cc_sea function

Identify Non-terrestrial Coordinates

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.

cc_sea(
  x,
  lon = "decimalLongitude",
  lat = "decimalLatitude",
  ref = NULL,
  scale = 110,
  value = "clean",
  speedup = TRUE,
  verbose = TRUE,
  buffer = NULL
)

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: SpatVector (geometry: polygons). Providing the geographic gazetteer. Can be any SpatVector (geometry: polygons), but the structure must be identical to rnaturalearth::ne_download(scale = 110, type = 'land', category = 'physical', returnclass = 'sf'). Default = rnaturalearth::ne_download(scale = 110, type = 'land', category = 'physical', returnclass = 'sf').
• 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.
• buffer: numeric. Units are in meters. If provided, a buffer is created around the sea polygon, or ref provided.

Returns

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 .

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.

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")

See Also

Other Coordinates: cc_aohi(), cc_cap(), cc_cen(), cc_coun(), cc_dupl(), cc_equ(), cc_gbif(), cc_inst(), cc_iucn(), cc_outl(), cc_urb(), cc_val(), cc_zero()