WhiteLabRt: Novel Methods for Reproduction Number Estimation, Back-Calculation, and Forecasting

A collection of functions related to novel methods for estimating R(t), created by the lab of Professor Laura White. Currently implemented methods include two-step Bayesian back-calculation and now-casting for line-list data with missing reporting delays, adapted in 'STAN' from Li (2021) <doi:10.1371/journal.pcbi.1009210>, and calculation of time-varying reproduction number assuming a flux between various adjacent states, adapted into 'STAN' from Zhou (2021) <doi:10.1371/journal.pcbi.1010434>.

Version:	1.0
Depends:	R (≥ 3.4.0)
Imports:	methods, Rcpp (≥ 0.12.0), RcppParallel (≥ 5.0.1), rstan (≥ 2.18.1), rstantools (≥ 2.4.0)
LinkingTo:	BH (≥ 1.66.0), Rcpp (≥ 0.12.0), RcppEigen (≥ 0.3.3.3.0), RcppParallel (≥ 5.0.1), rstan (≥ 2.18.1), StanHeaders (≥ 2.18.0)
Suggests:	knitr, rmarkdown
Published:	2024-07-31
DOI:	10.32614/CRAN.package.WhiteLabRt
Author:	Chad Milando [aut, cre], Tenglong Li [ctb], Zhenwei Zhou [ctb], Laura White [ctb]
Maintainer:	Chad Milando <cmilando at bu.edu>
License:	MIT + file LICENSE
NeedsCompilation:	yes
SystemRequirements:	GNU make
Language:	en-US
Materials:	README
CRAN checks:	WhiteLabRt results

Documentation:

Reference manual:	WhiteLabRt.pdf
Vignettes:	Backcalculating Reporting Delays Distributions from Linelist Data (source, R code) Spatial R(t) estimation with transfer estimates (source, R code)

Downloads:

Package source:	WhiteLabRt_1.0.tar.gz
Windows binaries:	r-devel: WhiteLabRt_1.0.zip, r-release: WhiteLabRt_1.0.zip, r-oldrel: WhiteLabRt_1.0.zip
macOS binaries:	r-release (arm64): WhiteLabRt_1.0.tgz, r-oldrel (arm64): WhiteLabRt_1.0.tgz, r-release (x86_64): WhiteLabRt_1.0.tgz, r-oldrel (x86_64): WhiteLabRt_1.0.tgz

Linking:

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