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 c
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 purpo
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)
DescList<-prop.
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 with
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 br
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 histor
Hello everyone,
I am studying a binomial trait across a phylogeny and I'm trying to
simulate specific numbers of evolutionary shifts (1, 5, 10 shifts)
across random trees.
Does anyone know how this can be done?
Any help is greatly appreciated
Cheers,
Antigoni
--
Antigoni Kaliontzopoulou
CIBI