calculate_measures: Calculate Summary Measures from Raw Accelerometer Data

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

Calculate Summary Measures from Raw Accelerometer Data

Description

Calculate Summary Measures from Raw Accelerometer Data

Usage

calculate_activity_counts(
  df,
  sample_rate = NULL,
  unit = "1 min",
  verbose = TRUE,
  ...
)

calculate_ac(df, sample_rate = NULL, unit = "1 min", verbose = TRUE, ...)

calculate_measures(
  df,
  unit = "1 min",
  fix_zeros = TRUE,
  fill_in = TRUE,
  by_second = FALSE,
  trim = FALSE,
  dynamic_range = NULL,
  calculate_mims = TRUE,
  calculate_ac = TRUE,
  flag_data = TRUE,
  flags = NULL,
  ensure_all_time = TRUE,
  verbose = TRUE,
  sample_rate = NULL,
  ...
)

calculate_ai(df, unit = "1 min", ensure_all_time = TRUE, verbose = FALSE)

calculate_activity_index(
  df,
  unit = "1 min",
  ensure_all_time = TRUE,
  verbose = FALSE
)

calculate_flags(df, unit = "1 min", ensure_all_time = TRUE)

calculate_n_idle(df, unit = "1 min", ensure_all_time = TRUE)

calculate_enmo(...)

calculate_ai_defined(...)

calculate_mad(df, unit = "1 min", ensure_all_time = TRUE, verbose = FALSE)

get_sample_rate(df, sample_rate = NULL)

calculate_auc(
  df,
  unit = "1 min",
  sample_rate = NULL,
  allow_truncation = FALSE,
  ensure_all_time = TRUE,
  verbose = TRUE
)

calculate_fast_mims(
  df,
  unit = "1 min",
  dynamic_range = NULL,
  sample_rate = NULL,
  allow_truncation = TRUE,
  ensure_all_time = TRUE,
  verbose = TRUE,
  ...
)

calculate_mims(
  df,
  unit = "1 min",
  dynamic_range = c(-6, 6),
  ensure_all_time = TRUE,
  ...
)

Arguments

df	An object with columns 'X', 'Y', and 'Z' or an object of class 'AccData'
sample_rate	sample rate of data, if not specified in header of object
unit	length of time to calculate measures over. a character string specifying a time unit or a multiple of a unit to be rounded to. Valid base units are 'second', 'minute', 'hour', 'day', 'week', 'month', 'bimonth', 'quarter', 'season', 'halfyear', and 'year'. Arbitrary unique English abbreviations as in the period constructor are allowed.
verbose	print diagnostic messages
...	additional arguments to pass to [MIMSunit::mims_unit]
fix_zeros	Should fix_zeros be run before calculating the measures?
fill_in	if fix_zeros = TRUE, should the zeros be filled in with the last
by_second	Should the last observation carried forward be done only within the same second?
trim	if fix_zeros = TRUE, should the time course be trimmed for zero values at the beginning and the end of the time course? observation carried forward?
dynamic_range	Dynamic range of the device, in gravity units
calculate_mims	Should MIMS units be calculated?
calculate_ac	Should Activity Counts from the activityCounts package be calculated?
flag_data	Should [SummarizedActigraphy::flag_qc()] be run? It will be executed after fix_zeros before any measure calculation
flags	the flags to calculate, passed to [SummarizedActigraphy::flag_qc()]
ensure_all_time	if TRUE, then all times from the first to last times will be in the output, even if data during that time was not in the input
allow_truncation	truncate small values

Value

A data set with the calculated features

Examples

file = system.file("extdata", "TAS1H30182785_2019-09-17.gt3x",
package = "SummarizedActigraphy")
res = read_actigraphy(file)
measures = calculate_measures(res, dynamic_range = NULL,
calculate_mims = FALSE)
auc = calculate_auc(res)

mims = calculate_mims(res, dynamic_range = NULL)

if (requireNamespace("data.table", quietly = TRUE)) {
   dt = data.table::as.data.table(res$data)
   out = calculate_measures(dt, calculate_mims = FALSE, flag_data = FALSE)
}

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