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) and Wallinga and Teunis (2004) .

EpiEstim

R build status Codecov test coverage DOI

A tool to estimate time varying instantaneous reproduction number during epidemics

This tool is described in the following paper:

A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics Anne Cori, Neil M. Ferguson, Christophe Fraser and Simon Cauchemez American Journal of Epidemiology 2013.

Reference manual

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install.packages("EpiEstim")

2.2-5 by Anne Cori, a year ago

https://github.com/mrc-ide/EpiEstim

Report a bug at https://github.com/mrc-ide/EpiEstim/issues

Browse source code at https://github.com/cran/EpiEstim

Authors: Anne Cori [aut, cre] , Simon Cauchemez [ctb] , Neil M. Ferguson [ctb] , Christophe Fraser [ctb] (ORCID: , Elisabeth Dahlqwist [ctb] (ORCID: , P. Alex Demarsh [ctb] , Thibaut Jombart [ctb] , Zhian N. Kamvar [ctb] , Justin Lessler [ctb] , Shikun Li [ctb] , Jonathan A. Polonsky [ctb] (ORCID: , Jake Stockwin [ctb] , Robin Thompson [ctb] , Rolina van Gaalen [ctb]

Documentation:   PDF Manual  

GPL (>= 2) license

Imports coarseDataTools, stats, graphics, reshape2, ggplot2, gridExtra, fitdistrplus, coda, incidence, scales, grDevices

Suggests testthat, utils, vdiffr, covr, knitr, rmarkdown

Imported by EpiLPS, ViroReportR, covid19india, earlyR, ern.

Suggested by EpiNova, projections.

See at CRAN

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