fairProportions: Calculate fair proportions phylogenetic diversity metric

In PuttickMacroevolution/motmot: Models of Trait Macroevolution on Trees

Description

Calculate fair proportions phylogenetic diversity metric Note that as.rateMatrix calls the CAIC function vcv.array multiple times and this can be slow for large phylogenies (though faster than using the "ape" equivalent vcv.phylo).

Usage

fairProportions(phy, nodeCount = FALSE)

Arguments

phy	An object of class phylo (see ape).
nodeCount	Logical - should root to tip node counts be returned (default is FALSE)

Value

Returns a matrix of fair proportion for all tips in phylogeny and node counts if selected.

Author(s)

Gavin Thomas

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.

Examples

data(anolis.tree)

fp <- fairProportions(anolis.tree)
fpNodes <- fairProportions(anolis.tree, nodeCount=TRUE)

PuttickMacroevolution/motmot documentation built on June 5, 2020, 7 p.m.