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.
