David,
on the top of my head, if no species measurement strictly corresponds to
zero, you may log-transform the data. You may then simulate Brownian
motion in log-transformed values, which will correspond to a boundary of
zero in a linear scale (i.e., the more negative the log number, the
Hello David, Enrico, et al.,
I may have lost track of what Dave was originally trying to do, and I am not
familiar with all of the options presently available in r for simulating
continuously valued traits along a specified phylogenetic tree. However, I
wanted to point out that MANY
I'm not sure that this is what Dave has in mind, but if anyone is
interested in simulating bounded evolution in R, I just added it to my
fastBM() function (code here:
http://anolis.oeb.harvard.edu/~liam/R-phylogenetics/fastBM/v0.3/fastBM.R).
In the process of evolving traits up the tree, I
Dear R phylogeneticists,
I am trying to make a species tree based on a newick file (at the end of this
message)of a pre-computed tree from microbesonline.org. I can read it into ape
but unlike with other files of the same format, there something weird going on
with the the node.labels and I
If someone were willing to mentor the R side, this might be a great
project idea for our Summer of Code participation [1], for which we
are pulling together the mentoring organization application right now.
-hilmar
[1]
Hi David, Liam and everyone,
Reflecting traits at boundaries or absorbing them is something that can be
done, but I guess I'd like to encourage everyone to think carefully about the
interpretation of such simulations. What are you trying to model and what does
it mean at the end? Doing these
p.s. an absorbing boundary might be a good model for something like the
disappearance of a gene or something. When it goes to such a low frequency it
goes extinct. Then in order to reevolve, it needs to mutate (basically
re-originate, which is a very rare event). But for reversible traits,
