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Identify Records Outside Natural Ranges

Source: R/cc_iucn.R
cc_iucn.Rd

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.

Usage

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 SpatialPolygonsDataFrame 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 decimal degrees. 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.

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”.

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.

See also

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

Examples

require(sp)
#> Loading required package: sp

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

range_species_A <- Polygon(cbind(c(-45,-45,-60,-60,-45),c(-10,-25,-25,-10,-10)))
range_species_B <- Polygon(cbind(c(15,15,32,32,15),c(10,-10,-10,10,10)))
range_A <- Polygons(list(range_species_A), ID = c("A"))
range_B <- Polygons(list(range_species_B), ID = c("B"))
range <- SpatialPolygons(list(range_A, range_B))
df <- data.frame(species = c("A", "B"), row.names = c("A", "B"))
range <- SpatialPolygonsDataFrame(range, data = as.data.frame(df))

cc_iucn(x = x, range = range, buffer = 10)
#> Testing natural ranges
#> Warning: GEOS support is provided by the sf and terra packages among others
#> Warning: no projection information for reference found, 
#>               assuming '+proj=longlat +datum=WGS84 +no_defs'
#> Removed 99 records.
#>    species decimallongitude decimallatitude
#> 85       A        -53.70508       -12.24963