Dear Fabio,
Andrew is correct in his answer regarding the new behavior of OUCH
(thanks Andrew). In the new version of OUCH, the hansen fit has been
modified so that the ancestral state at the root is no longer
estimated, but it is rather assumed to be in one of the regimes in the
dataset.
Dear Fabio,
In ouch v2 and up, the root state is not treated as a free parameter
and is not returned. One way to think about your question might be to
assume that the branches at the base of the tree have their own optimum,
and then treat that optimum as the root state. But in doing so, you
shoul
Hi Graham,
thanks for the reply.
I don't know if this a particular problem for my kind of data (various
characters), but I'm not receiving any "Theta zero" on the output.
Just thetas for each selective regime. Is this a version problem? I'm
with ouch v. 2.5-7
I do realize that in complex
Hi Fabio,
I believe the reconstructed condition at the root is given in OUCH's
output as Theta zero, in the list of thetas. Be careful with this
though, as when selection is strong and you have multiple optima, the
reconstructed root node value tends to be very (unrealistcally) small.
But
Dear all,
I'm trying to reconstruct the ancestral state of a small set of
morphometric traits. My problem is that these variables seams to be
strongly influenced by selection, something that would violate the
brownian-motion model. I tested various models for character evolution
using the
