Hi Miguel,
The output from vcv() is as expected. Maybe you need to have a look at the
reference cited in ?vcv to see how phylogenetic VCV is computed.
For instance, take a tree with 2 taxa, they look (phylogenetically)
independent:
R> vcv(read.tree(text = "(a:1,b:1);"))
a b
a 1 0
b 0 1
But if you add a third taxon outgroup of these two:
R> vcv(read.tree(text = "((a:1,b:1):1,c:1);"))
a b c
a 2 1 0
b 1 2 0
c 0 0 1
HTH
Emmanuel
----- Le 25 Sep 24, à 12:42, Miguel Hernández González
[email protected] a écrit :
> Good afternoon,
> My name is Miguel Hernández González and I am a PhD student at the University
> of
> Antwerp. I am currently trying to carry out a meta-analysis, but I am having
> problems to include the phylogenetic matrix in the models. When I create a
> matrix as shown in the screenshot, using the vcv function, many of the species
> are treated as a single group. Furthermore, it seems like the node with
> Somateria mollissima and Aythya affinis is being used as an outgroup, which
> gives back a 0 value in the matrix that causes a warning message when I try to
> run meta-analytical models in metafor. Could you help me understand what I am
> doing wrong?
> Thank you very much beforehand,
> Miguel
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