We discussed on the list a few months ago about using any correlation
matrix to simulate characters. At the moment, it's tedious to get the
correlation matrix from a corStruct object in ape, but I'll improve
that soon (following several requests) so that it'll be
straightforward to simulate (continous) traits under the available
models of evolution.
Emmanuel
Quoting Luke Harmon <lu...@uidaho.edu>:
Hi Christian (and everyone else),
You can do that with geiger, you just need to transform the tree
first. For example:
originalTree<-birthdeath.tree(b=0.1, d=0, taxa.stop=10)
transformedTree<-ouTree(originalTree, alpha=0.4)
sim.char(transformedTree, model.matrix=cbind(c(1, 0.5), c(0.5, 1)))
You can do something similar for EB, using exponentialchangeTree()
Luke
On Nov 5, 2009, at 3:13 PM, Christian Arnold wrote:
Hello,
I am desperately looking for a program or an R function that can
simulate the evolution of 2 continuous characters (with a given
correlation between the two characters) on a phylogenetic tree. I am
aware of the sim.char function of the GEIGER package; however, this
function only implements a Brownian model of evolution. I want to
simulate character evolution for 2 continuous characters (either
uncorrelated or with a correlation of 0.5) using alternative models
of evolution (e.g., OU model or an adaptive radiation / early burst
model).
Any help would be greatly appreciated!
Thanks!
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Luke Harmon
Assistant Professor
Biological Sciences
University of Idaho
208-885-0346
lu...@uidaho.edu
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