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: | 1.0.1 |
| 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: | 2024-08-16 |
| 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_1.0.1.tar.gz |
| Windows binaries: | r-devel: WhiteLabRt_1.0.1.zip, r-release: WhiteLabRt_1.0.1.zip, r-oldrel: WhiteLabRt_1.0.1.zip |
| macOS binaries: | r-release (arm64): WhiteLabRt_1.0.1.tgz, r-oldrel (arm64): WhiteLabRt_1.0.1.tgz, r-release (x86_64): WhiteLabRt_1.0.1.tgz, r-oldrel (x86_64): WhiteLabRt_1.0.1.tgz |
| Old sources: | WhiteLabRt archive |
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