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.
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
(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
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
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
