Read Actigraphy File
Arguments
- file
file to read
- ...
additional arguments to pass to function
- read_function
A custom function to read the data in.
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/Rtmp6zX4Yo
#> 1/1
#> Unzipping /home/runner/work/_temp/Library/SummarizedActigraphy/extdata/TAS1H30182785_2019-09-17.gt3x
#> === info.txt, log.bin extracted to /tmp/Rtmp6zX4Yo/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 0.515820741653442 seconds)
testthat::expect_equal(mean(res$data$X), -0.0742151351351352)
file = "blah.exe"
testthat::expect_error(read_actigraphy(file))
# \donttest{
url = paste0("https://github.com/THLfi/read.gt3x/files/",
"3522749/GT3X%2B.01.day.gt3x.zip")
destfile = tempfile(fileext = ".zip")
dl = utils::download.file(url, destfile = destfile, mode = "wb")
gt3x_file = utils::unzip(destfile, exdir = tempdir())
gt3x_file = gt3x_file[!grepl("__MACOSX", gt3x_file)]
path = gt3x_file
res = read_actigraphy(path)
#> Input is a .gt3x file, unzipping to a temporary location first...
#> Unzipping gt3x data to /tmp/Rtmp6zX4Yo
#> 1/1
#> Unzipping /tmp/Rtmp6zX4Yo/GT3X+ (01 day).gt3x
#> === info.txt, activity.bin, lux.bin extracted to /tmp/Rtmp6zX4Yo/GT3X+(01day)
#> GT3X information
#> $ Serial Number :"NEO1DXXXXXXXX"
#> $ Device Type :"GT3XPlus"
#> $ Firmware :"2.5.0"
#> $ Battery Voltage :"4.22"
#> $ Sample Rate :30
#> $ Start Date : POSIXct, format: "2012-06-27 10:54:00"
#> $ Stop Date : POSIXct, format: "2012-06-28 11:54:00"
#> $ Download Date : POSIXct, format: "2012-06-28 16:25:52"
#> $ Board Revision :"4"
#> $ Unexpected Resets :"0"
#> $ Sex :"Male"
#> $ Height :"172.72"
#> $ Mass :"69.8532249799612"
#> $ Age :"43"
#> $ Race :"White / Caucasian"
#> $ Limb :"Ankle"
#> $ Side :"Left"
#> $ Dominance :"Non-Dominant"
#> $ DateOfBirth :"621132192000000000"
#> $ Subject Name :"GT3XPlus"
#> $ Serial Prefix :"NEO"
#> $ Last Sample Time : 'POSIXct' num(0)
#> - attr(*, "tzone")= chr "GMT"
#> $ Acceleration Scale:341
#> $ Acceleration Min :"-6.0"
#> $ Acceleration Max :"6.0"
#> Parsing GT3X data via CPP.. expected sample size: 2700000
#> Using NHANES-GT3X format - older format
#> Sample size: 2700000
#> Scaling...
#> Done (in 2.36615514755249 seconds)
testthat::expect_equal(mean(res$data$X), -0.228406351135833)
dob = res$header$Value[res$header$Field == "DateOfBirth"]
if (length(dob) > 0) {
SummarizedActigraphy:::ticks2datetime(dob)
}
#> [1] "1969-04-17 GMT"
# }