Hi David,
It's a follow-up on your message.
David Williams wrote on 22/06/2011 07:31:
Dear R users and phylogeneticists,
I've been manipulating some phylo objects mostly with ape functions but
also with some phangorn functions. I'm a bit confused with some effects
of rerooting and the
Hi Morgan,
this is just stuff for thought, and remember, this is wrong anyway. But you
may try something like this:
1. compute pics,
2. take the pic value at the ancestral node subtending to your unknown tip,
3. pretend one of the two tips the pic was originally computed on is in fact
your
Also, the issue of predicting values for unknown tips using data from other
species in the tree is considered in this reference:
Garland, T., and A. R. Ives. 2000. Using the past to predict the present:
confidence intervals for regression equations in phylogenetic comparative
methods. American
The methods in the Garland and Ives (2000) paper are in our package of DOS PDAP
programs, and should also be functional in the PDAP module of Mesquite.
Cheers,
Ted
Theodore Garland, Jr.
Professor
Department of Biology
University of California, Riverside
Riverside, CA 92521
Office Phone: (951)
Of course Ted is right, but my problem with this computation, or with the
simple exercise I was proposing is well another: as a paleontologist I often
come across pretty exceptional phenotypes (dwarf hippos and elephants, huge
flightless birds, to make a few examples). When you use methods
Pasquale Raia said:
Of course Ted is right, but my problem with this computation, or
with the
simple exercise I was proposing is well another: as a
paleontologist I often
come across pretty exceptional phenotypes (dwarf hippos and
elephants, huge
flightless birds, to make a few
As the diversity of explicit models of trait evolution grow, it will
be interesting to see if any consensus develops about which models
hold most often in general and whether any insight is gained into
which conditions predict appearance of different models.
I think Joe is right that realizing a
David Bapst wrote:
I think Joe is right that realizing a model is an inaccurate or
imprecise description of reality should impel us to develop better
models of the world around us, because this partly how science moves
forward. However, I don't think pointing out that a model is deficient
Hello everyone. I just wanted to say thank you for all of the
responses so far and have thoroughly enjoyed the discussion. Just for
reference I thought I would explain what I am doing in more detail and
why I asked my original question.
I am interested in developing a practical method for using
Hi All,
I'm happy I have stimulated some discussion about this subject matter. For
some reason I can't imagine it looks this whole thing is going to be somehow
personal and I have not posted this last e-mail to the list as a consequence.
Joe, unfotunately I never attended a lecture of yours,
Folks --
I was intending my most recent message to be apologetic --
that I was perhaps overreactive. Certainly Pas has not
raised unreasonable objections or been obstructive with
my grants! (Others have).
Let me raise an issue so I understand him more clearly:
Pas, are you saying that you see
Pas said:
What I', trying to do now is writing a R routine to back-calculate
the expected branch lengths for the unusual critters, given the
fitted ancestral values and tip values of the phenotypes, and
assuming BM, in order to compare the actual branch lengths to the
expected. The
Hi Pas,
No worries, we have all done an accidental Reply All more than once!
I estimated ancestral (and tip) values for which I have real data via
BM assumption to see how good the fit is
Can you clarify? Unless you have some a priori hypothesis to test about a
particular tip (or set of
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