tip_grafts: Grafts tips on phylogenies

In mrhelmus/ieco: Functions used to perform integratice ecology research

Description

Places tips and clades where you want on a phylogeny. These functions are good for adding missing taxa in ecophylogenetic analyses when you have a good phylogeny, and only need to graft a few missing taxa with a good hypothesis as to where they should go.

tipXtip adds a tip halfway the distance between a supplied tip and its MRCA.

tipXnode adds a tip halfway the distance between a supplied set of nodes that define one edge

treeXnode adds a clade halfway the distance between a supplied set of nodes that define one edge

tree_scale linear scaling of a tree, use this to change the root age of a tree to the scale parameter, while scaling all branch lengths and node ages proportional to this change. Does not change relative relationships among nodes and tips.

Usage

tipXtip(tree, addtip, where.tip = NULL)

tipXnode(tree, addtip, where.nodes = NULL)

treeXnode(tree, addtree, where.nodes = NULL, tip.out = "tip.out")

tree_scale(tree, scale)

Arguments

tree	phylgeny of class phylo, this is the starting tree
addtip	name of the tip to add
where.tip	name of the tip
where.nodes	vector of two node numbers to insert the tip between
addtree	phylgeny of class phylo to add
tip.out	tip label of the outgroup tip that defines the stem of the clade to be grafted
scale	scalar to multiply all edges of a tree

Value

a phylo with the grafted tip

Author(s)

Matthew R. Helmus

See Also

bind.tip bind.tree

for tree_scale see the code at Phytools Blog and rescaleTree

mrhelmus/ieco documentation built on May 23, 2019, 7:37 a.m.