Type:	Package
Title:	Parse 'ActiGraph' 'GT3X'/'GT3X+' 'Accelerometer' Data
Version:	1.2.0
Description:	Implements a high performance C++ parser for 'ActiGraph' 'GT3X'/'GT3X+' data format (with extension '.gt3x') for 'accelerometer' samples. Activity samples can be easily read into a matrix or data.frame. This allows for storing the raw 'accelerometer' samples in the original binary format to reserve space.
License:	EUPL version 1.1 | EUPL version 1.2 [expanded from: EUPL]
Encoding:	UTF-8
LinkingTo:	Rcpp
Imports:	Rcpp, utils, R.utils, tools
RoxygenNote:	7.1.2
Suggests:	knitr, rmarkdown, testthat (≥ 2.1.0), data.table, zoo, readr, lubridate, zip
VignetteBuilder:	knitr
NeedsCompilation:	yes
Packaged:	2022-06-30 07:13:11 UTC; tuomo
Author:	Tuomo Nieminen [aut, cre], John Muschelli [aut], Patrick Bos [ctb], Vincent van Hees [ctb]
Maintainer:	Tuomo Nieminen <tuomo.a.nieminen@gmail.com>
Repository:	CRAN
Date/Publication:	2022-06-30 07:40:02 UTC

Convert an activity matrix to a data.frame

Description

Convert an activity matrix to a data.frame

Usage

## S3 method for class 'activity'
as.data.frame(x, ..., verbose = FALSE, add_light = FALSE)

Arguments

Value

An object of class activity_df which is also a data.frame with the following attributes (and more)

• subject_name : Subject name from info file

• time_zone : Time zone from info file

• missingness : Data frame with timestamps and the number of missing values associated.

See Also

Other gt3x-parsers: parse_gt3x_info(), print.gt3x_info(), read.gt3x()

Calculate the expected activity sample size from start time and last sample time in the info.txt of a gt3x directory

Description

Calculate the expected activity sample size from start time and last sample time in the info.txt of a gt3x directory

Usage

get_n_samples(x)

Arguments

See Also

Other gt3x-utils: is_gt3x(), ticks2datetime()

Path to read.gt3x package sample data

Description

Path to read.gt3x package sample data

Usage

gt3x_datapath(index = NULL, verbose = TRUE)

gt3x_filename(index = NULL, zipped = FALSE)

Arguments

Value

Character vector of files

See Also

Other file manipulations: is_gt3x(), list_gt3x(), unzip.gt3x()

Examples

## Not run: 
dir <- gt3x_datapath()
gt3x_filename <- gt3x_datapath(1)
stopifnot(!is.na(gt3x_datapath(2)))

## End(Not run)

testthat::expect_error(gt3x_filename(100))
testthat::expect_error(gt3x_filename(0))

Get url of github release

Description

Get url of github release

Usage

gt3x_dataurl(
  version = "v1.0",
  baseurl = "https://github.com/THLfi/read.gt3x/releases/download"
)

Arguments

Value

URL to file

See Also

Other sample-data: gt3x_download(), gt3x_url()

Download and unzip a zipped gt3x file

Description

Download and unzip a zipped gt3x file

Usage

gt3x_download(url, exdir, verbose = TRUE)

Arguments

Value

file path of exdir

See Also

Other sample-data: gt3x_dataurl(), gt3x_url()

Get url of gt3x sample file

Description

Get url of gt3x sample file

Usage

gt3x_url(index = NULL, filename = NULL)

Arguments

Value

file path

See Also

Other sample-data: gt3x_dataurl(), gt3x_download()

Check if files are .gt3x files

Description

Check if files are .gt3x files

Check if a .gt3x file or unzipped gt3x directory has both log.bin and info.txt

Usage

is_gt3x(path)

have_log_and_info(path, verbose = TRUE)

Arguments

Details

Checks if files have a .gt3x file extension

Value

Logical vector of the same length as path, which is TRUE if the corresponding path is a .gt3x file.

See Also

Other file manipulations: gt3x_datapath(), list_gt3x(), unzip.gt3x()

Other gt3x-utils: get_n_samples(), ticks2datetime()

Examples

is_gt3x("test.gt3x") # TRUE
is_gt3x("test") # FALSE
is_gt3x(NULL)

have_log_and_info(tempfile(), verbose = TRUE)

List full paths to all gt3x files in a directory

Description

List full paths to all gt3x files in a directory

Usage

list_gt3x(path)

Arguments

See Also

Other file manipulations: gt3x_datapath(), is_gt3x(), unzip.gt3x()

Examples

path <-
  system.file(
    "extdata",
    package = "read.gt3x")
list_gt3x(path)
## Not run: 
list_gt3x(gt3x_datapath())

## End(Not run)

Parse activity samples from a NHANES-GT3X file

Description

Parse activity samples from a NHANES-GT3X file

Usage

parseActivityBin(
  filename,
  max_samples,
  scale_factor,
  sample_rate,
  verbose = FALSE,
  debug = FALSE
)

Arguments

Value

Returns a matrix with max_samples rows and 3 columns, where the first 3 columns are the acceleration samples and the last column is timestamps in seconds (including hundredth of seconds) starting from 00:00:00 1970-01-01 UTC (UNIX time)

Parse activity samples from a GT3X file

Description

Parse activity samples from a GT3X file

Usage

parseGT3X(
  filename,
  max_samples,
  scale_factor,
  sample_rate,
  start_time,
  batch_begin = 0L,
  batch_end = 0L,
  verbose = FALSE,
  debug = FALSE,
  impute_zeroes = FALSE
)

Arguments

Value

Returns a matrix with max_samples rows and 3 columns with the acceleration samples. The matrix has attributes "time_index", "missingness", "start_time_log", "sample_rate", "impute_zeroes".

Parse activity samples from a GT3X file

Description

Parse activity samples from a GT3X file

Usage

parseLuxBin(filename, max_samples, scale_factor, max_value, verbose = FALSE)

Arguments

Value

Returns a vector with max_samples elements

Parse GT3X info.txt file

Description

Parse GT3X info.txt file

Usage

parse_gt3x_info(path, tz = "GMT")

extract_gt3x_info(path, tz = "GMT")

Arguments

Note

The input for parse_gt3x_info is a gt3x file, but the path for extract_gt3x_info is the info.txt file, which can also pass in a connection

See Also

Other gt3x-parsers: as.data.frame.activity(), print.gt3x_info(), read.gt3x()

Examples

gt3xfile <-
  system.file(
    "extdata", "TAS1H30182785_2019-09-17.gt3x",
    package = "read.gt3x")
parse_gt3x_info(gt3xfile)

## Not run: 
gt3xfile <- gt3x_datapath(1)
parse_gt3x_info(gt3xfile)

## End(Not run)

Print the contents of the activity data

Description

Print the contents of the activity data

Usage

## S3 method for class 'activity_df'
print(x, ...)

## S3 method for class 'activity_df'
head(x, ...)

## S3 method for class 'activity'
print(x, ...)

## S3 method for class 'activity'
head(x, ...)

Arguments

Print the contents of the info.txt file in a gt3x folder

Description

Print the contents of the info.txt file in a gt3x folder

Usage

## S3 method for class 'gt3x_info'
print(x, ...)

Arguments

See Also

Other gt3x-parsers: as.data.frame.activity(), parse_gt3x_info(), read.gt3x()

Read GT3X

Description

Read activity samples from a GT3X file as a matrix. Please note that all timestamps are in local time (of the device) even though they are represented as POSIXct with GMT timezone.

Usage

read.gt3x(
  path,
  verbose = FALSE,
  asDataFrame = FALSE,
  imputeZeroes = FALSE,
  flag_idle_sleep = FALSE,
  cleanup = FALSE,
  ...,
  add_light = FALSE
)

Arguments

Value

A numeric matrix with 3 columns (X, Y, Z) and the following attributes:

• start_time : Start time from info file in POSIXct format.

• subject_name : Subject name from info file

• time_zone : Time zone from info file

• missingness : Named integer vector. Names are POSIXct timestamps and values are the number of missing values.

Note

The timestamps in the .gt3x data format are saved in .NET format, which is nanoseconds in local time since 0001-01-01. This is a bit tricky to parse into an R datetime format. DateTimes are therefore represented as POSIXct format with the 'GMT' timezone attribute, which is false; the datetime actually represents local time.

See Also

Other gt3x-parsers: as.data.frame.activity(), parse_gt3x_info(), print.gt3x_info()

Examples

gt3xfile <-
  system.file(
    "extdata", "TAS1H30182785_2019-09-17.gt3x",
    package = "read.gt3x")
is_gt3x(gt3xfile)
have_log_and_info(gt3xfile, verbose = TRUE)

x <- read.gt3x(gt3xfile, imputeZeroes = FALSE, asDataFrame = FALSE,
verbose = TRUE)
attr(x, "features")
df2 <- as.data.frame(x, verbose = TRUE)
attr(df2, "features")
head(df2)
rm(x); gc(); gc()
rm(df2); gc()

x <- read.gt3x(gt3xfile, imputeZeroes = TRUE, asDataFrame = TRUE,
verbose = TRUE)

## Not run: 
# first unzip, then read
datadir <- gt3x_datapath()
gt3xfolders <- unzip.gt3x(datadir)
gt3xfile <- gt3xfolders[2]
# temporary unzip, read, convert to a data frame
gt3xfile <- gt3x_datapath(1)
memory.limit()
df <- read.gt3x(gt3xfile, asDataFrame = FALSE, verbose = 2)
head(df)
rm(df); gc(); gc()


df <- read.gt3x(gt3xfile, asDataFrame = TRUE, verbose = 2)
head(df)

## End(Not run)

## Not run: 



url <- paste0("https://github.com/THLfi/read.gt3x/",
"files/", "3522749/", "GT3X%2B.01.day.gt3x.zip")
destfile <- tempfile(fileext = ".zip")
dl <- download.file(url, destfile = destfile, mode = "wb")
gt3x_file <- unzip(destfile, exdir = tempdir())
gt3x_file <- gt3x_file[!grepl("__MACOSX", gt3x_file)]
path <- gt3x_file

res <- read.gt3x(path)

gz <- R.utils::gzip(path, remove = FALSE, overwrite = FALSE)
df2 <- read.gt3x(gz, asDataFrame = FALSE, verbose = 2)
head(df2)

rm(df2); gc(); gc()


## End(Not run)

Convert NET ticks to POSIXct datetime

Description

Convert NET ticks to POSIXct datetime

Usage

ticks2datetime(ticks, tz = "GMT")

datetime2ticks(x)

Arguments

Details

reference: https://stackoverflow.com/questions/35240874/r-net-ticks-to-timestamp-in-r

See Also

Other gt3x-utils: get_n_samples(), is_gt3x()

Other gt3x-utils: get_n_samples(), is_gt3x()

Examples

mystr = "599633592352500000"
x = read.gt3x::ticks2datetime(mystr)
x
out = read.gt3x::datetime2ticks(as.POSIXct("1901-03-02 08:40:35.25", tz = "UTC"))
out = as.character(out)
out
stopifnot(out == mystr)
read.gt3x::datetime2ticks(x = as.POSIXct(Sys.time(), tz = "EST"))

Unzip gt3x files

Description

unzip.gt3x() makes it convenient to unzip multiple .gt3x files.

Usage

unzip.gt3x(path, verbose = TRUE, ...)

Arguments

Details

A .gt3x file is a zipped directory with two files: log.bin and info.txt. This function simply unzips the contents of the directories.

Value

Returns a vector of paths to unzipped gt3x folders.

See Also

Other file manipulations: gt3x_datapath(), is_gt3x(), list_gt3x()

Examples

gt3xfile <-
  system.file(
    "extdata", "TAS1H30182785_2019-09-17.gt3x",
    package = "read.gt3x")
gt3xdirs <- unzip.gt3x(gt3xfile)
## Not run: 
# unzip a single .gt3x file
path <- gt3x_datapath(1)
gt3xdir <- unzip.gt3x(path)

# unzip multiple .gt3x files
dir <- gt3x_datapath()
gt3xdirs <- unzip.gt3x(dir)

## End(Not run)
tfile = tempfile()
testthat::expect_error(unzip.gt3x(c(dir, tfile)))
testthat::expect_error(unzip.gt3x(c("", "")))

Unzip a single gt3x file

Description

A .gt3x file is a zipped archive with two files: log.bin and info.txt. This function unzips the contents of the archive to a single folder. This is a helper for unzip.gt3x()

Usage

unzip_single_gt3x(
  path,
  dirname = basename(gsub(".gt3x$| ", "", path)),
  location = tempdir(),
  files = c("info.txt", "log.bin"),
  remove_original = FALSE,
  check_structure = TRUE,
  verbose = TRUE
)

Arguments