[R-sig-phylo] Detecting non-Brownian trait evolution

Emmanuel Paradis 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().

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
>>
>>
>>
>>
>>
>>
>>     [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> R-sig-phylo mailing list
>> R-sig-phylo at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> 
> _______________________________________________
> R-sig-phylo mailing list
> R-sig-phylo at r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> 

-- 
Emmanuel Paradis
IRD, Montpellier, France
   ph: +33 (0)4 67 16 64 47
  fax: +33 (0)4 67 16 64 40
http://ape.mpl.ird.fr/



More information about the R-sig-phylo mailing list