Salut Sandra,
I have experienced that the matrix given by vcv can lead to wrong results
if taken as a correlation matrix in the case of trees where the tips do not
have the same lengths.
I then built my own correlation, using the common branch length shared by
two tips, normalized by this same
Hi,
Xavier: if I understand correctly what you describe, this can be done with:
V - vcv(phy, corr = TRUE)
diag(V) - 0
vcv() returns the expected variance-covariance matrix under Brownian
motion for a given tree. If this tree is not ultrametric (I guess this
is what you mean with where the
Dear list,
I am trying to run a gls with an OU correlation structure using corMartins.
I first wanted to check whether i had a phylogenetic autocorrelation in my
trait, so i used the Moran's I index (Moran.I):
vcovm-vcv(corMartins(1,tree, fixed=T))
Moran.I(trait, vcovm, alt=greater)
And i
