Hello,
you may have a look at find.clusters (K-means based clustering) and gengraph
(transitive graph clusters) in adegenet too.
Cheers
Thibaut
From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on
behalf of Sam Brown
Hello,
I am using ape to obtain ancestral state estimates for continuous traits. Two
options are available, either maximum likelihood or a GLS method. I am
comparing the results of both methods and one difference between the two
puzzles me, I hope someone can enlighten me. Under GLS the
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Thank you all for your ideas. I'll probably explore further Liam's method.
sincerely,
john
On Tue, Mar 12, 2013 at 5:33 PM, Liam J. Revell liam.rev...@umb.edu wrote:
I did a little further exploration of this proposed method - the results
discussion are here:
Hi All,
Just a follow up on this. I was thinking about what Liam suggested, and I
think it's a different test to what I suggested, but maybe I'm wrong.
In particular, Liam's using squared contrasts in y, so that's asking
whether the absolute size of changes in y depends on x at the ancestral
Hi Rob -
Regarding your comment: However, I think that this test is not quite
the same as asking whether the rate of evolution of y depends on x. For
example, it's possible you could (correctly) see a relationship with
Liam's test even if there was no relationship between the rate of
Hi Liam,
I think you're right, and I'm wrong.
I included the reference below, which I left out of the last email.
Rob
[1] Freckleton, R.P. (2000) Phylogenetic tests of ecological and
evolutionary hypotheses: checking for phylogenetic independence. Funct.
Ecol. 14, 129134
On 16 March 2013
Rob Lanfear wrote:
In particular, Liam's using squared contrasts in y, so that's
asking whether the absolute size of changes in y depends on
x at the ancestral node. I might have missed something here,
but that sounds very similar in principle to Freckleton's
test of whether the
