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
earlyR_0.0.5.zip(r-4.5)earlyR_0.0.5.zip(r-4.4)earlyR_0.0.5.zip(r-4.3)
earlyR_0.0.5.tgz(r-4.4-any)earlyR_0.0.5.tgz(r-4.3-any)
earlyR_0.0.5.tar.gz(r-4.5-noble)earlyR_0.0.5.tar.gz(r-4.4-noble)
earlyR_0.0.5.tgz(r-4.4-emscripten)earlyR_0.0.5.tgz(r-4.3-emscripten)
earlyR.pdf |earlyR.html✨
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 site:https://www.repidemicsconsortium.org

On CRAN:

6.59 score 9 stars 96 scripts 236 downloads 3 mentions 2 exports 55 dependencies

Last updated 4 years agofrom:61ee8bd091. Checks:3 OK, 4 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 24 2025
R-4.5-winNOTEJan 24 2025
R-4.5-linuxNOTEJan 24 2025
R-4.4-winNOTEJan 24 2025
R-4.4-macNOTEJan 24 2025
R-4.3-winOKJan 24 2025
R-4.3-macOKJan 24 2025

Exports:get_Rsample_R

Dependencies:aweekclicoarseDataToolscodacolorspacecpp11distcretedplyrEpiEstimepitrixfansifarverfitdistrplusgenericsggplot2gluegridExtragtableincidenceisobandlabelinglatticelifecyclemagrittrMASSMatrixMatrixModelsmcmcMCMCpackmgcvmunsellnlmepillarpkgconfigplyrpurrrquantregR6RColorBrewerRcppreshape2rlangscalessodiumSparseMstringistringrsurvivaltibbletidyrtidyselectutf8vctrsviridisLitewithr

Early investigation of infectiousness using earlyR

Rendered fromearlyR.Rmdusingknitr::rmarkdownon Jan 24 2025.

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