Ape package - extracting distances between nodes

Question

I'm working with ape package currently. My idea is to extract tip labels corresponding to each node and also distances in between the nodes. How can I do this?

Thanks a lot for your help

Answer 1

Here is how to interpret distances between nodes/tips in a phylo object (note that for dispRity::tree.age you'll need to install dispRity from GitHub https://github.com/TGuillerme/dispRity):

set.seed(1)
tree <- rtree(5)
tree$node.label <- paste0("n", 6:9)
plot(tree)
nodelabels(tree$node.labe)
axisPhylo()

## The distance between each tip
cophenetic(tree)

## The height of each tip and node
library(dispRity)
dispRity::tree.age(tree, order = "present")

## The distance between each nodes/tips
distances <- cbind(tree$edge, tree$edge.length)
colnames(distances) <- c("from", "to", "distance")
distances

This distance table reads as from element (tip/node) n to element (tip/node) m. The numbering works as follow: 1 is the first tip in the tree (tree$tip.label[1]), 2 is the second etc... 6 (number of tips + 1) is the first node in the tree (tree$node.label[1]), etc.