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:	1.0.0
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

Documentation:

Reference manual:	rtestim.html , rtestim.pdf
Vignettes:	Delay-distributions (source, R code) rtestim Package Vignette (source, R code)

Downloads:

Package source:	rtestim_1.0.0.tar.gz
Windows binaries:	r-devel: rtestim_1.0.0.zip, r-release: rtestim_1.0.0.zip, r-oldrel: rtestim_1.0.0.zip
macOS binaries:	r-release (arm64): rtestim_1.0.0.tgz, r-oldrel (arm64): rtestim_1.0.0.tgz, r-release (x86_64): rtestim_1.0.0.tgz, r-oldrel (x86_64): rtestim_1.0.0.tgz

Linking:

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