Dear Rafa.
Try this to get the transition matrix, Q:
k<-nrow(ace$index.matrix)
Q<-matrix(ace$rates[ace$index.matrix],k,k)
diag(Q)<--rowSums(Q,na.rm=TRUE)
This should match what you get running:
as.Qmatrix(fitMk(tree,x,model="ARD"))
with phytools.
All the best, Liam
Liam J. Revell
Hi all,
I'm very confused trying to understand the output of ace::ape, specifically
the transition rates. I'm having a hard time understanding how the rates
are stored in the results.
For example, I used an ARD model on a trait with three states, denoted just
0, 1 and 2.
I know that the rates
