rtestim: Estimate the Effective Reproductive Number with Trend Filtering
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: |
1.0.2 |
| 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: |
2026-03-11 |
| 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 |
Documentation:
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