actiRhythm: Circadian Rest-Activity Rhythm Analysis

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.

Version:	0.1.0
Depends:	R (≥ 4.1)
Imports:	DBI, grDevices, ggplot2, Rcpp (≥ 1.0.0), Rdpack, RSQLite, scales, splines, stats, utils
LinkingTo:	Rcpp
Suggests:	ActCR, agcounts, cosinor, cosinor2, GGIR, GGIRread, knitr, nonlinearTseries, nparACT, openxlsx, pracma, read.gt3x, rmarkdown, testthat (≥ 3.0.0)
Published:	2026-07-29
DOI:	10.32614/CRAN.package.actiRhythm (may not be active yet)
Author:	Raymond Dacosta Azadda [aut, cre], CEAL Team [aut], Stacy Rasmus [aut]
Maintainer:	Raymond Dacosta Azadda <rdazadda at alaska.edu>
BugReports:	https://github.com/rdazadda/actiRhythm/issues
License:	MIT + file LICENSE
URL:	https://github.com/rdazadda/actiRhythm, https://rdazadda.github.io/actiRhythm/
NeedsCompilation:	yes
SystemRequirements:	C++17
Language:	en-US
Citation:	actiRhythm citation info
Materials:	README
CRAN checks:	actiRhythm results

Documentation:

Reference manual:	actiRhythm.html , actiRhythm.pdf
Vignettes:	Getting started with actiRhythm (source, R code) Output codebook (metrics data dictionary) (source, R code)

Downloads:

Package source:	actiRhythm_0.1.0.tar.gz
Windows binaries:	r-devel: not available, r-release: actiRhythm_0.1.0.zip, r-oldrel: not available
macOS binaries:	r-release (arm64): actiRhythm_0.1.0.tgz, r-oldrel (arm64): actiRhythm_0.1.0.tgz, r-release (x86_64): actiRhythm_0.1.0.tgz, r-oldrel (x86_64): actiRhythm_0.1.0.tgz

Linking:

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