flag_spike: Flag Spikes

In muschellij2/SummarizedActigraphy: Coerce 'Actigraphy' to Summarized Experiments

Flag Spikes

Description

Flag Spikes

Usage

flag_spike(df, spike_size = 11)

flag_interval_jump(df, verbose = FALSE)

flag_spike_second(df, spike_size = 11)

flag_device_limit(df, dynamic_range = NULL, epsilon = 0.05)

flag_contiguous_device_limit(df, dynamic_range = NULL, epsilon = 0.05)

flag_same_value(df, min_length = 1)

flag_all_zero(df, min_length = 3)

flag_impossible(df, min_length = 6)

Arguments

df	A data set of actigraphy
spike_size	size of "spike" - which is the absolute difference in contiguous observations on a single axis
verbose	print diagnostic messages
dynamic_range	dynamic range of the device, used to find the device limit.
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 = 3', then at least 3 'TRUE's in a row is required, any stretches of single 'TRUE' values or 2 'TRUE' followed by 'FALSE', will be set to 'FALSE'.

Value

A data set back

Note

'flag_spike' looks if 2 contiguous values, within each axis, are larger than a absolute size ('11' gravity units). The 'flag_spike_second' function groups the data by second, finds the range of values, within each axis, and determines if this range is greater than a specified size ('11' g).

Source

https://wwwn.cdc.gov/Nchs/Nhanes/2011-2012/PAXMIN_G.htm

Examples

file = system.file("extdata", "TAS1H30182785_2019-09-17.gt3x",
package = "SummarizedActigraphy")
res = read_actigraphy(file)
res = flag_spike(res)
res = flag_interval_jump(res)
res = flag_spike_second(res)
res = flag_same_value(res)
res = flag_device_limit(res)
res = flag_all_zero(res)
res = flag_impossible(res)

muschellij2/SummarizedActigraphy documentation built on Aug. 12, 2024, 5:35 p.m.