customAdd: Bind species to hypothesized relatives in a phylogeny

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

Bind species to hypothesized relatives in a phylogeny

Description

Given a data frame of species and taxonomic assignments, and an accepted phylogeny with some of those species in it, will add the missing species in next to a taxonomic relative. Optionally, can keep track of which named clades species are bound to.

Usage

customAdd(tree, addition.statements, no.trees)

Arguments

tree	An ape-style phylogenetic tree.
addition.statements	See details.
no.trees	The number of desired final trees with all missing species from groupings added.

Details

All the gory stuff.

Value

A list with two elements: (1) multiPhylo object with number of trees as determined by no.trees, and, if clade.membership was provided, (2) a list of data frames summarizing the addition results.

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.

eliotmiller/addTaxa documentation built on Sept. 29, 2024, 8:33 p.m.