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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 |
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) |
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 |
Please use the canonical form https://CRAN.R-project.org/package=WhiteLabRt to link to this page.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.