Use trend filtering, a type of regularized nonparametric regression, to estimate the instantaneous reproduction number, also called Rt. This value roughly says how many new infections will result from each new infection today. Values larger than 1 indicate that an epidemic is growing while those less than 1 indicate decline. For more details about this methodology, see Liu, Cai, Gustafson, and McDonald (2024) <doi:10.1371/journal.pcbi.1012324>.
| Version: | 1.0.0 |
| Depends: | R (≥ 3.6.2) |
| Imports: | checkmate, cli, dspline, ggplot2, Matrix, methods, Rcpp, rlang, tibble, tvdenoising, vctrs |
| LinkingTo: | BH, dspline, Rcpp, RcppEigen, testthat, tvdenoising |
| Suggests: | dplyr, forcats, knitr, nnet, rmarkdown, testthat (≥ 3.0.0), tidyr, xml2 |
| Published: | 2025-07-05 |
| DOI: | 10.32614/CRAN.package.rtestim |
| Author: | Daniel J. McDonald [aut, cre, cph], Jiaping Liu [aut], Zhenglun Cai [ctb] |
| Maintainer: | Daniel J. McDonald <daniel at stat.ubc.ca> |
| BugReports: | https://github.com/dajmcdon/rtestim/issues |
| License: | MIT + file LICENSE |
| URL: | https://github.com/dajmcdon/rtestim, https://dajmcdon.github.io/rtestim/ |
| NeedsCompilation: | yes |
| Materials: | README NEWS |
| CRAN checks: | rtestim results |
| Reference manual: | rtestim.pdf |
| Vignettes: |
Delay-distributions (source, R code) rtestim Package Vignette (source, R code) |
| Package source: | rtestim_1.0.0.tar.gz |
| Windows binaries: | r-devel: not available, r-release: not available, r-oldrel: not available |
| macOS binaries: | r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): rtestim_1.0.0.tgz, r-oldrel (x86_64): rtestim_1.0.0.tgz |
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