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
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.