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Temporal variation in taxon richness

Source: R/pbdb_temporal_functions.R
pbdb_richness.Rd

Returns a data frame of temporal variation in taxon richness in the indicated temporal extent and resolution from the provided occurrence data and optionally produces a plot from it.

Usage

pbdb_richness(
  data,
  rank = c("species", "genus", "family", "order", "class", "phylum"),
  res = 1,
  temporal_extent = c(0, 10),
  colour = "#0000FF30",
  bord = "#0000FF",
  ylab = "Richness",
  do_plot = TRUE
)

Arguments

data

Data frame from a query to PaleobioDB as returned by pbdb_occurrences(). Important: it is required to have information about the taxonomic classification of the occurrences in the data frame, to do that set the show parameter to "class" or "classext" (see Examples).

rank

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

res

Numeric. Sets the duration of the intervals in the temporal extent.

temporal_extent

Numeric vector to set the temporal extent (min, max).

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

Value

A data frame with the richness aggregated by the taxon rank in the specified temporal extent and resolution.

Examples

if (FALSE) {
  data <- pbdb_occurrences(
    limit = "all",
    vocab = "pbdb",
    base_name = "Canidae",
    show = "class"
  )
  pbdb_richness(data, rank = "species", res = 0.2, temporal_extent = c(0, 3))
}