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-4.7)earlyR_0.0.5.zip(r-4.6)earlyR_0.0.5.zip(r-4.5)
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✨
DESCRIPTION |NEWS
card.svg |card.png
earlyR/json (API)

# 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:

6.66 score 9 stars 113 scripts 239 downloads 3 mentions 2 exports 51 dependencies

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

Target	Result	Time
linux-devel-x86_64	NOTE	147
source / vignettes	OK	183
linux-release-x86_64	NOTE	152
macos-release-arm64	NOTE	121
macos-oldrel-arm64	NOTE	93
windows-devel	NOTE	94
windows-release	NOTE	94
windows-oldrel	NOTE	89
wasm-release	OK	122

Exports:get_R sample_R

Dependencies:aweek cli coarseDataTools coda cpp11 distcrete dplyr EpiEstim epitrix farver fitdistrplus generics ggplot2 glue gridExtra gtable incidence isoband labeling lattice lifecycle magrittr MASS Matrix MatrixModels mcmc MCMCpack pillar pkgconfig plyr purrr quantreg R6 RColorBrewer Rcpp reshape2 rlang S7 scales sodium SparseM stringi stringr survival tibble tidyr tidyselect utf8 vctrs viridisLite withr

Early investigation of infectiousness using earlyR

Rendered fromearlyR.Rmdusingknitr::rmarkdown

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

Help page	Topics
Estimate the Reproduction Number	get_R get_R.default get_R.incidence get_R.integer get_R.numeric
Plot earlyR objects	plot.earlyR points.earlyR
Print method for earlyR objects	print.earlyR
Get a sample of plausible Reproduction Numbers	sample_R

Package: earlyR 0.0.5

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

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)