Identify Fossils with Extreme Age Ranges
Removes or flags records with an unexpectedly large temporal range, based on a quantile outlier test.
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 )
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 |
lat |
character string. The column with the longitude coordinates.
Default = “decimallatitude”. To identify unique records if |
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
( |
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 |
uniq_loc |
logical. If TRUE only single records per location and time
point (and taxon if |
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. |
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”.
See https://ropensci.github.io/CoordinateCleaner/ for more details and tutorials.
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 = "")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.