read.gt3x

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The read.gt3x R package implements a high performance C++ parser for ActiGraph’s .gt3x data format. Read the binary accelerometer data (.gt3x) into an R data frame in a few seconds.

ActiGraph accelerometers

ActiGraph’s wearable accelerometer devices (e.g. GT9X Link) are used by both individuals and researchers to track movement. The devices measures proper acceleration in three directions: X (right-left), Y (forward-backward), Z (up-down). The measurement unit is the gravitational unit, g = 9.81m/s2

Data from the wearable ActiGraph devices is usually extracted and analyzed via a software called ActiLife. When data is extracted from the wearable ActiGraph device, it is saved as a .gt3x file. A gt3x file is a zip archive with two files: - info.txt
- log.bin

The log.bin file is a binary file which includes the raw activity samples, written to the wearable device during usage. The format of the binary file is described in detail in the GT3X github repository. info.txt is a simple text file with meta information related to the device.

Motivation for the package

ActiLife software provides a “Raw to Raw” import option, which reads the activity samples from a .gt3x file and writes them to a .csv file. However, this can be slow and the csv files can be large compared to the binary .gt3x format. Also, according to ActiGraph’s customer support, “A raw file exported via ActiLife is run through a proprietary band pass filter that will exclude movement considered outside of the human spectrum”, which might not be desirable for a researcher.

This package makes it easier and faster to read the raw accelerometer samples into R after extracting the data from the wearable device. No modification is done to the raw data. The package implements an efficient C++ parser which reads activity samples directly from the binary log.bin file inside the .gt3x archive. This allows for

Installation

You can install the read.gt3x package from GitHub, using the remotes package (available in CRAN).

remotes::install_github("THLfi/read.gt3x")

Basic usage

The read.gt3x package includes two sample .gt3x files which can be used to demonstrate reading the data.

library(read.gt3x)

First we need the path to a single gt3x file. We have one file included in the package:

gt3xfile <-
  system.file(
    "extdata", "TAS1H30182785_2019-09-17.gt3x",
    package = "read.gt3x")

And you can download larger and more extensive gt3x files if desired:

gt3xfile <- gt3x_datapath(1)

The read.gt3x() function can take as input a path to a single .gt3x file and will then read activity samples as an R matrix with three columns: X,Y,Z.

X <- read.gt3x(gt3xfile)
head(X)
#> Sampling Rate: 100Hz
#> Firmware Version: 1.7.2
#> Serial Number Prefix: TAS
#>          X      Y     Z
#> [1,] 0.000  0.008 0.996
#> [2,] 0.016  0.000 1.008
#> [3,] 0.020 -0.008 1.004
#> [4,] 0.016 -0.012 1.012
#> [5,] 0.016 -0.008 1.008
#> [6,] 0.008 -0.008 1.008
head(attributes(X)$time_index)
#> [1] 0 1 2 3 4 5
attributes(X)[setdiff(names(attributes(X)), c("dim", "dimnames", "time_index"))]
#> $missingness
#>                           time n_missing
#> 1568745610 2019-09-17 18:40:10       400
#> 1568745861 2019-09-17 18:44:21     10500
#> 1568745977 2019-09-17 18:46:17     55400
#> 1568746545 2019-09-17 18:55:45    112600
#> 1568747697 2019-09-17 19:14:57      3300
#> 1568747740 2019-09-17 19:15:40       100
#> 1568747741 2019-09-17 19:15:41       100
#> 1568747742 2019-09-17 19:15:42       500
#> 1568747759 2019-09-17 19:15:59       100
#> 1568747760 2019-09-17 19:16:00     24500
#> 
#> $total_records
#> [1] 33000
#> 
#> $start_time_param
#> [1] 1568745600
#> 
#> $start_time_info
#> [1] 1568745600
#> 
#> $sample_rate
#> [1] 100
#> 
#> $impute_zeroes
#> [1] FALSE
#> 
#> $add_light
#> [1] FALSE
#> 
#> $start_time
#> [1] "2019-09-17 18:40:00 GMT"
#> 
#> $stop_time
#> [1] "2019-09-18 19:00:00 GMT"
#> 
#> $last_sample_time
#> [1] "2019-09-17 19:20:05 GMT"
#> 
#> $subject_name
#> [1] "suffix_85"
#> 
#> $time_zone
#> [1] "-04:00:00"
#> 
#> $firmware
#> [1] "1.7.2"
#> 
#> $serial_prefix
#> [1] "TAS"
#> 
#> $acceleration_min
#> [1] "-8.0"
#> 
#> $acceleration_max
#> [1] "8.0"
#> 
#> $bad_samples
#> [1] FALSE
#> 
#> $old_version
#> [1] FALSE
#> 
#> $header
#> 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"
#> 
#> $class
#> [1] "activity" "matrix"   "array"

You can also convert the matrix to a data.frame with 4 columns: X,Y,Z,time

df <- as.data.frame(X)
head(df)
#> Sampling Rate: 100Hz
#> Firmware Version: 1.7.2
#> Serial Number Prefix: TAS
#>                  time     X      Y     Z
#> 1 2019-09-17 18:40:00 0.000  0.008 0.996
#> 2 2019-09-17 18:40:00 0.016  0.000 1.008
#> 3 2019-09-17 18:40:00 0.020 -0.008 1.004
#> 4 2019-09-17 18:40:00 0.016 -0.012 1.012
#> 5 2019-09-17 18:40:00 0.016 -0.008 1.008
#> 6 2019-09-17 18:40:00 0.008 -0.008 1.008
attributes(df)[setdiff(names(attributes(df)), c("names", "row.names"))]
#> $class
#> [1] "activity_df" "data.frame" 
#> 
#> $subject_name
#> [1] "suffix_85"
#> 
#> $time_zone
#> [1] "-04:00:00"
#> 
#> $missingness
#>                           time n_missing
#> 1568745610 2019-09-17 18:40:10       400
#> 1568745861 2019-09-17 18:44:21     10500
#> 1568745977 2019-09-17 18:46:17     55400
#> 1568746545 2019-09-17 18:55:45    112600
#> 1568747697 2019-09-17 19:14:57      3300
#> 1568747740 2019-09-17 19:15:40       100
#> 1568747741 2019-09-17 19:15:41       100
#> 1568747742 2019-09-17 19:15:42       500
#> 1568747759 2019-09-17 19:15:59       100
#> 1568747760 2019-09-17 19:16:00     24500
#> 
#> $old_version
#> [1] FALSE
#> 
#> $firmware
#> [1] "1.7.2"
#> 
#> $last_sample_time
#> [1] "2019-09-17 19:20:05 GMT"
#> 
#> $serial_prefix
#> [1] "TAS"
#> 
#> $sample_rate
#> [1] 100
#> 
#> $acceleration_min
#> [1] "-8.0"
#> 
#> $acceleration_max
#> [1] "8.0"
#> 
#> $header
#> 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"
#> 
#> $start_time
#> [1] "2019-09-17 18:40:00 GMT"
#> 
#> $stop_time
#> [1] "2019-09-18 19:00:00 GMT"
#> 
#> $total_records
#> [1] 33000
#> 
#> $bad_samples
#> [1] FALSE

Documentation

Documentation, hosted by GitHub pages.