Package: actiRhythm
Type: Package
Title: Circadian Rest-Activity Rhythm Analysis
Version: 0.1.0
Date: 2026-06-21
Authors@R: c(
    person(c("Raymond", "Dacosta"), "Azadda",
           email = "rdazadda@alaska.edu",
           role = c("aut", "cre")),
    person("CEAL Team", role = "aut"),
    person("Stacy", "Rasmus", role = "aut"))
Description: 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.
License: MIT + file LICENSE
URL: https://github.com/rdazadda/actiRhythm,
        https://rdazadda.github.io/actiRhythm/
BugReports: https://github.com/rdazadda/actiRhythm/issues
Language: en-US
Depends: R (>= 4.1)
Imports: DBI, grDevices, ggplot2, Rcpp (>= 1.0.0), Rdpack, RSQLite,
        scales, splines, stats, utils
LinkingTo: Rcpp
RdMacros: Rdpack
Suggests: ActCR, agcounts, cosinor, cosinor2, GGIR, GGIRread, knitr,
        nonlinearTseries, nparACT, openxlsx, pracma, read.gt3x,
        rmarkdown, testthat (>= 3.0.0)
SystemRequirements: C++17
VignetteBuilder: knitr
Encoding: UTF-8
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
NeedsCompilation: yes
Packaged: 2026-07-19 18:02:20 UTC; rdazadda
Author: Raymond Dacosta Azadda [aut, cre],
  CEAL Team [aut],
  Stacy Rasmus [aut]
Maintainer: Raymond Dacosta Azadda <rdazadda@alaska.edu>
Repository: CRAN
Date/Publication: 2026-07-29 16:40:34 UTC
Built: R 4.6.1; x86_64-w64-mingw32; 2026-09-02 03:45:08 UTC; windows
Archs: x64
