[R-sig-phylo] Detecting non-Brownian trait evolution
Emmanuel.Paradis at mpl.ird.fr
Tue Sep 9 16:35:55 CEST 2008
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().
> On Sep 9, 2008, at 9:48 AM, Alejandro Gonzalez Voyer wrote:
>> 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
>> with the heights of the nodes at which they are generated. Is there a
>> way of
>> implementing this analysis in R?
>> Thank you,
>> [[alternative HTML version deleted]]
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