Hi all,
I have a little problem with write.nexus. In part of my script, I need
to read
in some trees, write them out, then repeat. I find that they read back in
fine, but when I write them out the second time, there are no trees in the
files. Oddly, this problem doesn't occur if I use
Hi Gustavo,
I wrote a function to randomly prune one of the two alleles for each
species in
an alignment and tree list (say from MrBayes). I create a list of
names that I
want to drop, and I prune them out of the dataset and treelist (so I have a
matching dataset for each treefile). It's not
Hi Christoph,
There was some discussion following a similar question a year ago:
The question:
https://stat.ethz.ch/pipermail/r-sig-phylo/attachments/20080402/2e2b995e/attachment.pl
The threads:
https://stat.ethz.ch/pipermail/r-sig-phylo/2008-April/thread.html#35
I'll be interested to hear
Hi all,
Does any one know if there is R function for estimating delta to do a test of
the node density effect as described in Vendetti et al 2006? Pagel's
lab has a
web tool ( http://www.evolution.rdg.ac.uk/pe/index.html ) but it
doesn't report
the actual delta values.
Thanks in advance for
Hi all,
My lab has been reading literature related to the measurement of phylogenetic
signal and we are wondering about the application of Blomberg's K statistic to
discrete data and in particular discrete, unordered characters. We have seen
it applied to the latter in the literature, but it
Hi Marion,
About your questions, method (1) would still take into account phylogenetic
uncertainty, just among the 64 taxa instead of 116. It seems a shame, though,
to lose those extra taxa. I'm surprised SIMMAP can't deal with the short
branches.
Second, about the sample from MrBayes, you will
Hi Anne,
Have you looked at this paper?
#9702;Ives, A. R., P. E. Midford, and T. Garland Jr. 2007. Within-species
variation and measurement error in phylogenetic comparative methods.
Systematic
Biology 56:252-270.
You could also look on web of science at papers that have cited it (and
perhaps
