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.
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
} # }