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Calculate Summary Measures from Raw Accelerometer Data

Source: R/calculate_ac.R, R/calculate_measures.R
calculate_measures.Rd

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)
#> Input is a .gt3x file, unzipping to a temporary location first...
#> Unzipping gt3x data to /tmp/RtmpsiCePd
#> 1/1 
#> Unzipping /home/runner/work/_temp/Library/SummarizedActigraphy/extdata/TAS1H30182785_2019-09-17.gt3x
#>  === info.txt, log.bin extracted to /tmp/RtmpsiCePd/TAS1H30182785_2019-09-17
#> GT3X information
#>  $ Serial Number     :"TAS1H30182785"
#>  $ Device Type       :"Link"
#>  $ Firmware          :"1.7.2"
#>  $ Battery Voltage   :"4.18"
#>  $ Sample Rate       :100
#>  $ Start Date        : POSIXct, format: "2019-09-17 18:40:00"
#>  $ Stop Date         : POSIXct, format: "2019-09-18 19:00:00"
#>  $ Last Sample Time  : POSIXct, format: "2019-09-17 19:20:05"
#>  $ TimeZone          :"-04:00:00"
#>  $ Download Date     : POSIXct, format: "2019-09-17 19:20:05"
#>  $ Board Revision    :"8"
#>  $ Unexpected Resets :"0"
#>  $ Acceleration Scale:256
#>  $ Acceleration Min  :"-8.0"
#>  $ Acceleration Max  :"8.0"
#>  $ Subject Name      :"suffix_85"
#>  $ Serial Prefix     :"TAS"
#> Parsing GT3X data via CPP.. expected sample size: 240500
#> ---GT3X PARAMETERS
#> address: 0 key: 6 value: 1
#> address: 0 key: 7 value: 54703161
#> address: 0 key: 8 value: 8
#> address: 0 key: 9 value: 1534154836
#> address: 0 key: 13 value: 17235970
#> address: 0 key: 16 value: 3791650816
#> address: 0 key: 20 value: 0
#> address: 0 key: 21 value: 0
#> address: 0 key: 22 value: 0
#> address: 0 key: 23 value: 0
#> address: 0 key: 26 value: 2
#> address: 0 key: 28 value: 262013
#> address: 0 key: 29 value: 255
#> address: 0 key: 32 value: 16908288
#> address: 0 key: 37 value: 1024
#> address: 0 key: 38 value: 0
#> address: 0 key: 49 value: 2048
#> address: 0 key: 50 value: 88181047
#> address: 0 key: 51 value: 6.82667
#> address: 0 key: 55 value: 256
#> address: 0 key: 57 value: 333.87
#> address: 0 key: 58 value: 21
#> address: 0 key: 61 value: 2
#> address: 1 key: 0 value: 0
#> address: 1 key: 1 value: 872668711
#> address: 1 key: 2 (features)  value: 388
#> address: 1 key: 3 value: 1
#> address: 1 key: 4 value: 4294967131
#> address: 1 key: 5 value: 4294967095
#> address: 1 key: 6 value: 4294967149
#> address: 1 key: 7 value: 298
#> address: 1 key: 8 value: 286
#> address: 1 key: 9 value: 300
#> address: 1 key: 10 value: 100
#> address: 1 key: 12 (start time)  value: 1568745600
#> address: 1 key: 13 value: 1568833200
#> address: 1 key: 14 value: 1568745556
#> address: 1 key: 15 value: 74
#> address: 1 key: 16 value: 40
#> address: 1 key: 17 value: 72
#> address: 1 key: 20 value: 0
#> address: 1 key: 21 value: 0
#> address: 1 key: 33 value: 60000
#> address: 1 key: 34 value: 4294965247
#> address: 1 key: 35 value: 4294965190
#> address: 1 key: 36 value: 4294965237
#> address: 1 key: 37 value: 2051
#> address: 1 key: 38 value: 2000
#> address: 1 key: 39 value: 2048
#> address: 1 key: 40 value: 0
#> address: 1 key: 41 value: 1
#> address: 1 key: 42 value: 0
#> address: 1 key: 43 value: 4294967283
#> address: 1 key: 44 value: 0
#> address: 1 key: 45 value: 0
#> address: 1 key: 46 value: 0
#> ---END PARAMETERS
#> 
#> Activity with Sample Size of 0
#> payload start: 1568747741
#> total_records: 214100
#> max_samples: 240500
#> Activity with Sample Size of 0
#> payload start: 1568747759
#> total_records: 215900
#> max_samples: 240500
#> Total Records: 216000
#> Scaling...
#> Creating dimnames 
#> CPP returning 
#> Done (in 0.496452808380127 seconds)
measures = calculate_measures(res, dynamic_range = NULL,
calculate_mims = FALSE)
#> Fixing Zeros with fix_zeros
#> Flagging data
#> Flagging Spikes
#> Flagging Interval Jumps
#> Flagging Spikes at Second-level
#> Flagging Repeated Values
#> Flagging Device Limit Values
#> Flagging Zero Values
#> Flagging 'Impossible' Values
#> Calculating ai0
#> Calculating MAD
#> Joining AI and MAD
#> Calculating AC
#> Calculating Axis-Specific Activity Counts
#> Summing up Axes
#> Joining AC
#> Joining flags
auc = calculate_auc(res)
#> Absolute values
#> Calculting trapezoids
#> Replacing first value as NA
#> Calculating AUCs
# \donttest{
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)
}
#> Fixing Zeros with fix_zeros
#> Calculating ai0
#> Calculating MAD
#> Joining AI and MAD
#> Calculating AC
#> Calculating Axis-Specific Activity Counts
#> Summing up Axes
#> Joining AC