Hi,
ASReml is another option, which uses REML. It takes 1/10th of a second
on a 1000 tip phylogeny and is considerably more flexible.
fit-asreml(y~x,random=~giv(species),data=dat,ginverse=list(species=sm2asreml(Ainv)))
# with the data set up as:
ntips-1000
tree-rcoal(ntips) #
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
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)
# assuming
