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
Roxygen: list(markdown = TRUE)
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
Repository: https://rdazadda.r-universe.dev
Date/Publication: 2026-08-28 07:39:32 UTC
RemoteUrl: https://github.com/rdazadda/actirhythm
RemoteRef: HEAD
RemoteSha: c824a1b67e63184c4f927b88b859834e3407a0d2
NeedsCompilation: yes
Packaged: 2026-09-27 11:21:37 UTC; root
Author: Raymond Dacosta Azadda [aut, cre],
  CEAL Team [aut],
  Stacy Rasmus [aut]
Maintainer: Raymond Dacosta Azadda <rdazadda@alaska.edu>