It might be easier to use ace() in ape. A major advantage is it gives you the
uncertainty in the estimates, which is often substantial (and even so still an
underestimate, since there could be trends that aren't fit at all).
library(ape)
data(bird.orders)
x <- rnorm(23)
reconstruction <- ace(x, bird.orders)
and then you have the states at each node (with the node numbers):
print(reconstruction$ace)
and the confidence intervals:
print(reconstruction$CI95)
There are various ways to get node numbers for the node you care about; perhaps
the easiest is by specifying a pair of tips:
ape::getMRCA(bird.orders, c("Struthioniformes", "Tinamiformes"))
which will tell you the relevant node number of the reconstructions (the label
for the vector, not the index (i.e., use reconstruction$ace["26"] with the
quotes).
Hope this helps (and love to phytools in general, even if not the tool for
this),
Brian
From: R-sig-phylo <[email protected]> on behalf of Jaime Adrian
Cordova via R-sig-phylo <[email protected]>
Date: Thursday, November 20, 2025 at 6:00 PM
To: [email protected] <[email protected]>
Subject: [R-sig-phylo] Phytools connect ace values to tree
Hi colleagues,
I've conducted an ancestral state reconstruction for E.coli growth rates under
anaerobic conditions using phytools. I'd like to get a bit more detail out of
reconstruction, particularly with the ancestral values; however, I'm not
exactly sure how to match the values to the nodes in the phylogeny. In other
words, I'm able to map the values onto the map using contMap(), but I would
like to be able to say that the MRCA of a phylogroup is predicted to have a
certain growth rate, etc.
Can someone help me with this? Thanks!
Kind regards,
Jaime
Jaime A. Cordova Jr.
Pronouns: he/him/his/�l
Genetics PhD Candidate, Perna Lab
University of Wisconsin, Madison
NASA/JPL Solar System Ambassador
I tend to work at irregular hours, but I never expect others to do the same. If
I email you outside of your working hours, please do not feel obligated to
respond until you are comfortable doing so.
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