I am trying to calculate the variance-covariance matrix for a known tree but the ape function, vcv.phylo is not giving me expected results.
library(ape)
phy1 <- read.tree(text = "((a:6,b:6):4,c:10);")
plot(phy1, show.tip.label = TRUE, edge.width = 2)
ape::vcv.phylo(phy1)
a b c
a 10 4 0
b 4 10 0
c 0 0 10
However, I am expecting an output of:
a b c
a 10 6 4
b 6 10 4
c 4 4 10
I've been attempting different variations of this tree to get this output in the vcv matrix but I cannot seem to figure it out. Any ideas?