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Average Taxonomic Distinctness (Delta+)

Source: R/classical_indices.R
avtd.Rd

Calculates the average taxonomic distinctness (AvTD, Delta+) based on Clarke & Warwick (1998). This is a presence/absence-based measure of the average taxonomic distance between all pairs of species.

Usage

avtd(species, tax_tree, weights = NULL)

Arguments

species

Character vector of species names present in the community (presence-only data).

tax_tree

A data frame representing the taxonomic hierarchy.

weights

Optional numeric vector of weights for taxonomic levels.

Value

A numeric value representing the average taxonomic distinctness (Delta+).

References

Clarke, K.R. & Warwick, R.M. (1998). A taxonomic distinctness index and its statistical properties. Journal of Applied Ecology, 35, 523-531.

Examples

tax <- data.frame(
  Species = c("Quercus_robur", "Pinus_nigra", "Fagus_orientalis",
              "Abies_nordmanniana"),
  Genus = c("Quercus", "Pinus", "Fagus", "Abies"),
  Family = c("Fagaceae", "Pinaceae", "Fagaceae", "Pinaceae"),
  Order = c("Fagales", "Pinales", "Fagales", "Pinales"),
  stringsAsFactors = FALSE
)

spp <- c("Quercus_robur", "Pinus_nigra", "Fagus_orientalis")
avtd(spp, tax)
#> [1] 2.666667