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.
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
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.
Note
See https://ropensci.github.io/CoordinateCleaner/ for more details and tutorials.
Examples
require(sp)
#> Loading required package: 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)
#> Testing natural ranges
#> Warning: GEOS support is provided by the sf and terra packages among others
#> Warning: no projection information for reference found,
#> assuming '+proj=longlat +datum=WGS84 +no_defs'
#> Removed 99 records.
#> species decimallongitude decimallatitude
#> 85 A -53.70508 -12.24963