Hi all,
I'm looking for some advice on and thoughts regarding performing a
phylogenetic generalized least squares analysis in R.
I've tried GLS from the nlme package using corBrownian and corMartins from
the ape package and get one set of results (I've come to accept my dataset
isn't representing brownian evolution, so I've discarded those results,
leaving me with the OU results).
I've also tried PGLS from the cape package, having it estimate the 3
different Pagel parameters. After optimizing these parameters, I get
different results from those of the OU (corMartins) GLS analysis.
I'm wondering what is to blame for these drastically different results?
The different parameters that the two methods are estimating?
Is it the difference between using REML in the GLS vs. ML in the PGLS?
Do people have particular preferences for running these types of analyses?
Should I feel okay about estimating all three Pagel parameters at the same
time with PGLS?
Any insight or thoughts would be greatly appreciated.
Thanks,
Will
--
William Gearty
PhD Student, Paleobiology
Department of Geological and Environmental Sciences
Stanford School of Earth, Energy & Environmental Sciences
people.stanford.edu/wgearty
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