Dear Fabricia,
You can compute the mean distance between leaves in the tree. For each
pair of leaves, the distance between them equals the number of edges
that separate them. Unfortunately, I do not know any R function that
performs the computations but you can write your own function.
Since
Dear Fabricia,
I am the maintainer of the package.
Can you send me the tree that is responsible for the warnings please. It
might be because of unresolved nodes.
Sincerely
Michael Blum
Le 10/06/13 17:53, Fabricia Nascimento a écrit :
Hi,
I am trying to use the collies.test and maxlik.betaspl
Yes there is a current problem with the function as.phylo.
I rewrote a small function maxlik.betasplit2 which works without
as.phylo. I will update the package soon.
> maxlik.betasplit2(TR2,confidence.interval = "profile")
$max_lik
[1] 0.2103724
$conf_interval
[1] -1.017374 3.157280
maxlik.be
Dear Simon,
Normalization does not necessarily returns values between 0 and 1 but
returns the values of the summary statistics divided by the standard
deviation of the summary statistics that is expected under the Yule
model. If you want to use that renormalization to compare tree shapes
for
My admittedly biased advice would be to use the beta-splitting
statistic. The statistic is available in the apTreeshape package. What
is nice with this statistic is that its value should be interpretable
whatever the sizes of the trees you are looking at. Beta=0 is the yule
model, beta=-3/2 is
Dear all,
The package apTreeshape is back on CRAN
(http://cran.r-project.org/web/packages/apTreeshape/index.html). I hope
that this short interruption did not cause you too much trouble.
Sincerely,
Michael Blum
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Michael BLUM
Chargé de recherche (CR2 CNRS) (Research
