Hello Rob and Antigoni,
Would the following meet your purposes?
Cheers,
-Dave Bapst, UChicago
library(ape)
tree-rtree(30) #you can use your own tree here or rcoal() or whatever
Nchanges-10#number of shifts at nodes
nodeShifts-sample((2:Nnode(tree))+Ntip(tree),Nchanges)
Hello Dave,
from my part, yes, this does exactly what I wanted to do. As far as I
understood, it is also what Rob was suggesting.
Thanks to everyone for helping with this.
Cheers,
Antigoni
On 10/13/2011 07:02 AM, David Bapst wrote:
Hello Rob and Antigoni,
Would the following meet your
Hello again everyone,
forwarded is some code provided by Dave Bapst for simulating a certain
number of trait shifts in nodes AND tracking those changes as you go.
This code will simulate Nchanges shifts and give both tip (tipChar)
and node (intNodeChar) states at the end of the run.
Dave
Hi Liam,
thank you very much for this. Yes, the function works beautifully for
what we wanted to do and the code you sent greatly facilitates
implemantation.
I was, however, wondering whether you can somehow limit the shifts to
happen in nodes, to avoid character reversals across a single
Hi Antigoni,
I had been thinking about some of these kinds of simulations recently too.
One challenge I encountered (which is similar to your problem here, if I've
understood it) was how to make my simulations actually relevant.
Specifically, given a particular tree I needed to simulate data
Hi Antigoni.
I have a function in the new version of phytools called sim.history()
that might help with this. This version is not available yet on CRAN,
but it can be downloaded from my webpage:
http://anolis.oeb.harvard.edu/~liam/R-phylogenetics/. The function
generates stochastic
