CoordinateCleaner (version 3.0.1)

cf_range: Identify Fossils with Extreme Age Ranges

Description

Removes or flags records with an unexpectedly large temporal range, based on a quantile outlier test.

Usage

cf_range(
  x,
  lon = "decimalLongitude",
  lat = "decimalLatitude",
  min_age = "min_ma",
  max_age = "max_ma",
  taxon = "accepted_name",
  method = "quantile",
  mltpl = 5,
  size_thresh = 7,
  max_range = 500,
  uniq_loc = FALSE,
  value = "clean",
  verbose = TRUE
)

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”.

Arguments

x

data.frame. Containing fossil records with taxon names, ages, and geographic coordinates.

lon

character string. The column with the longitude coordinates. To identify unique records if uniq_loc = TRUE. Default = “decimalLongitude”.

lat

character string. The column with the longitude coordinates. Default = “decimalLatitude”. To identify unique records if uniq_loc = T.

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”.

method

character string. Defining the method for outlier selection. See details. Either “quantile” or “mad”. Default = “quantile”.

mltpl

numeric. The multiplier of the interquartile range (method == 'quantile') or median absolute deviation (method == 'mad') to identify outliers. See details. Default = 5.

size_thresh

numeric. The minimum number of records needed for a dataset to be tested. Default = 10.

max_range

numeric. A absolute maximum time interval between min age and max age. Only relevant for method = “time”.

uniq_loc

logical. If TRUE only single records per location and time point (and taxon if taxon != "") are used for the outlier testing. Default = T.

value

character string. Defining the output value. See value.

verbose

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

See Also

Other fossils: cf_age(), cf_equal(), cf_outl(), write_pyrate()

Examples

minages <- runif(n = 11, min = 0.1, max = 25)
x <- data.frame(species = c(letters[1:10], "z"),
                lng = c(runif(n = 9, min = 4, max = 16), 75, 7),
                lat = c(runif(n = 11, min = -5, max = 5)),
                min_ma = minages, 
                max_ma = minages + c(runif(n = 10, min = 0, max = 5), 25))

cf_range(x, value = "flagged", taxon = "")