Hi all,
Can anyone suggest an easy way of determining Strahler numbers of nodes on
a given phylogenetic tree (see http://en.wikipedia.org/wiki/Strahler_number for
details).
I have been trying this out (manually plotting the numbers) with another
set of metrics for estimating branching complexity
Hello all,
I've read some past posts and tried to figure this one out myself. It
appears that the short answer is if there are not some extinct lineages in
the tree with known trait values, it's difficult to do.
I have a data set of the current climatic niches of a continental radiation
of taxa.
We have a method in R, TreEvo, that can allow you to do things like have a
model where the optimum shifts through time according to some factor (like
external data on climate) or where there are constraints that change
through time: it's up on R-forge, and you can install the package, but it
If you want to do a Bayesian reconstruction for continuous traits with a
strong prior on the root - as Brian suggests - you can do this in the
phytools function anc.Bayes. The prior means variances need to be
provided in anc.Bayes(...,control=list(pr.var,pr.mean)). Unfortunately,
you need to
Hi Eliot and others,
You can also use the code contained in the fitContinuousMCMC package
available here -
https://www.eeb.ucla.edu/gradstudents/slater/Graham/code.html
And described in this paper -
http://onlinelibrary.wiley.com/doi/10./j.1558-5646.2012.01723.x/abstrac
t
To place a
Hi Alastair.
If I understand this correctly, you should be able to compute the
Strahler number for the tree (and all the nodes) with one post-order
tree traversal - which is easy if you reorder the tree pruningwise
using the ape function reorder.phylo.
I have written a function that I think
