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.
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.