Species' evolutionary distinctiveness
Calculates evolutionary distinctiveness measures for a suite of species by: a) equal splits (Redding and Mooers 2006) b) fair proportions (Isaac et al., 2007). Returns a datafram with species identifiers and species scores.
evol.distinct(tree, type = c("equal.splits", "fair.proportion"),
scale = FALSE, use.branch.lengths = TRUE)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. |
This function will return a vector of evolutionary distinctivenss for every species in the given tree. If only a subset of values are needed there are two, concetually distinct options: either prune the tree first and then pass the tree in or subset the resulting vector. These two options will provide very different outputs.
Karen Magnuson-Ford, Will Cornwell, Arne Mooers, Mark Vellend
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.
Mark Vellend, William K. Cornwell, Karen Magnuson-Ford, and Arne Mooers. In press. Measuring phylogenetic biodiversity. In: Biological diversity: frontiers in measurement and assessment. Edited by Anne Magurran and Brian McGill.
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