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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: 2.2-4
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: 2021-01-07
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.pdf
Vignettes: EpiEstim demonstration

Downloads:

Package source: EpiEstim_2.2-4.tar.gz
Windows binaries: r-devel: EpiEstim_2.2-4.zip, r-release: EpiEstim_2.2-4.zip, r-oldrel: EpiEstim_2.2-4.zip
macOS binaries: r-release (arm64): EpiEstim_2.2-4.tgz, r-oldrel (arm64): EpiEstim_2.2-4.tgz, r-release (x86_64): EpiEstim_2.2-4.tgz, r-oldrel (x86_64): EpiEstim_2.2-4.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.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.