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 (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")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},
}
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{https://github.com/mrc-ide/EpiEstim}}, commit={c18949d93fe4dcc384cbcae7567a788622efc781},
}