delta.tree {geiger}R Documentation

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 <1 disproportionately increase the length of internal nodes (slow-down).
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 signal.
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.

Details

Value

Phylogenetic tree in ape format

Note

Author(s)

Luke J. Harmon

References

PAGEL

See Also

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)


[Package geiger version 0.2-6 Index]