tag_create: Create a 'tag' object

In Rafnuss/GeoPressureR: Global Positioning by Atmospheric Pressure

Create a tag object

Description

Create a GeoPressureR tag object from the data collected by a tracking device. The function can read data formatted according to three manufacturers SOI, Migratetech or Lund CAnMove, as well as according to the GeoLocator Data package standard and also accept manual data.frame as input. Pressure data is required for the GeoPressureR workflow but can be allowed to be missing with assert_pressure = FALSE.

Usage

tag_create(
  id,
  manufacturer = NULL,
  crop_start = NULL,
  crop_end = NULL,
  directory = glue::glue("./data/raw-tag/{id}"),
  pressure_file = NULL,
  light_file = NULL,
  acceleration_file = NULL,
  temperature_external_file = NULL,
  temperature_internal_file = NULL,
  magnetic_file = NULL,
  assert_pressure = TRUE,
  quiet = FALSE
)

Arguments

id	unique identifier of a tag.
manufacturer	One of NULL, "soi", "migratetech", "bas", "lund", "prestag" or "manual".
crop_start	remove all data before this date (POSIXct or character in UTC).
crop_end	remove all data after this date (POSIXct or character in UTC).
directory	path of the directory where the tag files can be read.
pressure_file	name of the file with pressure data. Full pathname or finishing with extensions (e.g., "*.pressure", "*.deg" or "*_press.xlsx").
light_file	name of the file with light data. Full pathname or finishing with extensions (e.g., "*.glf", "*.lux" or "*_acc.xlsx").
acceleration_file	name of the file with acceleration data. Full pathname or finishing with extensions (e.g., "*.acceleration", "*.deg" or "*_acc.xlsx").
temperature_external_file	name of the file with temperature data. Full pathname or finishing with extensions (e.g., "*.temperature", "*.airtemperature" or "*.deg"). External or air temperature is generally for temperature sensor on directed outward from the bird.
temperature_internal_file	name of the file with temperature data . Full pathname or finishing with extensions (e.g., "*.bodytemperature"). Internal or body temperature is generally for temperature sensor on directed inward (between bird and tag).
magnetic_file	name of the file with magnetic/accelerometer data. Full pathname or finishing with extensions (e.g., "*.magnetic").
assert_pressure	logical to check that the return tag has pressure data.
quiet	logical to hide messages about the progress.

Details

The current implementation can read files from the following three sources:

• GeoLocator Data Package (gldp)

  • pressure_file = "pressure.csv"(optional)

  • light_file = "light.csv" (optional)

  • acceleration_file = "acceleration.csv" (optional)

  • temperature_external_file = "temperature.csv" (optional)

  • temperature_external_file = "airtemperature.csv" (optional)

  • magnetic_file = "magnetic.csv" (optional)

• Swiss Ornithological Institute (soi)

  • pressure_file = "*.pressure"

  • light_file = "*.glf" (optional)

  • acceleration_file = "*.acceleration" (optional)

  • temperature = "*.temperature" (optional)

  • airtemperature = "*.airtemperature" (optional)

  • magnetic = "*.magnetic" (optional)

• Migrate Technology (migratetech):

  • pressure_file = "*.deg"

  • light_file = "*.lux" (optional)

  • acceleration_file = "*.deg" (optional)

• British Antarctic Survey (bas), aquired by Biotrack Ltd in 2011, renamed Lotek in 2019 . Only works for light data (assert_pressure = FALSE)

  • light_file = "*.lig"

• Lund CAnMove (lund)

  • pressure_file = "*_press.xlsx"

  • light_file = "*_acc.xlsx" (optional)

  • acceleration_file = "*_acc.xlsx" (optional)

• BitTag/PresTag (prestag)

  • pressure_file = "*.txt"

You can also enter the data manually (manufacturer = "manual") by providing the data.frame to pressure_file:

• pressure_file: data.frame with column date and value.

• light_file: (optional) data.frame with column date and value.

• acceleration_file: (optional) data.frame with column date and value.

You can still create a tag without pressure data using assert_pressure = TRUE. This tag won't be able to run the traditional GeoPressureR workflow, but you can still do some analysis.

By default manufacturer = NULL, the manufacturer is determined automatically from the content of the directory. You can also specify manually the file with a full pathname or the file extension using a regex expression (e.g., "*.pressure" matches any file ending with pressure).

Please create an issue on Github if you have data in a format that is not yet supported.

This function can be used to crop the data at specific date, for instance to remove pre-equipment or post-retrieval data.

Value

a GeoPressureR tag object containing

• param parameter object (see param_create())

• pressure data.frame with columns: date and value

• light (optional) same structure as pressure

• temperature_external (optional) same structure as pressure

• temperature_internal (optional) same structure as pressure

• acceleration (optional) data.frame with columns: date, value, act and pit.

  • value is the activity computed as the sum of the difference in acceleration on the z-axis (i.e. jiggle). In the SOI sensor, it is summarised from 32 measurements at 10Hz

  • pitch is the relative position of the bird’s body relative to the z axis. In the SOI sensor, it is an average over 32 measurements at 10Hz.

• magnetic (optional) data.frame with columns: date, magnetic_x, magnetic_y, magnetic_z , acceleration_x, acceleration_y and acceleration_z

See Also

GeoPressureManual

Other tag: print.tag(), tag_set_map()

Examples

withr::with_dir(system.file("extdata", package = "GeoPressureR"), {
  # Read all sensor file
  tag <- tag_create("18LX")

  print(tag)

  # Read only pressure and crop date
  tag <- tag_create("18LX",
    light_file = NULL,
    acceleration_file = NULL,
    crop_start = "2017-08-01",
    crop_end = "2017-08-05"
  )

  print(tag)

  # You can also specify the exact file in case multiple files with the
  # same extension exist in your directory (migratetech data)
  tag <- tag_create("CB621",
    pressure_file = "CB621_BAR.deg",
    light_file = "CB621.lux",
    acceleration_file = NULL
  )

  print(tag)

  # You can specify the data manually with
  pressure <- data.frame(
    date = as.POSIXct(c(
      "2017-06-20 00:00:00 UTC", "2017-06-20 01:00:00 UTC",
      "2017-06-20 02:00:00 UTC", "2017-06-20 03:00:00 UTC"
    ), tz = "UTC"),
    value = c(1000, 1000, 1000, 1000)
  )
  tag_create(id = "xxx", pressure_file = pressure)
})

Rafnuss/GeoPressureR documentation built on April 17, 2025, 12:58 p.m.