I would have to see your code to know 100% for certain - but your results make
intuitive sense, so let me just guess. When you have OU under a very high alpha
(which is what you are getting here), then you are modeling a process following
a random walk with an extremely high tendency to be pulled towards the OU
optimum value. In this case, characters do not retain any information about
their past states, and so the best guess for every node in the tree is the
mean of all of the characters. You can check to see if the value you are
getting back is actually the mean of all of your tips.
To me, what this means is that if you think the model is correct (lambda or OU)
then you have no information about any of the ancestral character states in the
tree.
lh
On Nov 8, 2012, at 3:14 PM, Zachary Chejanovski sliv...@life.bio.sunysb.edu
wrote:
Hi,
I am attempting to estimate ancestral states using the following methods-
APE::ace, GEIGER::getancstates, as well as this method recommend by Liam
Revell for reconstructing under an OU model:
ou-fitContinuous(tree,data,model=OU)$Trait1
anc.mins-vector()
N-length(tree$tip)
M-tree$Nnode
outree-ouTree(tree,ou$alpha)
for(i in 1:M+N){
anc.mins[i-N]-ace(data,multi2di(root(outree,node=i)),method=pic)$ace[1]
names(anc.mins)[i-N]-i
}
Here are the parameter estimates for one of my traits:
$Lambda
lnl betalambda aic aicc k
1 -121.4771 31.33674 0.4057359 248.9541 250.2173 3
$OU
lnl beta alpha convergence
message k aic aicc
1 -120.7098 281.9509 0.08288029 0 CONVERGENCE: REL_REDUCTION_OF_F
= FACTR*EPSMCH 3 247.4196 248.6828
When I do not transform the tree (i.e. Brownian Motion), the values returned
seem valid. But when I transform the tree using either lambdaTree, ouTree. or
even the exponentialTree, all the values returned are almost identical and
when I plot them on the phylogeny, it is evident that they do not make sense
in regards to the tip values.
Any help on this would be greatly appreciated.
Thank you,
Zac
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Luke Harmon
Associate Professor
Biological Sciences
University of Idaho
208-885-0346
lu...@uidaho.edu
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