A function to calculate the temporal range of fossil taxa from occurrence data.
Usage
tax_range_time(
occdf,
name = "genus",
min_ma = "min_ma",
max_ma = "max_ma",
by = "FAD",
plot = FALSE
)
Arguments
- occdf
dataframe
. A dataframe of fossil occurrences containing at least three columns: names of taxa, maximum age and minimum age (seename
,min_ma
, andmax_ma
arguments). These ages should constrain the age range of the fossil occurrence and are assumed to be in millions of years before present.- name
character
. The name of the column you wish to be treated as the input names, e.g. "genus" (default).- min_ma
character
. The name of the column you wish to be treated as the minimum limit of the age range, e.g. "min_ma" (default).- max_ma
character
. The name of the column you wish to be treated as the maximum limit of the age range, e.g. "max_ma" (default).- by
character
. How should the output be sorted? Either: "FAD" (first-appearance date; default), "LAD" (last-appearance data), or "name" (alphabetically by taxon names).- plot
logical
. Should a plot of the ranges be generated?
Value
A dataframe
containing the following columns:
unique taxa (taxon
), taxon ID (taxon_id
), first appearance of taxon
(max_ma
), last appearance of taxon (min_ma
), duration of temporal
range (range_myr
), and number of occurrences per taxon (n_occ
) is
returned.
Details
The temporal range(s) of taxa are calculated by extracting all
unique taxa (name
column) from the input occdf
, and checking their first
and last appearance. The temporal duration of each taxon is also calculated.
A plot of the temporal range of each taxon is also returned if plot = TRUE
.
If the input data columns contain NAs, these should be removed prior to
function call.
Note: this function provides output based solely on the user input data. The true duration of a taxon is likely confounded by uncertainty in dating occurrences, and incomplete sampling and preservation.