : SARS-CoV-2 as a case-study, medRxiv pre-print.

Nash RK, Cori A, Nouvellet P. Estimating the epidemic reproduction number from temporally aggregated incidence data: a statistical modelling approach and software tool. (medRxiv pre-print)

Citing this code resource

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

@misc{Cori2022, author={Cori, A and Kamvar, ZN and Stockwin, J and Jombart, T and Dahlqwist, E and FitzJohn, R and Thompson, R and Nash, RK and Wardle, J and Bhatia, S},
year={2022},
title={{EpiEstim v2.2-4: A tool to estimate time varying instantaneous reproduction number during epidemics}},
publisher={GitHub}, journal={GitHub repository},
howpublished = {\url{https://github.com/mrc-ide/EpiEstim}},
}