cc_cap function

Identify Coordinates in Vicinity of Country Capitals.

Removes or flags records within a certain radius around country capitals. Poorly geo-referenced occurrence records in biological databases are often erroneously geo-referenced to capitals.

cc_cap(
  x,
  lon = "decimalLongitude",
  lat = "decimalLatitude",
  species = "species",
  buffer = 10000,
  geod = TRUE,
  ref = NULL,
  verify = FALSE,
  value = "clean",
  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 .
• species: character string. The column with the species identity. Only required if verify = TRUE.
• buffer: The buffer around each capital coordinate (the centre of the city), where records should be flagged as problematic. Units depend on geod. Default = 10 kilometres.
• geod: logical. If TRUE the radius around each capital is calculated based on a sphere, buffer is in meters and independent of latitude. If FALSE the radius is calculated assuming planar coordinates and varies slightly with latitude. Default = TRUE. See https://seethedatablog.wordpress.com/ for detail and credits.
• ref: SpatVector (geometry: polygons). Providing the geographic gazetteer. Can be any SpatVector (geometry: polygons), but the structure must be identical to countryref. Default = countryref.
• verify: logical. If TRUE records are only flagged if they are the only record in a given species flagged close to a given reference. If FALSE, the distance is the only criterion
• 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 .

Note

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

Examples

## Not run:

x <- data.frame(species = letters[1:10],
                decimalLongitude = c(runif(99, -180, 180), -47.882778),
                decimalLatitude = c(runif(99, -90, 90), -15.793889))

cc_cap(x)
cc_cap(x, value = "flagged")
## End(Not run)

See Also

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