cc_counR Documentation

Identify Coordinates Outside their Reported Country

Description

Removes or flags mismatches between geographic coordinates and additional country information (usually this information is reliably reported with specimens). Such a mismatch can occur for example, if latitude and longitude are switched.

Usage

cc_coun(
  x,
  lon = "decimallongitude",
  lat = "decimallatitude",
  iso3 = "countrycode",
  value = "clean",
  ref = NULL,
  ref_col = "iso_a3",
  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”.

iso3

a character string. The column with the country assignment of each record in three letter ISO code. Default = “countrycode”.

value

character string. Defining the output value. See value.

ref

a SpatialPolygonsDataFrame. Providing the geographic gazetteer. Can be any SpatialPolygonsDataFrame, but the structure must be identical to rnaturalearth::ne_countries(scale = "medium"). Default = rnaturalearth::ne_countries(scale = "medium")

ref_col

the column name in the reference dataset, containing the relevant ISO codes for matching. Default is to "iso_a3_eh" which refers to the ISO-3 codes in the reference dataset. See notes.

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

The ref_col argument allows to adapt the function to the structure of alternative reference datasets. For instance, for rnaturalearth::ne_countries(scale = "small"), the default will fail, but ref_col = "iso_a3" will work.

With the default reference, records are flagged if they fall outside the terrestrial territory of countries, hence records in territorial waters might be flagged. See https://ropensci.github.io/CoordinateCleaner/ for more details and tutorials.

See Also

Other Coordinates: cc_cap(), cc_cen(), cc_dupl(), cc_equ(), cc_gbif(), cc_inst(), cc_iucn(), cc_outl(), cc_sea(), cc_urb(), cc_val(), cc_zero()

Examples


## Not run: 
x <- data.frame(species = letters[1:10], 
                decimallongitude = runif(100, -20, 30), 
                decimallatitude = runif(100, 35,60),
                countrycode = "RUS")

cc_coun(x, value = "flagged")#non-terrestrial records are flagged as wrong. 

## End(Not run)