Appearance of new taxa and extinctions across time

Returns a data frame with the appearance of new taxa and their last appearances across time in the provided data and optionally produces a plot from it, showing the new appearances or last appearances.

Usage

pbdb_orig_ext(
  data,
  rank = c("species", "genus", "family", "order", "class", "phylum"),
  temporal_extent,
  res,
  orig_ext = 1,
  colour = "#0000FF30",
  bord = "#0000FF",
  ylab = NULL,
  do_plot = TRUE
)

Arguments

data

Data frame from a query to PaleobioDB as returned by pbdb_occurrences(). Important: it is required to show the name of the families, orders, etc. in the data frame, to do that set: show = c("classext", "ident") (see Examples).

rank

The taxon rank to be analyzed. Its default value is "species".

temporal_extent

Vector to set the temporal extent (min, max)

res

Numeric. Sets the intervals of the temporal extent.

orig_ext

Set to 1 to plot the number new appearances, or to 2 to plot the number of extinctions.

colour

Colour of the area of the polygon in the plot.

bord

Colour of the border of the polygon.

ylab

A label for the y axis.

do_plot

Logical value indicating whether to produce a plot (TRUE by default).

Value

A data frame with the number of first appearances and extinctions of the selected taxon rank across time.

Examples

if (FALSE) {
  canidae <- pbdb_occurrences(
    limit = "all", vocab = "pbdb",
    base_name = "Canidae", show = "classext"
  )

  # Plot of the evolutionary rates
  pbdb_orig_ext(
    canidae,
    rank = "genus",
    orig_ext = 1,
    temporal_extent = c(0, 10), res = 1
  )

  # Plot of the extinction rates
  pbdb_orig_ext(
    canidae,
    rank = "genus",
    orig_ext = 2,
    temporal_extent = c(0, 10), res = 1
  )
}