R: Add species to genus on a phylogeny

add.species.to.genus {phytools}

R Documentation

Add species to genus on a phylogeny

Description

This function adds an additional species to a genus on a phylogeny.

Usage

add.species.to.genus(tree, species, genus=NULL, where=c("root","random"))

Arguments

`tree`	an object of class `"phylo"`.
`species`	string contain species name in the format `"Genus_species"` or `"Genus species"`.
`genus`	optional argument containing the genus to which `species` is to be attached. If `NULL` then `genus` will be extracted from `species`.
`where`	location to attach `species` to the tree. `where="root"` will cause the species to be attached to the MRCA of all members of `genus`. `where="random"` will cause `species` to be attached at random to the subtree descended from the MRCA of all members of `genus`.

Details

If genus contains only one species and where="root", then species will be attached midway along the branch leading to the one species. If where="random" then species will be added at a random position along the edge. If genus cannot be found in the tree, then the original tree is returned and a warning printed. If the tree is not ultrametric, then the resultant tree may not contain branch lengths and a warning will be printed. If genus is non-monophyletic then species will be attached to the most inclusive group containing members of genus and a warning will be printed.

Value

An object of class "phylo".

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.