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 beta lambda 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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