CoordinateCleaner: cc_iucn – R documentation

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cc_iucn

Identify Records Outside Natural Ranges

Description

Removes or flags records outside of the provided natural range polygon, on a per species basis. Expects one entry per species. See the example or https://www.iucnredlist.org/resources/spatial-data-download for the required polygon structure.

Usage

cc_iucn(
  x,
  range,
  lon = "decimallongitude",
  lat = "decimallatitude",
  species = "species",
  buffer = 0,
  value = "clean",
  verbose = TRUE
)

Arguments

`x`	data.frame. Containing geographical coordinates and species names.
`range`	a SpatialPolygonsDataFrame of natural ranges for species in x. Must contain a column named as indicated by `species`. See details.
`lon`	character string. The column with the longitude coordinates. Default = “decimallongitude”.
`lat`	character string. The column with the latitude coordinates. Default = “decimallatitude”.
`species`	a character string. The column with the species name. Default = “species”.
`buffer`	numerical. The buffer around each species' range, from where records should be flagged as problematic, in decimal degrees. Default = 0.
`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

Download natural range maps in suitable format for amphibians, birds, mammals and reptiles from https://www.iucnredlist.org/resources/spatial-data-download. 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”.

Note

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

Examples

require(sp)

x <- data.frame(species = c("A", "B"),
decimallongitude = runif(100, -170, 170),
decimallatitude = runif(100, -80,80))

range_species_A <- Polygon(cbind(c(-45,-45,-60,-60,-45),c(-10,-25,-25,-10,-10)))
range_species_B <- Polygon(cbind(c(15,15,32,32,15),c(10,-10,-10,10,10)))
range_A <- Polygons(list(range_species_A), ID = c("A"))
range_B <- Polygons(list(range_species_B), ID = c("B"))
range <- SpatialPolygons(list(range_A, range_B))
df <- data.frame(species = c("A", "B"), row.names = c("A", "B"))
range <- SpatialPolygonsDataFrame(range, data = as.data.frame(df))

cc_iucn(x = x, range = range, buffer = 10)

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