CoordinateCleaner: cc_urb – R documentation

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cc_urb

Identify Records Inside Urban Areas

Description

Removes or flags records from inside urban areas, based on a geographic gazetteer. Often records from large databases span substantial time periods (centuries) and old records might represent habitats which today are replaced by city area.

Usage

cc_urb(
  x,
  lon = "decimallongitude",
  lat = "decimallatitude",
  ref = NULL,
  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”.
`ref`	a SpatialPolygonsDataFrame. Providing the geographic gazetteer with the urban areas. See details. By default rnaturalearth::ne_download(scale = 'medium', type = 'urban_areas'). Can be any `SpatialPolygonsDataframe`, but the structure must be identical to `rnaturalearth::ne_download()`.
`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”.

Note

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

Examples

## Not run: 
x <- data.frame(species = letters[1:10],
                decimallongitude = runif(100, -180, 180),
                decimallatitude = runif(100, -90,90))

cc_urb(x)
cc_urb(x, value = "flagged")

## 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