Good morning.
dichot_tree$edge.length-runif(n=nrow(dichot_tree$edge),min=0,max=1)
dichot_tree$edge.length[dichot_tree$edge.length1]-1
Why did you elect to do this? This just has the effect of setting all
the branch lengths of the tree to 1.
Question 1:_ Ace (from Paradis et al., ape
Hi Milton.
phytools has a function, ratebystate, that tests this hypothesis using
the admittedly ad hoc approach of correlating the squared contrasts
the states at each node. To read more about this method you can see some
posts on my blog: http://blog.phytools.org/search?q=ratebystate.
Hello all,
I have a question that is perhaps esoteric, since it's on a method I don't see
used often. I am looking at the dynamics of body size evolution, and have come
upon ancestor-vs-change plots described in Alroy 2000 (Understanding the
dynamics of evolutionary trends, Paleobiology). This
In Paleo, you can (well, arguably) see the ancestor and descendent pair, so
you can assess the amount of change and the ancestral state. Using just
info at the tips, you are inferring from N taxa N-1 ancestral states and
2N-2 rates of change. That seems a lot to ask from data, especially since
the
Hello all,
Very sorry for the double e-mail, I forgot to attach the plot mentioned.
Milton
From: R-sig-phylo r-sig-phylo-boun...@r-project.org on behalf of Milton Tan
mzt0...@tigermail.auburn.edu
Sent: Friday, April 24, 2015 2:14 PM
To:
Milton Tan asked:
I have a question that is perhaps esoteric, since it's on a method I don't
see used often. I am looking at the dynamics of body size evolution, and have
come upon ancestor-vs-change plots described in Alroy 2000 (Understanding
the dynamics of evolutionary trends,
