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Identify Non-terrestrial Coordinates

Source: R/cc_sea.R
cc_sea.Rd

Removes or flags coordinates outside the reference landmass. Can be used to restrict datasets to terrestrial taxa, or exclude records from the open ocean, when depending on the reference (see details). Often records of terrestrial taxa can be found in the open ocean, mostly due to switched latitude and longitude.

Usage

cc_sea(
  x,
  lon = "decimalLongitude",
  lat = "decimalLatitude",
  ref = NULL,
  scale = 110,
  value = "clean",
  speedup = TRUE,
  verbose = TRUE,
  buffer = NULL
)

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

SpatVector (geometry: polygons). Providing the geographic gazetteer. Can be any SpatVector (geometry: polygons), but the structure must be identical to rnaturalearth::ne_download(scale = 110, type = 'land', category = 'physical', returnclass = 'sf'). Default = rnaturalearth::ne_download(scale = 110, type = 'land', category = 'physical', returnclass = 'sf').

scale

the scale of the default reference, as downloaded from natural earth. Must be one of 10, 50, 110. Higher numbers equal higher detail. Default = 110.

value

character string. Defining the output value. See value.

speedup

logical. Using heuristic to speed up the analysis for large data sets with many records per location.

verbose

logical. If TRUE reports the name of the test and the number of records flagged.

buffer

numeric. Units are in meters. If provided, a buffer is created around the sea polygon, or ref provided.

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

In some cases flagging records close of the coastline is not recommendable, because of the low precision of the reference dataset, minor GPS imprecision or because a dataset might include coast or marshland species. If you only want to flag records in the open ocean, consider using a buffered landmass reference, e.g.: buffland.

Note

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

See also

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

Examples

x <- data.frame(species = letters[1:10], 
                decimalLongitude = runif(10, -30, 30), 
                decimalLatitude = runif(10, -30, 30))
                
cc_sea(x, value = "flagged")
#> Testing sea coordinates
#> Reading layer `ne_110m_land' from data source `/tmp/RtmpXOhoah/ne_110m_land.shp' using driver `ESRI Shapefile'
#> Simple feature collection with 127 features and 3 fields
#> Geometry type: POLYGON
#> Dimension:     XY
#> Bounding box:  xmin: -180 ymin: -90 xmax: 180 ymax: 83.64513
#> Geodetic CRS:  WGS 84
#> Flagged 6 records.
#>  [1] FALSE  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE