breakthem?
library(help = ape)
or:
packageVersion("ape")
In many cases, a problem can be solved by updating ape and R.
tr$edge.length
tr <- ladderize(tr) # right-ladderized by default
plot(tr)
tr <- ladderize(tr, FALSE) # left-ladderized
plot(tr)
lm(picy ~ picx - 1)
BEGIN TREES;
TRANSLATE
0 Pongo,
1 Pan,
etc ...
s <- phy$edge[, 2] <= Ntip(phy)
phy$edge[s, 2] <- phy$edge[s, 2] + 1L
par(ljoin = 2, lend = 2)
breakthem?
tr.bak <- tr
We then need to identify the long edge(s). This could done by plotting the tree and then printing the edge numbers:
plot(tr)
edgelabels()
i <- which(tr$edge.length > 1)
We then modify the length of these edges with a small value, for instance the mean of the shorter branch lengths:tr$edge.length[i] <- mean(tr$edge.length[-i])
We can now plot the modified tree and show the (originally) long branches with, for instance, dashed lines:
edge.style <- rep(1, Nedge(tr))
edge.style[i] <- 2
plot(tr, edge.lty = edge.style)
plot(tr)
edgelabels("//", i, frame = "n")
//:
plot(tr)
edgelabels(edge = i, pch = 19, col = "white")
edgelabels("//", i, frame = "n")