geiger (version 0.2-5)

delta.tree: Tree transformations

Description

Apply various transformation to the branches of a phylogenetic tree; These are meant to correspond with changing the model of phenotypic evolution for discrete or continuous characters

Usage

delta.tree(phy, delta, rescale = F)
lambda.tree(phy, lambda)
tworate.tree(phy, breakPoint, f) 
linearchange.tree(phy, endf)
rescale.tree(phy, total.length)

Arguments

phy

Phylogenetic tree

delta

Delta value. This is the transformation suggested by Pagel as a test for a slow-down or speed-up. Value of delta >1 disproporionately increase the length of external nodes (speed-up), where as values

lambda

Lambda value. This performs a transformation that was advocated by Pagel as a test of phylogenetic signal. Values of lambda are alwasys less than one. Each internal edge is multiplied by lambda, having the effect of reducing or eliminating phylogenetic

rescale

if TRUE, rescale tree to a total length of one before applying transformation

breakPoint

This splits the tree into two parts determined by the breakpoint

f

Branch lengths to the right of the breakpoint (i.e., toward the tips) are multiplied by some factor f. Thus, if f is greater than 1, these branches are made longer, whereas if f is less than 1 these branches are made shorter.

endf

This causes the rate of change to increase or decrease linearly, with the ratio of the beginning rate to the ending rate equal to endf

total.length

This is a general function that rescales the root to tip length of the tree to some pre-specified value.

Value

• Phylogenetic tree in ape format

References

PAGEL

Examples

data(geospiza)
attach(geospiza)

delta.tree(geospiza.tree, 0.5)->g2
plot(g2)
lambda.tree(geospiza.tree, 0.5)->g3
plot(g3)
tworate.tree(geospiza.tree, 0.5, 0.5)->g4
plot(g4)
linearchange.tree(geospiza.tree, 0.1)->g5
plot(g5)