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.
evol_distinct(
tree,
type = c("equal.splits", "fair.proportion"),
scale = FALSE,
use.branch.lengths = TRUE,
...
)an object of class phylo.
a) equal splits (Redding and Mooers 2006) or b) fair proportions (Isaac et al., 2007)
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.
If use.branch.lengths=FALSE, then all branch lengths are changed to 1.
Further arguments passed to or from other methods.
a named vector with species scores.
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.
tree <- ape::rcoal(10)
evol_distinct(tree)
#> t5 t4 t6 t9 t2 t3 t8 t10
#> 0.6717092 0.6717092 1.0438740 0.6128804 0.6128804 0.2777347 0.2777347 0.3398900
#> t7 t1
#> 0.3398900 0.9133170
evol_distinct(tree, type = "fair.proportion")
#> t5 t4 t6 t9 t2 t3 t8 t10
#> 0.6662238 0.6662238 0.9637152 0.6584452 0.6584452 0.3432634 0.3432634 0.4054188
#> t7 t1
#> 0.4054188 0.6512021