earlyR: Estimation of Transmissibility in the Early Stages of a Disease Outbreak

Implements a simple, likelihood-based estimation of the reproduction number (R0) using a branching process with a Poisson likelihood. This model requires knowledge of the serial interval distribution, and dates of symptom onsets. Infectiousness is determined by weighting R0 by the probability mass function of the serial interval on the corresponding day. It is a simplified version of the model introduced by Cori et al. (2013) <doi:10.1093/aje/kwt133>.

Version: 0.0.5
Depends: R (≥ 3.3.0)
Imports: stats, distcrete, EpiEstim, epitrix, ggplot2
Suggests: testthat, vdiffr, roxygen2, incidence, knitr, rmarkdown, projections, covr
Published: 2020-10-27
DOI: 10.32614/CRAN.package.earlyR
Author: Thibaut Jombart [aut, cre], Anne Cori [aut], Pierre Nouvellet [aut], Janetta Skarp [aut], Zhian N. Kamvar [ctb], Tim Taylor ORCID iD [ctb]
Maintainer: Thibaut Jombart <thibautjombart at gmail.com>
BugReports: https://github.com/reconhub/earlyR/issues
License: MIT + file LICENSE
URL: https://www.repidemicsconsortium.org/earlyR/
NeedsCompilation: no
Materials: NEWS
In views: Epidemiology
CRAN checks: earlyR results


Reference manual: earlyR.pdf
Vignettes: Early investigation of infectiousness using earlyR


Package source: earlyR_0.0.5.tar.gz
Windows binaries: r-devel: earlyR_0.0.5.zip, r-release: earlyR_0.0.5.zip, r-oldrel: earlyR_0.0.5.zip
macOS binaries: r-release (arm64): earlyR_0.0.5.tgz, r-oldrel (arm64): earlyR_0.0.5.tgz, r-release (x86_64): earlyR_0.0.5.tgz, r-oldrel (x86_64): earlyR_0.0.5.tgz
Old sources: earlyR archive


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