Hi all,
I've noticed that apTreeshape's _colless_ and _colless.test_ functions can give
normalised/standardised Ic values outside the expected range of 0-1.
For example,
getcolless - function(tips) {
# randomly generate a tree, and get the normalized Colless score.
Dear Simon,
Normalization does not necessarily returns values between 0 and 1 but
returns the values of the summary statistics divided by the standard
deviation of the summary statistics that is expected under the Yule
model. If you want to use that renormalization to compare tree shapes
for
try
diag(vcv.phylo(your.tree))
Cheers,
Simon.
On 03/09/12 19:17, boyang zhe wrote:
Hi, everyone
I am new to ape and R programming. I have an unrooted tree. I use
root() function to reroot the tree by one outgroup. and then I try to
extract root to tip distance. the tree$edge.length only
Hi. Try:
diag(vcv.phylo(tree))
nodeHeights in phytools will also give you a matrix with all the heights of
internal and terminal nodes in the same order as tree$edge.
- Liam
Liam J. Revell
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
