Package: rtestim 1.0.2.9001

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>.

Authors:Daniel J. McDonald [aut, cre, cph], Jiaping Liu [aut], Zhenglun Cai [ctb]

rtestim_1.0.2.9001.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
rtestim/json (API)
NEWS

# Install 'rtestim' in R:
install.packages('rtestim', repos = c('https://dajmcdon.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/dajmcdon/rtestim/issues

Pkgdown/docs site:https://dajmcdon.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • cancovid - Canadian Incident COVID-19 Cases

On CRAN:

Conda:

cpp

6.33 score 8 stars 38 scripts 510 downloads 7 exports 47 dependencies

Last updated from:fa078efe99. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK190
linux-devel-x86_64OK189
source / vignettesOK251
linux-release-arm64OK191
linux-release-x86_64OK205
macos-release-arm64OK140
macos-release-x86_64OK222
macos-oldrel-arm64OK133
macos-oldrel-x86_64OK334
windows-develOK251
windows-releaseOK196
windows-oldrelOK169
wasm-releaseOK154

Exports:confbandconfigure_rt_admmcv_estimate_rtdelay_calculatordiscretize_gammaestimate_rtinterpolate_rt

Dependencies:backportsBHbriocallrcheckmateclicpp11crayondescdiffobjdsplineevaluatefarverfsggplot2gluegtableisobandjsonlitelabelinglatticelifecyclemagrittrMatrixpillarpkgbuildpkgconfigpkgloadpraiseprocessxpsR6RColorBrewerRcppRcppEigenrlangrprojrootS7scalestestthattibbletvdenoisingutf8vctrsviridisLitewaldowithr

rtestim Package Vignette

Rendered fromrtestim.Rmdusingknitr::rmarkdownon May 14 2026.

Last update: 2025-08-06
Started: 2023-07-08