Package 'actiread'

Convert vectors ensuring no new NA

Description

Convert vectors ensuring no new NA

Usage

acti_convert_sensorlogger_time(x)

Arguments

x

a vector

Value

A converted 'vector' the same length as 'x' or errors if there are introduced NAs.

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Decompress an Activity-data File

Description

Decompresses .bz2, .gz, and .xz files to a temporary file. If extension is NULL, the destination extension is inferred after removing the compression extension from path.

Usage

acti_decompress_file(path, extension = NULL)

Arguments

path	Path to an activity-data file, optionally compressed.
extension	Output file extension. Defaults to NULL, which infers the extension from path after removing its compression extension.

Value

A list with path, the usable file path, and temporary, which is TRUE when a temporary decompressed file was created. Callers should delete path when temporary is TRUE.

Examples

file = acti_decompress_file(acti_example_cwa())
if (file$temporary) {
  unlink(file$path)
}

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Activity/Actigraphy Example Data

Description

Activity/Actigraphy Example Data

Usage

acti_example_gt3x()

acti_example_cwa()

acti_example_geneactiv()

acti_example_sensorlog_file()

acti_example_sensorlogger_file()

acti_example_sensorlogger_location_file()

Value

A file path

Examples

library(actiread)
acti_example_gt3x()
acti_example_cwa()
acti_example_sensorlogger_file()

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Read CWA File with actipy

Description

Read CWA File with actipy

Usage

acti_py_read_cwa(
  path,
  lowpass_hz = FALSE,
  calibrate_gravity = FALSE,
  detect_nonwear = FALSE,
  resample_hz = FALSE,
  ...,
  tz = "UTC",
  apply_tz = TRUE,
  verbose = TRUE
)

Arguments

path	Path to cwa file
lowpass_hz	Frequency of low pass filter
calibrate_gravity	perform gravity calibration method of van Hees et al. 2014 https://doi.org/10.1152/japplphysiol.00421.2014
detect_nonwear	Flag nonwear episodes in the data by setting them to NA. Non-wear episodes are inferred from long periods of no movement. 90 minute munte windows based on 10-second rolling windows with a threshold of 0.015g standard deviation tolerance
resample_hz	Target frequency (Hz) to resample the signal. If "uniform", uses the device's sample rate to fix sampling errors. Pass FALSE to disable.
...	additional arguments to pass to actipy.read_device
tz	time zone for the data time, passed to desiredtz argument in GGIRread::readAxivity. If NULL or "", no time conversion is done.
apply_tz	turn the time column into a POSIXct and apply the timezone
verbose	print diagnostic messages, higher values = more verbosity.

Value

A tibble with attributes of a header, sample rate, and transformations

Examples

if (requireNamespace("reticulate", quietly = TRUE) &&
    requireNamespace("arrow", quietly = TRUE)) {
    if (reticulate::py_module_available("actipy") &&
      reticulate::py_module_available("pyarrow")) {
        data = acti_py_read_cwa(acti_example_cwa())
    }
}

---

Read CWA File

Description

Read CWA File

Usage

acti_read_cwa(
  path,
  start = 0,
  end = Inf,
  tz = "UTC",
  ...,
  apply_tz = TRUE,
  verbose = TRUE
)

acti_read_cwa_header(path)

Arguments

path	Path to cwa file
start	where to start in the file, passed to GGIRread::readAxivity
end	where to end in the file, passed to GGIRread::readAxivity
tz	time zone for the data time, passed to desiredtz argument in GGIRread::readAxivity. If NULL or "", no time conversion is done.
...	additional arguments to pass to GGIRread::readAxivity()
apply_tz	turn the time column into a POSIXct and apply the timezone
verbose	print diagnostic messages, higher values = more verbosity.

Value

A tibble with attributes of a header, sample rate, and transformations

Examples

data = acti_read_cwa(acti_example_cwa())
data = acti_read_cwa(
  acti_example_cwa(),
  tz = NULL,
  apply_tz = FALSE,
  verbose = FALSE
)

---

Read GENEActiv Binary File

Description

Read GENEActiv Binary File

Usage

acti_read_geneactiv(
  path,
  start = 0,
  end = Inf,
  tz = "UTC",
  ...,
  verbose = TRUE
)

acti_read_geneactiv_header(path)

Arguments

path	Path to geneactiv binary file
start	where to start in the file, passed to GGIRread::readGENEActiv
end	where to end in the file, passed to GGIRread::readGENEActiv
tz	time zone for the data time, passed to desiredtz argument in GGIRread::readGENEActiv. If NULL or "", no time conversion is done.
...	additional arguments to pass to GGIRread::readGENEActiv()
verbose	print diagnostic messages, higher values = more verbosity.

Value

A tibble with attributes of a header, sample rate, and transformations

Examples

data = acti_read_cwa(acti_example_cwa())
data = acti_read_cwa(
  acti_example_cwa(),
  tz = NULL,
  apply_tz = FALSE,
  verbose = FALSE
)

---

Read GT3X file

Description

Read GT3X file

Usage

acti_read_gt3x(
  path,
  asDataFrame = TRUE,
  imputeZeroes = TRUE,
  verbose = TRUE,
  ...,
  fill_zeroes = TRUE,
  apply_tz = FALSE,
  check_attributes = TRUE,
  tz = "GMT"
)

acti_info_gt3x(path, ...)

Arguments

path	Path to gt3x file
asDataFrame	convert to an activity_df, see as.data.frame.activity
imputeZeroes	Impute zeros in case there are missingness? Default is FALSE, in which case the time series will be incomplete in case there is missingness.
verbose	print diagnostic messages, higher values = more verbosity.
...	additional arguments to pass to read.gt3x::read.gt3x()
fill_zeroes	Rows with all zeros will be filled in with the last observation carried forward as is done with ActiLife. Recommended
apply_tz	Apply the timezone from the header TimeZone attribute, if available
check_attributes	Check that the attributes are included This is a sanity check, including checking that sample_rate is in the attributes.
tz	timezone to project the data into. The data read in via read.gt3x::read.gt3x() says the timezone is GMT, but the time values is in the native timezone. So this data is projected into the correct time zone and then forced into the timezone given by tz. Set to NULL to not apply this forcing.

Value

A data.frame

Examples

library(actiread)
data = acti_read_gt3x(acti_example_gt3x())
data = acti_read_gt3x(
  acti_example_gt3x(),
  tz = NULL,
  apply_tz = FALSE,
  verbose = FALSE,
  fill_zeroes = FALSE
)
info = acti_info_gt3x(acti_example_gt3x())

---

Read SensorLog Data

Description

Read SensorLog Data

Usage

acti_read_sensorlog(file, verbose = FALSE, robust = FALSE)

acti_sensorlog_csv_spec()

acti_sensorlog_csv_colnames_mapping()

Arguments

file	A character vector of SensorLog files, usually from unzipping the file
verbose	print diagnostic messages. Either logical or integer, where higher values are higher levels of verbosity.
robust	if TRUE then acti_rewrite_sensorlog_csv is run on the data to try to fix any shifts with the data.

Value

A data.frame of data

Examples

library(actiread)
file = acti_example_sensorlog_file()
df = acti_read_sensorlog(file)
head(df)

---

Require actipy for reticulate

Description

Require actipy for reticulate

Usage

acti_require_actipy(..., python_version = "3.9")

Arguments

...	additional arguments to pass to reticulate::py_require
python_version	version of python passed to reticulate::py_require

Value

invisible NULL

---

Rewrite a CSV that may have issues with export from SensorLog

Description

Rewrite a CSV that may have issues with export from SensorLog

Usage

acti_rewrite_sensorlog_csv(
  file,
  outfile = tempfile(fileext = ".csv"),
  verbose = FALSE
)

Arguments

file	Input CSV file
outfile	Output CSV file
verbose	Print Diagnostic messages

Value

A file path to the new CSV

Examples

sl_file = actiread::acti_example_sensorlog_file()
tfile = tempfile()
files = utils::unzip(sl_file, exdir = tfile)
result = actiread::acti_rewrite_sensorlog_csv(files)

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Read SensorLogger Data

Description

Read SensorLogger Data

Usage

acti_sensorlogger_location_colnames_mapping()

acti_sensorlogger_location_spec()

acti_read_sensorlogger_location(file, ...)

acti_read_sensorlogger(file, verbose = FALSE, ...)

acti_read_sensorlogger_general(file, ..., verbose = FALSE)

Arguments

file	A character vector of SensorLogger files, usually from unzipping the file, or a zip file of SensorLogger files
...	additional arguments to pass to readr::read_csv(). If verbose = FALSE, then progress = FALSE and show_col_types = FALSE, unless otherwise overridden
verbose	print diagnostic messages. Either logical or integer, where higher values are higher levels of verbosity.

Value

A data.frame of data

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Transform timezone offset to timezone

Description

Transform timezone offset to timezone

Usage

tzoffset_to_tz(x)

Arguments

x	A character vector

Value

A character vector

Examples

tzoffset_to_tz(c("+00:00", "-05:00", "+01:00"))

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