singleSpeciesTree: Create a single-species tree

In eliotmiller/addTaxa: An R package for adding missing taxa to phylogenies

Create a single-species tree

Description

Generate a single-species tree with appropriate stem branch length

Usage

singleSpeciesTree(tree, tip)

Arguments

tree	An ape-style phylogenetic tree.
tip	A character vector corresponding to one of the species in the phylogeny.

Details

Ape cannot readily deal with single-species trees. This functions will extract a single-species tree with appropriate branch length to the most recent common ancestor. The tree cannot be plotted, but it can be used for analyses.

Value

A single-species phylo object.

References

Mast et al. 2015. Paraphyly changes understanding of timing and tempo of diversification in subtribe Hakeinae (Proteaceae), a giant Australian plant radiation. American Journal of Botany.

Examples

#load a molecular tree up
data(bird.families)

#extract a single-species tree
tree <- singleSpeciesTree(bird.families, "Rheidae")

eliotmiller/addTaxa documentation built on Feb. 3, 2024, 12:19 a.m.