Hi Antigoni.
The other responders are correct, but just to be a little more concrete:
# using ape & nlme
library(ape); library(nlme)
# assuming your data are contained in named vectors x & y
y<-y[names(x)]
fit<-gls(y~x,data.frame(x,y),correlation=corPagel(1,tree,fixed=FALSE),method="ML")
# assum
Hi Antigoni,
I would also suggest looking at the caper package by Orme et al.
(http://cran.r-project.org/web/packages/caper/index.html) it has PGLS with
lambda transforms and it allows you to look at the likelihood surface for the
lambda estimate as well.
Sam
---
Hi Antigoni
try the new package by Carl Boettiger "pmc"
it seems to be suited EXACTLY for you purpose (if I did not misanderstand...)
ciaoo
paolo
Da: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] per
conto di Alejandro Gonzalez Voye
Hi Antigoni
You can try ape (and nlme) with the functions gls and corPagel (the latter to
define the covariance structure, ie the evolutionary model) and also caper (I
don't know the exact function there).
Cheers
Alejandro
_
Dr. Alejandro Gonzalez Voyer
E
Hello everyone,
I am trying to implement Liam Revell's suggestion on the evaluation of
Pagel's lambda simultaneous to fitting PGLS to minimize the effects of
wrong model selection (OLS vs. PGLS) on species data (i.e. Revell 2010,
Methods in Ecology and Evolution 1: 319-329).
Does anyone know
