cc_inst function

Identify Records in the Vicinity of Biodiversity Institutions

Removes or flags records assigned to the location of zoos, botanical gardens, herbaria, universities and museums, based on a global database of ~10,000 such biodiversity institutions. Coordinates from these locations can be related to data-entry errors, false automated geo-reference or individuals in captivity/horticulture.

cc_inst(
  x,
  lon = "decimalLongitude",
  lat = "decimalLatitude",
  species = "species",
  buffer = 100,
  geod = FALSE,
  ref = NULL,
  verify = FALSE,
  verify_mltpl = 10,
  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: numerical. The buffer around each institution, where records should be flagged as problematic, in decimal degrees. Default = 100m.
• 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 institutions. Default = institutions
• verify: logical. If TRUE, records close to institutions are only flagged, if there are no other records of the same species in the greater vicinity (a radius of buffer * verify_mltpl).
• verify_mltpl: numerical. indicates the factor by which the radius for verify exceeds the radius of the initial test. Default = 10, which might be suitable if geod is TRUE, but might be too large otherwise.
• 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

Note: the buffer radius is in degrees, thus will differ slightly between different latitudes.

Examples

x <- data.frame(species = letters[1:10],
                decimalLongitude = c(runif(99, -180, 180), 37.577800),
                decimalLatitude = c(runif(99, -90,90), 55.710800))

#large buffer for demonstration, using geod = FALSE for shorter runtime
cc_inst(x, value = "flagged", buffer = 10, geod = FALSE)

## Not run:

#' cc_inst(x, value = "flagged", buffer = 50000) #geod = T
## End(Not run)

See Also

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