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
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 <-
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
