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Geographic Cleaning of Coordinates from Biologic Collections

Source: R/clean_coordinates.R
clean_coordinates.Rd

Cleaning geographic coordinates by multiple empirical tests to flag potentially erroneous coordinates, addressing issues common in biological collection databases.

Usage

clean_coordinates(
  x,
  lon = "decimalLongitude",
  lat = "decimalLatitude",
  species = "species",
  countries = NULL,
  tests = c("capitals", "centroids", "equal", "gbif", "institutions", "outliers", "seas",
    "zeros"),
  capitals_rad = 10000,
  centroids_rad = 1000,
  centroids_detail = "both",
  inst_rad = 100,
  outliers_method = "quantile",
  outliers_mtp = 5,
  outliers_td = 1000,
  outliers_size = 7,
  range_rad = 0,
  zeros_rad = 0.5,
  capitals_ref = NULL,
  centroids_ref = NULL,
  country_ref = NULL,
  country_refcol = "iso_a3",
  country_buffer = NULL,
  inst_ref = NULL,
  range_ref = NULL,
  seas_ref = NULL,
  seas_scale = 50,
  seas_buffer = NULL,
  urban_ref = NULL,
  aohi_rad = NULL,
  value = "spatialvalid",
  verbose = TRUE,
  report = FALSE
)

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”.

species

a character string. A vector of the same length as rows in x, with the species identity for each record. If NULL, tests must not include the "outliers" or "duplicates" tests.

countries

a character string. The column with the country assignment of each record in three letter ISO code. Default = “countrycode”. If missing, the countries test is skipped.

tests

a vector of character strings, indicating which tests to run. See details for all tests available. Default = c("capitals", "centroids", "equal", "gbif", "institutions", "outliers", "seas", "zeros")

capitals_rad

numeric. The radius around capital coordinates in meters. Default = 10000.

centroids_rad

numeric. The radius around centroid coordinates in meters. Default = 1000.

centroids_detail

a character string. If set to ‘country’ only country (adm-0) centroids are tested, if set to ‘provinces’ only province (adm-1) centroids are tested. Default = ‘both’.

inst_rad

numeric. The radius around biodiversity institutions coordinates in metres. Default = 100.

outliers_method

The method used for outlier testing. See details.

outliers_mtp

numeric. The multiplier for the interquartile range of the outlier test. If NULL outliers.td is used. Default = 5.

outliers_td

numeric. The minimum distance of a record to all other records of a species to be identified as outlier, in km. Default = 1000.

outliers_size

numerical. The minimum number of records in a dataset to run the taxon-specific outlier test. Default = 7.

range_rad

buffer around natural ranges. Default = 0.

zeros_rad

numeric. The radius around 0/0 in degrees. Default = 0.5.

capitals_ref

a data.frame with alternative reference data for the country capitals test. If missing, the countryref dataset is used. Alternatives must be identical in structure.

centroids_ref

a data.frame with alternative reference data for the centroid test. If NULL, the countryref dataset is used. Alternatives must be identical in structure.

country_ref

a SpatVector as alternative reference for the countries test. If NULL, the rnaturalearth:ne_countries('medium', returnclass = "sf") dataset is used.

country_refcol

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

country_buffer

numeric. Units are in meters. If provided, a buffer is created around each country polygon.

inst_ref

a data.frame with alternative reference data for the biodiversity institution test. If NULL, the institutions dataset is used. Alternatives must be identical in structure.

range_ref

a SpatVector of species natural ranges. Required to include the 'ranges' test. See cc_iucn for details.

seas_ref

a SpatVector as alternative reference for the seas test. If NULL, the rnaturalearth::ne_download(scale = 110, type = 'land', category = 'physical', returnclass = "sf") dataset is used.

seas_scale

The scale of the default landmass reference. Must be one of 10, 50, 110. Higher numbers equal higher detail. Default = 50.

seas_buffer

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

urban_ref

a SpatVector as alternative reference for the urban test. If NULL, the test is skipped. See details for a reference gazetteers.

aohi_rad

numeric. The radius around aohi coordinates in meters. Default = 1000.

value

a character string defining the output value. See the value section for details. one of ‘spatialvalid’, ‘summary’, ‘clean’. Default = ‘spatialvalid’.

verbose

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

report

logical or character. If TRUE a report file is written to the working directory, summarizing the cleaning results. If a character, the path to which the file should be written. Default = FALSE.

Value

Depending on the output argument:

“spatialvalid”

an object of class spatialvalid similar to x with one column added for each test. TRUE = clean coordinate entry, FALSE = potentially problematic coordinate entries. The .summary column is FALSE if any test flagged the respective coordinate.

“flagged”

a logical vector with the same order as the input data summarizing the results of all test. TRUE = clean coordinate, FALSE = potentially problematic (= at least one test failed).

“clean”

a data.frame similar to x with potentially problematic records removed

Details

The function needs all coordinates to be formally valid according to WGS84. If the data contains invalid coordinates, the function will stop and return a vector flagging the invalid records. TRUE = non-problematic coordinate, FALSE = potentially problematic coordinates.

  • capitals tests a radius around adm-0 capitals. The radius is capitals_rad.

  • centroids tests a radius around country centroids. The radius is centroids_rad.

  • countries tests if coordinates are from the country indicated in the country column. Switched off by default.

  • duplicates tests for duplicate records. This checks for identical coordinates or if a species vector is provided for identical coordinates within a species. All but the first records are flagged as duplicates. Switched off by default.

  • equal tests for equal absolute longitude and latitude.

  • gbif tests a one-degree radius around the GBIF headquarters in Copenhagen, Denmark.

  • institutions tests a radius around known biodiversity institutions from instiutions. The radius is inst_rad.

  • outliers tests each species for outlier records. Depending on the outliers_mtp and outliers.td arguments either flags records that are a minimum distance away from all other records of this species (outliers_td) or records that are outside a multiple of the interquartile range of minimum distances to the next neighbour of this species (outliers_mtp). Three different methods are available for the outlier test: "If “outlier” a boxplot method is used and records are flagged as outliers if their mean distance to all other records of the same species is larger than mltpl * the interquartile range of the mean distance of all records of this species. If “mad” the median absolute deviation is used. In this case a record is flagged as outlier, if the mean distance to all other records of the same species is larger than the median of the mean distance of all points plus/minus the mad of the mean distances of all records of the species * mltpl. If “distance” records are flagged as outliers, if the minimum distance to the next record of the species is > tdi.

  • ranges tests if records fall within provided natural range polygons on a per species basis. See cc_iucn for details.

  • seas tests if coordinates fall into the ocean.

  • urban tests if coordinates are from urban areas. Switched off by default

  • validity checks if coordinates correspond to a lat/lon coordinate reference system. This test is always on, since all records need to pass for any other test to run.

  • zeros tests for plain zeros, equal latitude and longitude and a radius around the point 0/0. The radius is zeros.rad.

Note

Always tests for coordinate validity: non-numeric or missing coordinates and coordinates exceeding the global extent (lon/lat, WGS84). See https://ropensci.github.io/CoordinateCleaner/ for more details and tutorials.

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

See also

Other Wrapper functions: clean_dataset(), clean_fossils()

Examples



exmpl <- data.frame(species = sample(letters, size = 250, replace = TRUE),
                    decimalLongitude = runif(250, min = 42, max = 51),
                    decimalLatitude = runif(250, min = -26, max = -11))

test <- clean_coordinates(x = exmpl, 
                          tests = c("equal"))
#> Testing coordinate validity
#> Flagged 0 records.
#> Testing equal lat/lon
#> Flagged 0 records.
#> Flagged 0 of 250 records, EQ = 0.
                                    
if (FALSE) { # \dontrun{
#run more tests
test <- clean_coordinates(x = exmpl, 
                          tests = c("capitals", 
                          "centroids","equal", 
                          "gbif", "institutions", 
                          "outliers", "seas", 
                          "zeros"))
} # }
                                 
                                    
summary(test)
#>     .val     .equ .summary 
#>        0        0        0