Dear Alejandro, Paolo, and Liam,
thanks so much for your feedback on this - I was able to get Liam's
method to work on my trees and data. Very useful to be able to do!
Alejandro is right about BayesTraits, but indeed my data is continuous,
so I was disappointed to find out that BayesTraits
Dear phylo-sig list people,
I want to do ancestral state reconstruction (preferably with ace) with
one (or more) of the internal nodes 'fixed' for a range / a distribution
of values. For instance, I want a node leading to one particular clade
that is present a subset of my trees to have a
Hi AnneMarie,
I dont really know if this makes sense; in fact
ancestral state reconstruction is an ** a posteriori
estimation ** of nodal values starting from tips
observations.
A trick could be to add a false taxon lnked to that
node and giving to it a 0 branch length (i.e.
plitomized - you can
Hi AnneMarie,
The way Paolo suggests would be the best/right way to do this. We're
working on some methods for incorporating fossil info in comparative
methods and I have some code that will do this that i can send you
off-list if you would like. I should add that, at least based on what
Hi Annemarie,
I do think this makes sense - *if* (and this may be a big if,
depending on your data) we have a value for a hypothetical ancestor for
which we are very confident and which we are sure belongs at a
particularly ancestral node.
In that case, you could indeed use ace() by
...@ucla.edu]
Sent: Thursday, June 30, 2011 10:09 AM
To: r-sig-phylo@r-project.org
Subject: Re: [R-sig-phylo] ancestral state reconstruction with fixed internal
node(s)
Hi AnneMarie,
The way Paolo suggests would be the best/right way to do this. We're
working on some methods for incorporating fossil
