Le 09.09.2008 16:13, Brian O'Meara a écrit :
You could look at OUCH, which implements Ornstein-Uhlenbeck models
(Hansen, 1997; Butler & King, 2004), to compare the fit of OU models vs
a single rate Brownian motion model as another way of testing for
non-Brownian evolution.
I cowrote a paper (O'Meara et al., 2006) that develops tests comparing
single rate and multiple rate Brownian motion models (the latter a
rejection of the basic BM model) -- there's now an implementation of the
most basic test (censored two-rate) in the R package TreEvo, available
from R-forge, not CRAN. It works, but I haven't written documentation
yet, and it depends on phylobase (also R-forge, not CRAN).
For the node height test, ape's pic function can generate contrasts. If
you can figure out the node order in which it returns them, you could
then compare the pics vs. the node heights that way. There may be other
packages that do this, too.
branching.times() will return the node heights in the same order than
the contrasts returned by pic().
EP
Best,
Brian
On Sep 9, 2008, at 9:48 AM, Alejandro Gonzalez Voyer wrote:
Hello,
I want to analyze whether the evolution of certain traits within a clade
fits a niche-filling model. I've looked at GEIGER and the different tests
offered within that package to analyze the tempo and mode of evolution of
continuous traits. I also wanted to implement the Node height test: where
one tests whether the absolute value of independent contrasts is
correlated
with the heights of the nodes at which they are generated. Is there a
way of
implementing this analysis in R?
Thank you,
Alejandro
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