CoordinateCleaner: cc_sea – R documentation

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cc_sea

Identify Non-terrestrial Coordinates

Description

Removes or flags coordinates outside the reference landmass. Can be used to restrict datasets to terrestrial taxa, or exclude records from the open ocean, when depending on the reference (see details). Often records of terrestrial taxa can be found in the open ocean, mostly due to switched latitude and longitude.

Usage

cc_sea(
  x,
  lon = "decimallongitude",
  lat = "decimallatitude",
  ref = NULL,
  scale = 110,
  value = "clean",
  speedup = TRUE,
  verbose = TRUE
)

Arguments

`x`	data.frame. Containing geographical coordinates and species names.
`lon`	character string. The column with the longitude coordinates. Default = “decimallongitude”.
`lat`	character string. The column with the latitude coordinates. Default = “decimallatitude”.
`ref`	a SpatialPolygonsDataFrame. Providing the geographic gazetteer. Can be any SpatialPolygonsDataFrame, but the structure must be identical to rnaturalearth::ne_download(scale = 110, type = 'land', category = 'physical'). Default = rnaturalearth::ne_download(scale = 110, type = 'land', category = 'physical')
`scale`	the scale of the default reference, as downloaded from natural earth. Must be one of 10, 50, 110. Higher numbers equal higher detail. Default = 110.
`value`	character string. Defining the output value. See value.
`speedup`	logical. Using heuristic to speed up the analysis for large data sets with many records per location.
`verbose`	logical. If TRUE reports the name of the test and the number of records flagged.

Details

In some cases flagging records close of the coastline is not recommendable, because of the low precision of the reference dataset, minor GPS imprecision or because a dataset might include coast or marshland species. If you only want to flag records in the open ocean, consider using a buffered landmass reference, e.g.: buffland.

Value

Depending on the ‘value’ argument, either a data.frame containing the records considered correct by the test (“clean”) or a logical vector (“flagged”), with TRUE = test passed and FALSE = test failed/potentially problematic . Default = “clean”.

Note

See https://ropensci.github.io/CoordinateCleaner/ for more details and tutorials.

Examples

x <- data.frame(species = letters[1:10], 
                decimallongitude = runif(10, -30, 30), 
                decimallatitude = runif(10, -30, 30))
                
cc_sea(x, value = "flagged")

CoordinateCleaner

Automated Cleaning of Occurrence Records from Biological Collections

v2.0-18

GPL-3

Authors

Alexander Zizka [aut, cre], Daniele Silvestro [ctb], Tobias Andermann [ctb], Josue Azevedo [ctb], Camila Duarte Ritter [ctb], Daniel Edler [ctb], Harith Farooq [ctb], Andrei Herdean [ctb], Maria Ariza [ctb], Ruud Scharn [ctb], Sten Svanteson [ctb], Niklas Wengstrom [ctb], Vera Zizka [ctb], Alexandre Antonelli [ctb], Irene Steves [rev] (Irene reviewed the package for ropensci, see <https://github.com/ropensci/onboarding/issues/210>), Francisco Rodriguez-Sanchez [rev] (Francisco reviewed the package for ropensci, see <https://github.com/ropensci/onboarding/issues/210>)

Initial release