rtestim: Estimate the Effective Reproductive Number with Trend Filtering (original) (raw)
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 |
| BugReports: | https://github.com/dajmcdon/rtestim/issues |
| License: | MIT + file |
| URL: | https://github.com/dajmcdon/rtestim,https://dajmcdon.github.io/rtestim/ |
| NeedsCompilation: | yes |
| Materials: | README, NEWS |
| CRAN checks: | rtestim results |
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