phytools: getExtant – R documentation

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getExtant

Returns a list of the extant or extinct lineages in a tree containing non-contemporaneous tips

Description

The function getExtant takes a tree as input and returns a vector containing the names of all the tips that have a height above the root that is equal (to a degree of numerical precision determined by tol) to the height of the highest tip.

getExtinct returns the complement.

Usage

getExtant(tree, tol=1e-8)
getExtinct(tree, tol=1e-8)

Arguments

`tree`	a phylogeny stored as an object of class `"phylo"` with some tips that are non-contemporaneous (i.e., end before the present).
`tol`	a tolerance value to account for numerical imprecision.

Value

A vector with the tip names of extant or extinct species in the tree.

Author(s)

Liam Revell liam.revell@umb.edu

References

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.