Hi all,
I tried the function written by Liam, it works pretty well! As an indication
for users, do not use an ultrametric tree, you'd get an error like this:
Error in chol.default(x, pivot = FALSE) :
the leading minor of order 140 is not positive definite
Error in pd.solve(varcov) : x appea
Hi Pasquale,
To follow up on my earlier message, I have written a preliminary version
of a simple function to simultaneously estimate the evolutionary
parameters and ancestral states for Brownian evolution with a trend
using likelihood. I will paste it at the end of this email. I have
confi
(Apologies if you receive multiple copies.)
Over the next 3 weeks we will be pulling together NESCent's
application to the 2011 Google Summer of Code as a mentoring
organization. This is a call for all prospective mentors, primary and
secondary, to step forward.
Participating as an organi
Dear all,
Can somebody tell whether one should subtract degrees of freedom when applying
pgls with a phylogeny containing soft polytomies?
cheers, Popko Wiersma
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The package phylobase uses NCL to parse Newick files which provides some
information when a non-valid file is being imported. It's not perfect, but
it will at least give you an idea of the part that is not correctly
formated.
-- François
On Sun, Feb 20, 2011 at 22:31, Ben Bolker wrote:
> O
James: it's not the space that is the problem, but one label has
parentheses:
'Rubus idaeus U06825.1(2)'
Deleting or substituting these parentheses with(out) the spaces and/or
quotes solves the problem for read.tree(). I remind that this behaviour
is expected and discussed in ape's FAQ.
Ben