I just wanted to clarify one thing. Agus wrote:
" Under the case of phylo dependence, all off-diagonal values are expected
to
be non zero "
That is incorrect for species on opposite sides of the root of the
phylogenetic tree, as they have zero shared phylogenetic history in the
context of the
Hello,
I used the code insertion that Emmanuel provided, and that solved my issue.
Thank you all for the help and discussion!
Pascal, if you're looking for a tutorial, this is the first one I found
when I started:
http://www.phytools.org/eqg/Exercise_3.2/
I've found it *very* helpful. I've also
Many thanks to all for your very helpful references, commands and examples.
For the sake of future readers, a summary of the off-list discussions and
further reading.
Andrew Hipp provided a very didactic way to look at the vcv matrix as a
triangular distance matrix
library(geiger)
tr <-