chrono_scale {fossilbrush}

chrono_scale

Description

Convenience function to apply user-specified chronostratigraphy to fossil datasets. The function relies on a lookup table generated based on the named intervals in the PBDB in early 2021. First and last interval names in the supplied dataset are matched against this lookup table, by default using 'get("GTS_2020)", to get GTS_2020 numeric ages. If the dataset contains intervals which are not present in the lookup table, they will not be matched and the user will be warned. To get around this possibility, the user can also supply the original numeric ages which will be used as default ages if an interval cannot be matched, to ensure that the returned vectors of numeric ages do not contain NAs.

Usage

chrono_scale(
  x,
  tscale = "GTS_2020",
  srt = "early_interval",
  end = "late_interval",
  max_ma = NULL,
  min_ma = NULL,
  verbose = TRUE
)

Arguments

x

A data.frame containing, minimally two columns corresponding respectively to the first and last intervals of the data. Values should only be present in the second column where the minimum age interval for a row is different to the maximum age interval. Otherwise the values should be NA and the ages returned will be based on the interval specified in the first column, in line with PBDB formatting.

tscale

A character string specifying one of the inbuilt chronostratigraphic timescales (currently GTS 2020 only) or a data.frame supplied by the user. If the latter, this must contain columns named 'Interval', 'FAD', 'LAD', specifying the interval names to be matched and their lower and upper age in Ma

srt

A character of length 1 specifing the column name of the first interval field in x

end

A character of length 1 specifing the column name of the last interval field in x

max_ma

If not NULL, a character of length 1 specifing the column name of the original numeric maximum age field in x, to be used as fall back values if interval names cannot all be matched

min_ma

If not NULL, a character of length 1 specifing the column name of the original numeric minimum age field in x, to be used as fall back values if interval names cannot all be matched

verbose

A logical indicating if warning messages should be displayed or otherwise

Value

The dataframe, x, with two additional columns containing the revised first and last numeric ages of the data, with column names GTS_FAD and GTS_LAD respectively

Examples

# example dataset
data("brachios")
# add GTS_2020 dates
brachios <- chrono_scale(brachios, srt = "early_interval", end = "late_interval",
                          max_ma = "max_ma", min_ma = "min_ma")