Calculate Summary Measures from Raw Accelerometer Data

Usage

acti_calculate_measures(
  data,
  unit = "1 min",
  fix_zeros = TRUE,
  dynamic_range = NULL,
  calculate_mims = TRUE,
  calculate_ac = TRUE,
  flag_data = TRUE,
  flags = NULL,
  ensure_all_time = TRUE,
  verbose = TRUE,
  sample_rate = NULL,
  ...
)

acti_calculate_ai(
  data,
  unit = "1 min",
  ensure_all_time = TRUE,
  verbose = FALSE
)

acti_calculate_activity_index(
  data,
  unit = "1 min",
  ensure_all_time = TRUE,
  verbose = FALSE
)

acti_calculate_flags(data, unit = "1 min", ensure_all_time = TRUE)

acti_calculate_n_idle(data, unit = "1 min", ensure_all_time = TRUE)

acti_calculate_enmo(...)

acti_calculate_ai_defined(...)

acti_calculate_mad(
  data,
  unit = "1 min",
  ensure_all_time = TRUE,
  verbose = FALSE
)

acti_calculate_auc(
  data,
  unit = "1 min",
  sample_rate = NULL,
  allow_truncation = FALSE,
  ensure_all_time = TRUE,
  verbose = TRUE
)

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

acti_calculate_mims(
  data,
  unit = "1 min",
  dynamic_range = c(-6, 6),
  ensure_all_time = TRUE,
  ...
)

Arguments

data: An object with columns `X`, `Y`, and `Z` or an object of class `AccData`
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 `lubridate::period()` constructor are allowed.
fix_zeros: Should `actibase::acti_fill_zeros()` be run before calculating the measures?
dynamic_range: Dynamic range of the device, in gravity units
calculate_mims: Should MIMS units be calculated?
calculate_ac: Should Activity Counts from the `agcounts` package be calculated?
flag_data: Should the downstream overlay `flag_qc()` be run? It will be executed after `fix_zeros` before any measure calculation
flags: the flags to calculate, passed to the downstream overlay `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
verbose: print diagnostic messages
sample_rate: sample rate of data, if not specified in header of object
...: additional arguments to pass to `MIMSunit::mims_unit()`
allow_truncation: truncate small values

Value

A data set with the calculated features

Examples

file = actiread::acti_example_gt3x()
res = actiread::acti_read_gt3x(file, verbose = FALSE)
res = res[1:12000, ]
measures = acti_calculate_measures(
  res,
  dynamic_range = NULL,
  calculate_mims = FALSE,
  calculate_ac = FALSE,
  flag_data = FALSE
)
#> Fixing Zeros with fix_zeros
#> Calculating ai0
#> Calculating MAD
#> Joining AI and MAD
auc = acti_calculate_auc(res)
#> Absolute values
#> Calculting trapezoids
#> Replacing first value as NA
#> Calculating AUCs
# \donttest{
mims = acti_calculate_mims(res, dynamic_range = NULL)
#> Warning: NAs introduced by coercion
#> Error in check_dynamic_range(data, dynamic_range = dynamic_range): length(dynamic_range) == 2 is not TRUE
# }
if (requireNamespace("data.table", quietly = TRUE)) {
   dt = data.table::as.data.table(res)
   out = acti_calculate_measures(dt, calculate_mims = FALSE, flag_data = FALSE,
     calculate_ac = FALSE)
}
#> Fixing Zeros with fix_zeros
#> Calculating ai0
#> Calculating MAD
#> Joining AI and MAD