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Flag Spikes

Source: R/flag_spike.R
acti_flag_spike.Rd

Flag Spikes

Usage

acti_flag_spike(data, spike_size = 11, sample_rate = NULL, by_axis = FALSE)

acti_flag_interval_jump(
  data,
  verbose = TRUE,
  window_seconds = 1,
  min_repeats = 10,
  min_distinct = 3,
  min_separation = 0.5,
  by_axis = FALSE,
  digits = 3,
  chunk_windows = 50000L
)

acti_flag_spike_second(
  data,
  spike_size = 11,
  window_seconds = 1,
  min_spikes = 13,
  max_change_seconds = 0.1,
  sample_rate = NULL,
  by_axis = FALSE
)

acti_flag_device_limit(data, dynamic_range = NULL, epsilon = 0.05)

acti_flag_adjacent_device_limit_samples(
  data,
  dynamic_range = NULL,
  epsilon = 0.05,
  sample_rate = NULL
)

acti_flag_contiguous_device_limit(
  data,
  dynamic_range = NULL,
  epsilon = 0.05,
  sample_rate = NULL
)

acti_flag_same_value(data, min_length = 1, sample_rate = NULL)

acti_flag_all_zero(data, min_length = 3, sample_rate = NULL)

acti_flag_impossible(
  data,
  min_length = 7,
  change_threshold = 0.01,
  magnitude_threshold = 1.25,
  sample_rate = NULL,
  dynamic_range = NULL
)

Arguments

data

A data set of actigraphy

spike_size

size of "spike" - which is the absolute difference in contiguous observations on a single axis

sample_rate

Sampling frequency; extracted from data when omitted.

by_axis

If TRUE, also return one indicator per axis.

verbose

print diagnostic messages

window_seconds

Width of each window used by acti_flag_spike_second.

min_repeats

Minimum occurrences of an axis value in a window.

min_distinct

Minimum number of frequent axis values required.

min_separation

Minimum separation between retained values.

digits

Number of decimal places used when grouping axis values.

chunk_windows

Number of windows processed together to bound memory.

min_spikes

Minimum number of qualifying extrema in a window.

max_change_seconds

Maximum time between an extremum and a qualifying large change; the CDC rule uses less than 0.1 seconds.

dynamic_range

Device dynamic range. When omitted, it is read from the data with get_dynamic_range(); data-based estimates are rejected.

epsilon

A small adjustment so that if values are within the device limit, but minus epsilon, still flagged as hitting the limit. For example, if dynamic_range = c(-6, 6) and epsilon = 0.05, then any value <= -5.95 or >= 5.95 gravity units will be flagged

min_length

minimum length of the condition for contiguous samples. If min_length = 7, then at least 7 TRUEs in a row is required, any stretches of single TRUE values or 2 TRUE followed by FALSE, will be set to FALSE.

change_threshold

Maximum absolute change between adjacent samples on each axis for a stable run to qualify. The default is 0.01 g.

magnitude_threshold

Minimum vector magnitude required at both ends of each stable adjacent pair. The default is 1.25 g.

Value

A data set back

Details

These functions provide configurable sample-level and window-level signal indicators. Thresholds and run or window lengths are arguments; they do not encode a specific device or study's quality-control scheme. When continuity is checked, sample_rate is extracted with get_sample_rate() unless supplied explicitly.

Note

acti_flag_spike compares adjacent observations by axis. The acti_flag_spike_second checks for repeated local extrema followed by a large change within the requested time, then counts them within each window.

Examples

res = acti_raw_data
res = acti_flag_spike(res)
res = acti_flag_interval_jump(res)
#> Processed X windows 2405 of 2405
#> Processed Y windows 2405 of 2405
#> Processed Z windows 2405 of 2405
res = acti_flag_spike_second(res)
res = acti_flag_same_value(res)
res = acti_flag_device_limit(res)
res = acti_flag_all_zero(res)
res = acti_flag_impossible(res)