evol_distinct: Species' evolutionary distinctiveness

In darunabas/phyloregion: Biogeographic Regionalization and Macroecology

Species' evolutionary distinctiveness

Description

Calculates evolutionary distinctiveness measures for a suite of species by: a) equal splits (Redding and Mooers 2006) b) fair proportions (Isaac et al., 2007). This a new implementation of the picante function evol.distinct however allowing multifurcations and can be orders of magnitude faster.

Usage

evol_distinct(
  tree,
  type = c("equal.splits", "fair.proportion"),
  scale = FALSE,
  use.branch.lengths = TRUE,
  ...
)

Arguments

tree	an object of class phylo.
type	a) equal splits (Redding and Mooers 2006) or b) fair proportions (Isaac et al., 2007)
scale	The scale option refers to whether or not the phylogeny should be scaled to a depth of 1 or, in the case of an ultrametric tree, scaled such that branch lengths are relative.
use.branch.lengths	If use.branch.lengths=FALSE, then all branch lengths are changed to 1.
...	Further arguments passed to or from other methods.

Value

a named vector with species scores.

Author(s)

Klaus Schliep

References

Redding, D.W. and Mooers, A.O. (2006). Incorporating evolutionary measures into conservation prioritisation. Conservation Biology, 20, 1670–1678.

Isaac, N.J.B., Turvey, S.T., Collen, B., Waterman, C. and Baillie, J.E.M. (2007). Mammals on the EDGE: conservation priorities based on threat and phylogeny. PLoS ONE, 2, e296.

See Also

evol.distinct, phyloregion

Examples

tree <- ape::rcoal(10)
evol_distinct(tree)
evol_distinct(tree, type = "fair.proportion")

darunabas/phyloregion documentation built on Oct. 27, 2024, 10:01 p.m.