delta.tree {geiger} | R Documentation |
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
delta.tree(phy, delta, rescale = F) lambda.tree(phy, lambda) tworate.tree(phy, breakPoint, f) linearchange.tree(phy, endf) rescale.tree(phy, total.length)
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. |
Phylogenetic tree in ape format
Luke J. Harmon
PAGEL
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)