Excellent. I have added those function to phytools on GitHub, so they
can be installed using devtools as follows:
library(devtools)
install_github("liamrevell/phytools")
Glad it was of help. - Liam
Liam J. Revell, Associate Professor of Biology
University of Massachusetts Boston
web:
Thank you very much! That actually solved my problem.
I couldn't express myself clearly but that was what I wanted.. that nodes
with the same maximum path length to the tips should have the same height..
>From a layman perspective that way to compute branch lengths is actually
more logic for a
Hi Carlos.
After thinking about this, I realized that what you probably want is not
a node depth based on the number of nodes above that node - but the
based on the maximum number of nodes separating that node from any leaf.
I just posted a second solution for this on my blog here:
Hi Carlos.
The edge lengths used for plotting (and thus the 'merge depths') are
completely arbitrary when none are supplied. The algorithm used to
compute the edge lengths is in the documentation for compute.brlen as
follows:
"Grafen's (1989) computation of branch lengths: each node is
Dear list,
TL;DR: When I plot the newick tree A,B),C,D),E),(((F,G),H),I));
shouldn't ((A,B),C,D) merge at the same level as ((F,G),H)?
Or in a phylogenetic tree it doesn't matter?
library(ape)
newickTree <- read.tree(text="A,B),C),E),(((F,G),H),I));")
plot(newickTree)
goes just fine but
