cc_iucn function

Identify Records Outside Natural Ranges

Removes or flags records outside of the provided natural range polygon, on a per species basis. Expects one entry per species. See the example or https://www.iucnredlist.org/resources/spatial-data-download for the required polygon structure.

cc_iucn(
  x,
  range,
  lon = "decimalLongitude",
  lat = "decimalLatitude",
  species = "species",
  buffer = 0,
  value = "clean",
  verbose = TRUE
)

Arguments

• x: data.frame. Containing geographical coordinates and species names.
• range: a SpatVector of natural ranges for species in x. Must contain a column named as indicated by species. See details.
• lon: character string. The column with the longitude coordinates. Default = decimalLongitude .
• lat: character string. The column with the latitude coordinates. Default = decimalLatitude .
• species: a character string. The column with the species name. Default = species .
• buffer: numerical. The buffer around each species' range, from where records should be flagged as problematic, in meters. Default = 0.
• value: character string. Defining the output value. See value.
• verbose: logical. If TRUE reports the name of the test and the number of records flagged.

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

Download natural range maps in suitable format for amphibians, birds, mammals and reptiles from https://www.iucnredlist.org/resources/spatial-data-download. Note: the buffer radius is in degrees, thus will differ slightly between different latitudes.

Note

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

Examples

library(terra)

x <- data.frame(species = c("A", "B"),
decimalLongitude = runif(100, -170, 170),
decimalLatitude = runif(100, -80,80))

range_species_A <- cbind(c(-45,-45,-60,-60,-45), c(-10,-25,-25,-10,-10))
rangeA <- terra::vect(range_species_A, "polygons")
range_species_B <- cbind(c(15,15,32,32,15), c(10,-10,-10,10,10))
rangeB <- terra::vect(range_species_B, "polygons")
range <- terra::vect(list(rangeA, rangeB))
range$binomial <- c("A", "B")

cc_iucn(x = x, range = range, buffer = 0)

See Also

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