Package: earlyR 0.0.5

Thibaut Jombart

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>.

Authors:Thibaut Jombart [aut, cre], Anne Cori [aut], Pierre Nouvellet [aut], Janetta Skarp [aut], Zhian N. Kamvar [ctb], Tim Taylor [ctb]

earlyR_0.0.5.tar.gz
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earlyR_0.0.5.tgz(r-4.6-any)earlyR_0.0.5.tgz(r-4.5-any)
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earlyR_0.0.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
earlyR/json (API)
NEWS

# Install 'earlyR' in R:
install.packages('earlyR', repos = c('https://reconhub.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/reconhub/earlyr/issues

Pkgdown/docs site:https://www.repidemicsconsortium.org

On CRAN:

Conda:

6.59 score 9 stars 97 scripts 286 downloads 3 mentions 2 exports 51 dependencies

Last updated from:61ee8bd091. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE154
source / vignettesOK244
linux-release-x86_64NOTE168
macos-release-arm64NOTE109
macos-oldrel-arm64NOTE105
windows-develNOTE95
windows-releaseNOTE99
windows-oldrelNOTE102
wasm-releaseOK133

Exports:get_Rsample_R

Dependencies:aweekclicoarseDataToolscodacpp11distcretedplyrEpiEstimepitrixfarverfitdistrplusgenericsggplot2gluegridExtragtableincidenceisobandlabelinglatticelifecyclemagrittrMASSMatrixMatrixModelsmcmcMCMCpackpillarpkgconfigplyrpurrrquantregR6RColorBrewerRcppreshape2rlangS7scalessodiumSparseMstringistringrsurvivaltibbletidyrtidyselectutf8vctrsviridisLitewithr

Early investigation of infectiousness using earlyR

Rendered fromearlyR.Rmdusingknitr::rmarkdownon May 08 2026.

Last update: 2020-10-27
Started: 2017-05-30

Readme and manuals

Help Manual

Help pageTopics
Estimate the Reproduction Numberget_R get_R.default get_R.incidence get_R.integer get_R.numeric
Plot earlyR objectsplot.earlyR points.earlyR
Print method for earlyR objectsprint.earlyR
Get a sample of plausible Reproduction Numberssample_R