CoordinateCleaner: cc_coun – R documentation

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cc_coun

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.

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)

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