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

Peer review:

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

On CRAN:

2 exports 9 stars 2.06 score 55 dependencies 3 mentions 198 downloads

Last updated 4 years agofrom:61ee8bd091

Exports:get_Rsample_R

Dependencies:aweekclicoarseDataToolscodacolorspacecpp11distcretedplyrEpiEstimepitrixfansifarverfitdistrplusgenericsggplot2gluegridExtragtableincidenceisobandlabelinglatticelifecyclemagrittrMASSMatrixMatrixModelsmcmcMCMCpackmgcvmunsellnlmepillarpkgconfigplyrpurrrquantregR6RColorBrewerRcppreshape2rlangscalessodiumSparseMstringistringrsurvivaltibbletidyrtidyselectutf8vctrsviridisLitewithr