Hi Sergio.
You didn't specify what BM vf are, but if:
BM-corBrownian(1,phy)
## and
vf-diag(vcv(phy))
then, yes, this is correct. There is a function in phytools, phy.resid,
that also does this calculation.
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of
Dear all,
I just read this paper: Revell, L. J. (2009). Size‐correction and principal
components for interspecific comparative studies. Evolution, 63(12),
3258-3268. There is no coding for R, but it says it can be made using APE.
From what I could understand this is as simples as:
Hello,
I'm sorry for not specifying that. But yes, that's exactly it. Thanks for
the help.
Cheers,
Sérgio.
2015-06-15 12:47 GMT+01:00 Liam J. Revell liam.rev...@umb.edu:
Hi Sergio.
You didn't specify what BM vf are, but if:
BM-corBrownian(1,phy)
## and
vf-diag(vcv(phy))
then, yes,
What about using Tracer instead? It's well-maintained with quite recent
versions.
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Hi Nicholas,
There is actually a new version of AWTY rewritten for R (RWTY) by Dan Warren.
Here is a link to the github. As far as I’m aware it is functional.
https://github.com/danlwarren/RWTY https://github.com/danlwarren/RWTY
Cheers
Pete
On Jun 15, 2015, at 10:43 AM, Daniel Fulop
A kludgy solution to achieve Dave's original use case of fixing
not-quite-right phylo objects is to do:
phy - read.tree(text=write.tree(phy))
It converts the tree to Newick and reads it back in.
It's not as good a solution as using a validator (great addition, Emanuel!)
to find and fix the
Hi,
There is a new R implementation of AWTY https://github.com/danlwarren/RWTY
Haven't used it myself but I think this will probably alleviate this issue.
Cheers,
Matt
On Mon, Jun 15, 2015 at 7:43 AM, Daniel Fulop dfulop@gmail.com wrote:
What about using Tracer instead? It's
Hi Brian,
I was already aware of the read.tree(write.tree()) fix, however I've
run into (corner?) cases where a particular sorting of edges or
whatever can lead to a loss of tip taxa using the
read.tree(write.tree()) approach; plus, read.tree(write.tree()) gets
completely flabbergasted by
Whoops, I meant a 'function in ape?'
-Dave
On Mon, Jun 15, 2015 at 10:26 AM, David Bapst dwba...@gmail.com wrote:
Hi Brian,
I was already aware of the read.tree(write.tree()) fix, however I've
run into (corner?) cases where a particular sorting of edges or
whatever can lead to a loss of tip
Hi David.
I'm not sure about this, but changing to:
tree-read.newick(text=write.tree(tree))
tree-collapse.singles(tree)
may work. I believe that write.tree will write trees with singletons
read.newick in phytools should be able to read them.
All the best, Liam
Liam J. Revell, Assistant
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