Create a tag object — tag_create • GeoPressureR

Create a GeoPressureR tag object from the data collected by a tracking device. This data needs to include at least pressure and optionally a light and/or acceleration.

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

Swiss Ornithological Institute (soi)
- pressure_file = "*.pressure"
- light_file = "*.glf" (optional)
- acceleration_file = "*.acceleration" (optional)
Migrate Technology (migratetech):
- pressure_file = "*.deg"
- light_file = "*.lux" (optional)
- acceleration_file = "*.deg" (optional)
Lund CAnMove (lund)
- pressure_file = "*_press.xlsx"
- light_file = "*_acc.xlsx" (optional)
- acceleration_file = "*_acc.xlsx" (optional)

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.

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.

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_file = NULL,
  quiet = FALSE
)

Arguments

id: unique identifier of a tag.
manufacturer: One of NULL, "soi", "migratetech", "lund" 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_file: name of the file with temperature data. Full pathname or finishing with extensions (e.g., "*.temperature", "*.deg").
quiet: logical to hide messages about the progress.

Value

a GeoPressureR tag object containing

param parameter object (see param_create)
pressure data.frame with columns for date and value
light (optional) same structure as pressure
acceleration (optional) same structure as pressure

Examples

setwd(system.file("extdata", package = "GeoPressureR"))

# Read all sensor file
tag <- tag_create("18LX")
#> ✔ Read ./data/raw-tag/18LX/18LX_20180725.pressure
#> ✔ Read ./data/raw-tag/18LX/18LX_20180725.glf
#> ✔ Read ./data/raw-tag/18LX/18LX_20180725.acceleration
#> ✔ Read ./data/raw-tag/18LX/18LX_20180725.temperature

print(tag)
#> 
#> ── GeoPressureR `tag` object for 18LX ──────────────────────────────────────────
#> Note: All green texts are fields of `tag` (i.e., `tag$field`).
#> 
#> ── Parameter param 
#> Run `tag$param` to display full table
#> 
#> ── Sensors data 
#> Manufacturer: soi
#> Date range: 2017-07-27 to 2017-08-09 23:30:00
#> • pressure: 672 datapoints
#> • acceleration: 4032 datapoints
#> • light: 4032 datapoints
#> • temperature: 2448 datapoints
#> 
#> ── Stationary periods stap 
#> ✖ No stationary periods defined yet. Use `tag_label()`

# 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"
)
#> ✔ Read ./data/raw-tag/18LX/18LX_20180725.pressure
#> ✔ Read ./data/raw-tag/18LX/18LX_20180725.glf
#> ✔ Read ./data/raw-tag/18LX/18LX_20180725.acceleration
#> ✔ Read ./data/raw-tag/18LX/18LX_20180725.temperature

print(tag)
#> 
#> ── GeoPressureR `tag` object for 18LX ──────────────────────────────────────────
#> Note: All green texts are fields of `tag` (i.e., `tag$field`).
#> 
#> ── Parameter param 
#> Run `tag$param` to display full table
#> 
#> ── Sensors data 
#> Manufacturer: soi
#> Date range: 2017-08-01 to 2017-08-04 23:30:00
#> • pressure: 192 datapoints
#> • acceleration: 1152 datapoints
#> • light: 1152 datapoints
#> • temperature: 2448 datapoints
#> 
#> ── Stationary periods stap 
#> ✖ No stationary periods defined yet. Use `tag_label()`

# 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
)
#> ✔ Read ./data/raw-tag/CB621/CB621_BAR.deg
#> ✔ Read ./data/raw-tag/CB621/CB621_BAR.deg
#> ✔ Read ./data/raw-tag/CB621/CB621.lux

print(tag)
#> 
#> ── GeoPressureR `tag` object for CB621 ─────────────────────────────────────────
#> Note: All green texts are fields of `tag` (i.e., `tag$field`).
#> 
#> ── Parameter param 
#> Run `tag$param` to display full table
#> 
#> ── Sensors data 
#> Manufacturer: migratetech
#> Date range: 2021-06-15 21:38:35 to 2021-06-16 05:08:35
#> • pressure: 16 datapoints
#> • light: 14 datapoints
#> • temperature: 16 datapoints
#> 
#> ── Stationary periods stap 
#> ✖ No stationary periods defined yet. Use `tag_label()`

# 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)
#> List of 2
#>  $ param   :List of 8
#>   ..$ id                  : chr "xxx"
#>   ..$ GeoPressureR_version:Classes 'package_version', 'numeric_version'  hidden list of 1
#>   .. ..$ : int [1:3] 3 2 1
#>   ..$ pressure_file       : chr "manual"
#>   ..$ light_file          : chr "manual"
#>   ..$ acceleration_file   : chr "manual"
#>   ..$ temperature_file    : chr "manual"
#>   ..$ manufacturer        : chr "manual"
#>   ..$ directory           : 'glue' chr "./data/raw-tag/xxx"
#>   ..- attr(*, "class")= chr "param"
#>  $ pressure:'data.frame':	4 obs. of  2 variables:
#>   ..$ date : POSIXct[1:4], format: "2017-06-20 00:00:00" "2017-06-20 01:00:00" ...
#>   ..$ value: num [1:4] 1000 1000 1000 1000
#>  - attr(*, "class")= chr "tag"

Create a `tag` object

Usage

Arguments

Value

See also

Examples