Dear Brad,
here are some solutions for your problems. I assume unrooted trees
here and ignore the position of the root, so you may additionaly check
for the position of the root.
On 3/24/11, Ruhfel Brad ruh...@gmail.com wrote:
Dear all,
I am wondering if there is some way using R to sort a
Hi,
Klaus beat me to it, but since there are more ways to do it ;-)
Two functions in the APE package are handy: is.monophyletic(), and
all.equal.phylo(). See the help for options.
They could be used in wrapper functions, like this
filter.mono - function (x, grp) {
fun - function (x)
Thanks for tracking this down, Emmanuel. I'm forwarding this to the
TreeBASE developers list for consideration.
BTW the phylobase implementation uses NCL (NEXUS Class Library, in C+
+) for parsing NEXUS. Given the difference, probably ape does not?
-hilmar
On Mar 25, 2011, at 12:00
Dear all,
I am trying to figure out how to automate something in R. Any suggestions much
appreciated.
In general I am trying to summarize the results of ancestral area
reconstructions done using Lagrange on 1000 trees from BEAST. These results
would then be summarized and reported based on
Hello all,
I was using prop.part() to identify nodes shared between several topologies,
when I discovered a strange error, where prop.part() was underestimating the
number of partitions found in common. I was able to fix the error for some
comparisons by outputting the trees as Newick strings and
Hmmm. I am not familiar with what this program is doing, but I thought that
Pagel's lambda is supposed to be constrained in the range of zero to one. Note
that Grafen's (1989) rho and the OU transform (d) or ACDC transform (g) of
Blomberg et al. (2003) and Lavin et al. (2008) can exceed one.
