Geographic and Temporal Cleaning of Records from Fossil Collections

Cleaning records by multiple empirical tests to flag potentially erroneous coordinates and time-spans, addressing issues common in fossil collection databases. Individual tests can be activated via the tests argument:

clean_fossils(
  x,
  lon = "decimalLongitude",
  lat = "decimalLatitude",
  min_age = "min_ma",
  max_age = "max_ma",
  taxon = "accepted_name",
  tests = c("agesequal", "centroids", "equal", "gbif", "institutions", "spatiotemp",
    "temprange", "validity", "zeros"),
  countries = NULL,
  centroids_rad = 0.05,
  centroids_detail = "both",
  inst_rad = 0.001,
  outliers_method = "quantile",
  outliers_threshold = 5,
  outliers_size = 7,
  outliers_replicates = 5,
  zeros_rad = 0.5,
  centroids_ref = NULL,
  country_ref = NULL,
  inst_ref = NULL,
  value = "spatialvalid",
  verbose = TRUE,
  report = FALSE
)

Arguments

x: data.frame. Containing fossil records, containing taxon names, ages, and geographic coordinates..
lon: character string. The column with the longitude coordinates. Default = “decimalLongitude”.
lat: character string. The column with the latitude coordinates. Default = “decimalLatitude”.
min_age: character string. The column with the minimum age. Default = “min_ma”.
max_age: character string. The column with the maximum age. Default = “max_ma”.
taxon: character string. The column with the taxon name. If “”, searches for outliers over the entire dataset, otherwise per specified taxon. Default = “accepted_name”.
tests: vector of character strings, indicating which tests to run. See details for all tests available. Default = c("centroids", "equal", "gbif", "institutions", "temprange", "spatiotemp", "agesequal", "zeros")
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.
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_threshold: numerical. The multiplier for the interquantile range for outlier detection. The higher the number, the more conservative the outlier tests. See cf_outl for details. Default = 3.
outliers_size: numerical. The minimum number of records in a dataset to run the taxon-specific outlier test. Default = 7.
outliers_replicates: numeric. The number of replications for the distance matrix calculation. See details. Default = 5.
zeros_rad: numeric. The radius around 0/0 in degrees. Default = 0.5.
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.
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.
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

agesequal tests for equal minimum and maximum age.
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.
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.
spatiotemp test for records which are outlier in time and space. See below for details.
temprange tests for records with unexpectedly large temporal ranges, using a quantile-based outlier test.
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. The outlier detection in ‘spatiotemp’ is based on an interquantile range test. In a first step a distance matrix of geographic distances among all records is calculate. Subsequently a similar distance matrix of temporal distances among all records is calculated based on a single point selected by random between the minimum and maximum age for each record. The mean distance for each point to all neighbours is calculated for both matrices and spatial and temporal distances are scaled to the same range. The sum of these distanced is then tested against the interquantile range and flagged as an outlier if \(x > IQR(x) + q_75 * mltpl\). The test is replicated ‘replicates’ times, to account for temporal uncertainty. Records are flagged as outliers if they are flagged by a fraction of more than ‘flag_thresh’ replicates. Only datasets/taxa comprising more than ‘size.thresh’ records are tested. Note that geographic distances are calculated as geospheric distances for datasets (or taxa) with fewer than 10,000 records and approximated as Euclidean distances for datasets/taxa with 10,000 to 25,000 records. Datasets/taxa comprising more than 25,000 records are skipped.

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.

Examples