EpiEstim: Estimate Time Varying Reproduction Numbers from Epidemic Curves

Tools to quantify transmissibility throughout an epidemic from the analysis of time series of incidence as described in Cori et al. (2013) <doi:10.1093/aje/kwt133> and Wallinga and Teunis (2004) <doi:10.1093/aje/kwh255>.

Version: 2.2-5
Depends: R (≥ 2.10)
Imports: coarseDataTools (≥ 0.6-4), stats, graphics, reshape2, ggplot2, gridExtra, fitdistrplus, coda, incidence (≥ 1.7.0), scales, grDevices
Suggests: testthat, utils, vdiffr, covr, knitr, rmarkdown
Published: 2025-06-27
DOI: 10.32614/CRAN.package.EpiEstim
Author: Anne Cori ORCID iD [aut, cre], Simon Cauchemez [ctb], Neil M. Ferguson ORCID iD [ctb], Christophe Fraser ORCID iD [ctb], Elisabeth Dahlqwist ORCID iD [ctb], P. Alex Demarsh [ctb], Thibaut Jombart ORCID iD [ctb], Zhian N. Kamvar ORCID iD [ctb], Justin Lessler ORCID iD [ctb], Shikun Li [ctb], Jonathan A. Polonsky ORCID iD [ctb], Jake Stockwin [ctb], Robin Thompson ORCID iD [ctb], Rolina van Gaalen [ctb]
Maintainer: Anne Cori <a.cori at imperial.ac.uk>
BugReports: https://github.com/mrc-ide/EpiEstim/issues
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL: https://github.com/mrc-ide/EpiEstim
NeedsCompilation: no
Materials: README, NEWS
In views: Epidemiology
CRAN checks: EpiEstim results

Documentation:

Reference manual: EpiEstim.html , EpiEstim.pdf
Vignettes: EpiEstim demonstration (source, R code)

Downloads:

Package source: EpiEstim_2.2-5.tar.gz
Windows binaries: r-devel: EpiEstim_2.2-5.zip, r-release: EpiEstim_2.2-5.zip, r-oldrel: EpiEstim_2.2-5.zip
macOS binaries: r-release (arm64): EpiEstim_2.2-5.tgz, r-oldrel (arm64): EpiEstim_2.2-5.tgz, r-release (x86_64): EpiEstim_2.2-5.tgz, r-oldrel (x86_64): EpiEstim_2.2-5.tgz
Old sources: EpiEstim archive

Reverse dependencies:

Reverse imports: covid19india, earlyR, EpiLPS, ern
Reverse suggests: covidmx, projections

Linking:

Please use the canonical form https://CRAN.R-project.org/package=EpiEstim to link to this page.