R Observatory: Metrics for actiRhythm version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

actiRhythm

0.1.0

Circadian Rest-Activity Rhythm Analysis

0packages depend

184downloads / year

67.9%test coverage

11/13checks pass

Overview

About

Maintained by Raymond Dacosta AzaddaFirst published 2026-07-291 releasesCRAN page ↗GitHub ↗

Quantifies the circadian rest-activity rhythm, the roughly 24-hour cycle of activity and rest, from activity counts and raw accelerometer recordings. Analyses run on an activity-count vector and its timestamps, and a built-in reader loads 'ActiGraph' '.agd' files (an 'SQLite' database) directly. Computes nonparametric metrics (interdaily stability (IS) and intradaily variability (IV) following Witting et al. (1990) doi:10.1016/0006-3223(90)90523-5; relative amplitude (RA), the least-active 5-hour window (L5), and the most-active 10-hour window (M10) following Van Someren et al. (1999) doi:10.3109/07420529908998724), cosinor models with a rhythmicity test, confidence ellipses, population-mean cosinor, and two-group parameter comparison (Cornelissen (2014) doi:10.1186/1742-4682-11-16; Marler et al. (2006) doi:10.1002/sim.2466), period estimation by Lomb-Scargle (Lomb (1976) doi:10.1007/BF00648343; Scargle (1982) doi:10.1086/160554) and chi-square (Sokolove and Bushell (1978) doi:10.1016/0022-5193(78)90022-X) periodograms with bootstrap confidence intervals and a sliding-window spectrogram, fractal and nonlinear measures (Peng et al. (1994) doi:10.1103/PhysRevE.49.1685; Kantelhardt et al. (2002) doi:10.1016/S0378-4371(02)01383-3), the Sleep Regularity Index (Phillips et al. (2017) doi:10.1038/s41598-017-03171-4), social jet lag, rest-activity state transitions, and locomotor inactivity during sleep (Winnebeck et al. (2018) doi:10.1016/j.cub.2017.11.063). It also reads raw accelerometer files ('ActiGraph' '.gt3x', 'Axivity' '.cwa', 'GENEActiv' '.bin'), auto-calibrates them (van Hees et al. (2014) doi:10.1152/japplphysiol.00421.2014), and derives the ENMO, MAD, and z-angle metrics with diary-free sleep-period detection (van Hees et al. (2018) doi:10.1038/s41598-018-31266-z), cross-checked against 'GGIR'. A batch mode runs the analysis over a folder of files and writes a multi-sheet 'Excel' workbook.

Install

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

install.packages("actiRhythm", 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("rdazadda/actiRhythm")

Development version from rdazadda/actiRhythm. 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-actirhythm

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-actiRhythm

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-actiRhythm

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-oldrel-macos-arm64
NOTE r-release-macos-arm64

Slowest check: 17.0 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.27

67.9%

Coverage · measured lines

100%

Documentation · exports

10

Dependencies · direct

Check history

NOTE2026-07-31
6 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-07-30
5 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 1,113 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 60%
Documented parameters: 95%
Return-value docs: 100%
References docs: 60%

Downloads

184

CRAN downloads in the past year

Rank #24,432 · ~1/day · ~15/mo

Releases R versions

Daily download trend is not available in this view yet.

18430 days

18490 days

1841 year

Compare downloads with other packages →

Also on7 r2u2 autocran

Repository

GitHub ↗ rdazadda/actirhythm

0Stars

0Forks

0Open issues

0Open PRs

0Releases

Last activity 2026-07-18

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/rdazadda/actirhythm on 2026-08-09.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1

Imports (10)

DBIgrDevicesggplot2 Rcpp Rdpack RSQLite scalessplinesstatsutils

LinkingTo (1)

Rcpp

Suggests (14)

ActCR agcounts cosinor cosinor2 GGIR GGIRread knitr nonlinearTseries nparACT openxlsx pracma read.gt3x rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Raymond Dacosta Azadda

Author, Maintainer

Authors (3)

Raymond Dacosta Azadda

Author, Maintainer

CEAL Team

Author

Stacy Rasmus

Author

Listed in earlier versions (1)

Raymond Dacosta

no longer listed · 0.1.0

Package Timeline

1 release. R releases are shown for context.

0.1.0Latest
2026-07-29 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-07-29
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("actiRhythm")

Format

Azadda, R. D., CEAL Team, & Rasmus, S. (2026). actiRhythm: Circadian Rest-Activity Rhythm Analysis (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.actiRhythm

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 actiRhythm version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-08-11. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-11, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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