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Identify Records in the Vicinity of Biodiversity Institutions

Source: R/cc_inst.R
cc_inst.Rd

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.

Usage

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.

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

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

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()

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)
#> Testing biodiversity institutions
#> Flagged 1 records.
#>   [1]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
#>  [13]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
#>  [25]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
#>  [37]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
#>  [49]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
#>  [61]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
#>  [73]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
#>  [85]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
#>  [97]  TRUE  TRUE  TRUE FALSE

if (FALSE) { # \dontrun{
#' cc_inst(x, value = "flagged", buffer = 50000) #geod = T
} # }