R Observatory: Metrics for rtestim version 1.0.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

rtestim

1.0.2Package record

Estimate the Effective Reproductive Number with Trend Filtering

0packages depend

4.1Kdownloads / year

52.3%test coverage

13/13flavors OK

Overview

About

Maintained by Daniel J. McDonaldCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("rtestim", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("dajmcdon/rtestim")

Development version from dajmcdon/rtestim. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-rtestim

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-rtestim

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-rtestim

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 4.2 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
WARNING12 OK, 1 WARNING2026-06-08
OK13 OK2026-05-02

Show 3 earlier changesHide 3 earlier changes

NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.2

READMEYes · 181 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.0.2Citation fileNoWebsiteYes · pkgdown

The repository also keeps web-only articles.

Help pages: 14
Examples that run: 100%13 run in a plain check
Exported functions with examples: 100%
Documented parameters: 93%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

rtestim Package Vignette HTML

How these are measured

Downloads

4.1K

CRAN downloads in the past year

Rank #10,778 · ~11/day · ~339/mo

Releases R versions

Daily download trend is not available in this view yet.

33030 days

97590 days

4.1K1 year

Compare downloads with other packages →

Also on360 r2u2 autocran

How downloads are counted

Repository

dajmcdon/rtestim ↗Account: dajmcdon

8Stars

2Forks

1Open issues

0Open PRs

3Releases

422Commits

17Commit identities

422 commits · Last activity 2026-05-14 · 0% stars, 30d · Default branch at 1.0.2.9001, ahead of CRAN 1.0.2 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 91%
Median days to close, 50 most recently updated closed issues: 38
Median days to close, 50 most recently updated closed PRs: 3

Stars over time

2025-10-22 · 72026-07-07 · 8

How these are measured

PracticesBeta

10 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/dajmcdon/rtestim on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (1)

CODEOWNERS

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-05-14 · The repository has a site deploy workflow

pkgdown site last built 2026-05-14

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 2 practices

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

22 external dependencies (excludes base and recommended)

Installing rtestim adds 46 packages (23 with compiled code, 39 MB of source tarballs). Heaviest: BH 14 MB, ggplot2 6.0 MB, Rcpp 1.8 MB.

Depends (1)

R >= 3.6.2

Imports (11)

checkmate cli dspline ggplot2MatrixmethodsRcpp rlang tibble tvdenoising vctrs

LinkingTo (6)

BH dspline Rcpp RcppEigen testthat tvdenoising

Suggests (8)

dplyr forcats knitrnnetrmarkdown testthat tidyr xml2

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Daniel J. McDonald

Jiaping Liu

Author

Zhenglun Cai

Contributor

Releases (3)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.0.2Latest
record
2026-03-11 · current release · diff ↗
1.0.1
record
2025-10-24 · diff ↗
1.0.0
record
2025-07-05
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-07-05
Total releases: 3 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.6.2
Bundled data: 5.0 KB / 1 file
Download size: 1.0 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("rtestim")

Format

McDonald, D. J., Cai, Z., & Liu, J. (2026). rtestim: Estimate the Effective Reproductive Number with Trend Filtering (Version 1.0.2) [Computer software]. https://doi.org/10.32614/CRAN.package.rtestim

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for rtestim version 1.0.2 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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