CoordinateCleaner: cc_inst – R documentation

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cc_inst

Identify Records in the Vicinity of Biodiversity Institutions

Description

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 = TRUE,
  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, in this case buffer is in degrees. Default = TRUE. See https://seethedatablog.wordpress.com/ for detail and credits.
`ref`	SpatialPointsDataFrame. Providing the geographic gazetteer. Can be any SpatialPointsDataFrame, 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.

Details

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

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”.

Examples

x <- data.frame(species = letters[1:10], 
                decimallongitude = runif(100, -180, 180), 
                decimallatitude = runif(100, -90,90))

#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)

CoordinateCleaner

Automated Cleaning of Occurrence Records from Biological Collections

v2.0-18

GPL-3

Authors

Alexander Zizka [aut, cre], Daniele Silvestro [ctb], Tobias Andermann [ctb], Josue Azevedo [ctb], Camila Duarte Ritter [ctb], Daniel Edler [ctb], Harith Farooq [ctb], Andrei Herdean [ctb], Maria Ariza [ctb], Ruud Scharn [ctb], Sten Svanteson [ctb], Niklas Wengstrom [ctb], Vera Zizka [ctb], Alexandre Antonelli [ctb], Irene Steves [rev] (Irene reviewed the package for ropensci, see <https://github.com/ropensci/onboarding/issues/210>), Francisco Rodriguez-Sanchez [rev] (Francisco reviewed the package for ropensci, see <https://github.com/ropensci/onboarding/issues/210>)

Initial release