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Taxonomic Distinctness (Delta*)

Source: R/classical_indices.R
delta_star.Rd

Calculates the taxonomic distinctness (Delta*) from Warwick & Clarke (1995). This is the average weighted path length between individuals of different species only.

Usage

delta_star(community, tax_tree, weights = NULL)

Arguments

community

A named numeric vector of species abundances.

tax_tree

A data frame with taxonomic hierarchy.

weights

Optional numeric vector of path weights for each taxonomic level. If NULL, a linear scale is used (1, 2, 3, ...).

Value

A numeric value representing taxonomic distinctness (Delta*).

Details

$$\Delta^* = \frac{\sum\sum_{i<j} w_{ij} x_i x_j} {\sum\sum_{i<j} x_i x_j}$$

References

Warwick, R.M. & Clarke, K.R. (1995). New 'biodiversity' measures reveal a decrease in taxonomic distinctness with increasing stress. Marine Ecology Progress Series, 129, 301-305.

See also

delta() for taxonomic diversity (including same-species), avtd() and vartd() for presence/absence measures.

Examples

comm <- c(sp1 = 5, sp2 = 3, sp3 = 3, sp4 = 1, sp5 = 3)
tax <- data.frame(
  Species = paste0("sp", 1:5),
  Genus = c("G1", "G1", "G2", "G2", "G2"),
  Family = c("F1", "F1", "F1", "F2", "F2"),
  stringsAsFactors = FALSE
)
delta_star(comm, tax)
#> [1] 1.651163