Cosinor Rhythmicity Test

Tests whether a rhythm of the given period is present, using the Halberg zero-amplitude F-test (H0: amplitude = 0) on the single-component cosinor fit, and reports the percent rhythm (the proportion of variance the cosinor explains, R^2). It reuses cosinor.analysis as the single fitting engine, so the MESOR/amplitude/acrophase and valid-day gating are identical.

Usage

rhythmicity.test(
  counts,
  timestamps,
  period = 24,
  alpha = 0.05,
  wear_time = NULL,
  min_valid_hours = 10,
  cosinor_result = NULL
)

Arguments

counts

Numeric vector of activity counts (or any activity measure).

timestamps

POSIXct timestamps, one per count.

period

Rhythm period in hours (default 24).

alpha

Significance level for the rhythmic flag (default 0.05).

wear_time

Optional logical wear-time mask passed to the cosinor fit.

min_valid_hours

Minimum valid hours per day for the cosinor fit.

cosinor_result

Optional existing cosinor.analysis result to test without refitting; when supplied, counts/timestamps are ignored.

Value

An object of class actiRhythm_rhythmicity: a list with the F statistic, numerator/denominator degrees of freedom (df1, df2), p_value, percent_rhythm (and r_squared), a logical rhythmic flag, and the cosinor parameters.

References

Nelson W, Tong YL, Lee JK, Halberg F (1979). “Methods for cosinor-rhythmometry.” Chronobiologia, 6(4), 305–323.

Examples

ts <- seq(as.POSIXct("2024-01-01", tz = "UTC"), by = 60, length.out = 1440)
h <- as.numeric(format(ts, "%H"))
counts <- pmax(0, 100 + 80 * cos(2 * pi * (h - 14) / 24))
rhythmicity.test(counts, ts)
#> Cosinor Rhythmicity Test (Halberg zero-amplitude F-test)
#> 
#> H0: amplitude = 0 (no rhythm)
#>   Period:         24 h
#>   F(2, 21):        Inf
#>   P-value:        <1e-300
#>   Percent rhythm: 100.0% (R-squared = 1.0000)
#>   Rhythmic:       YES (alpha = 0.05)