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Detect main sleep periods using the Crespo algorithm

Source: R/sleep_periods.R
detect_sleep_crespo.Rd

Identifies the main sleep period(s) in an actigraphy recording using the algorithm described in Crespo et al. (2012). The method applies an adaptive median filter to the activity signal, mitigates spuriously long zero runs, and thresholds the result at a quantile of the filtered signal. Morphological closing and opening operations are then used to smooth the binary sleep/wake estimate.

Usage

detect_sleep_crespo(
  x,
  epoch_h = NULL,
  median_filter_h = 8,
  pad_h = 1,
  sleep_quantile = 1/3,
  morph_size = 61L,
  consec_zeros_thr = 15L,
  awake_zeros_thr = 2L,
  sleep_zeros_thr = 30L,
  zero_mitigation_q = 0.33,
  min_short_window_thr = 1
)

Arguments

x

A tibble as returned by detect_offwrist_bimodal() (or prepare_actigraphy() if off-wrist detection is skipped), containing columns datetime, activity, and state.

epoch_h

numeric(1). Number of epochs per hour. If NULL (default), estimated automatically from the median inter-epoch interval in datetime.

median_filter_h

numeric(1). Length of the preprocessing median filter window in hours. Default is 8.

pad_h

numeric(1). Padding length in hours added before the adaptive median filter. Default is 1.

sleep_quantile

numeric(1). Quantile of the filtered activity used as the sleep/wake threshold. Default is 1/3.

morph_size

integer(1). Size of the structuring element used in morphological closing/opening. Default is 61 epochs.

consec_zeros_thr

integer(1). Runs of zeros longer than this threshold are treated as invalid (zero mitigation). Default is 15.

awake_zeros_thr

integer(1). Threshold for consecutive zeros within wake periods. Default is 2.

sleep_zeros_thr

integer(1). Threshold for consecutive zeros within sleep periods. Default is 30.

zero_mitigation_q

numeric(1). Quantile of activity used to determine the mitigation level for invalid zero runs. Default is 0.33.

min_short_window_thr

numeric(1). Minimum value of the adaptive median threshold; if the fitted quantile falls below this, the threshold is clamped here. Default is 1.0.

Value

The input tibble x with state and sleep columns updated. Sleep epochs have state == 1 and sleep == 1; off-wrist epochs (state == 4) are preserved and excluded from the sleep column.

References

Crespo, C., Aboy, M., Fernández, J. R., & Mojón, A. (2012). Automatic identification of activity-rest periods based on actigraphy. Journal of Medical and Biological Engineering, 32(4), 249–256. doi:10.5405/jmbe.1033

See also

detect_naps_crespo() for secondary sleep period (nap) detection.

Examples

if (FALSE) { # \dontrun{
rec  <- read_acttrust("recordings/P001.txt")
prep <- prepare_actigraphy(rec)
prep <- detect_offwrist_bimodal(prep)
prep <- detect_sleep_crespo(prep)
} # }