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
University of Massachusetts Boston [Assoc. Prof.]
Universidad Católica de la Ssma Concepción [Adj. Res.]
On 6/7/2021 6:52 PM, Rafael S Marcondes wrote:
EXTERNAL SENDER
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 are stored in $rates and the indices of $rates are
given in $index.matrix:
ace$index.matrix
[,1] [,2] [,3]
[1,] NA35
[2,]1 NA6
[3,]24 NA
ace$rates
[1] 0.107923960 0.012997878 0.0 0.008488054 0.0 0.073339853
But how do the ace$index.matrix columns and rows correspond to my character
states?
Thanks for any help!
Rafa
*--*
*Rafael Sobral Marcondes, Ph.D.*
Pronouns: he/him
*"Eu quase que nada não sei. Mas desconfio de muita coisa"*
*"I almost don't know nothing. But I suspect many things"*
-João Guimarães Rosa, Brazilian novelist
(Portuguese original and free English translation by me)
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