[R-sig-phylo] ancestral state reconstruction with fixed internal node(s)

ppiras at uniroma3.it ppiras at uniroma3.it
Thu Jun 30 18:40:35 CEST 2011


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 then resolve this during
computation using multi2di() ) and assigning your
desired trait value.

I'm not sure if this helps....

Best
Paolo






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 value
from 0.2-0.5, and
then do the ancestral state reconstruction with this
restriction on that
node.

I have been searching the archives and the net for
discussion of this
(but maybe with the wrong search terms), and I cannot
find anything
about it - not how to do it in R or in any other
package.

Thanks for your input!
Annemarie

--
Annemarie Verkerk, MA
Evolutionary Processes in Language and Culture (PhD
student)
Max Planck Institute for Psycholinguistics
P.O. Box 310, 6500AH Nijmegen, The Netherlands
+31 (0)24 3521 185
http://www.mpi.nl/research/research-projects/evolutionary-processes

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