Hi Hai-Dong,

The R implementation of phylogenetic eigenvectors is found in package MPSEM. For more detail and bioinformatic workflow, please check this article: https://cran.r-project.org/web/packages/MPSEM/vignettes/MPSEM.pdf

I wish you good luck with your analysis.

Best,

Tegegn

Dear Tegegn,

Thank you very much! I will try MPSEM packge.

Regards,

Hai-Dong

Looking at the basics of the method, it seems simple to fit by yourself. You need to run a principal coordinate analysis (function pcoa in ape package) on a phylogenetic distance matrix, and then use the loadings of some of the axes as inputs in a linear regression (trait ~ pcoa1 + pcoa2...). The R² of the regression between the trait and selected eigenvectors is an estimate of phylogenetic signal. Also check the package PVR.

You should keep in mind that this method has been critized

Article The best of both worlds: Phylogenetic eigenvector regression...

Cheers