find_farthest_tip_pair: Find the two most distant tips in a tree.

Description

Given a phylogenetic tree, find the two most phylogenetically distant tips (to each other) in the tree.

Usage

find_farthest_tip_pair(tree, as_edge_counts = FALSE)

Arguments

tree

A rooted tree of class "phylo". While the tree must be rooted for technical reasons, the outcome does not actually depend on the rooting.

as_edge_counts

Logical, specifying whether to count phylogenetic distance in terms of edge counts instead of cumulative edge lengths. This is the same as setting all edge lengths to 1.

Value

A named list with the following elements:

tip1

An integer between 1 and Ntips, specifying the first of the two most distant tips.

tip2

An integer between 1 and Ntips, specifying the second of the two most distant tips.

distance

Numeric, specifying the phylogenetic (patristic) distance between the farthest_tip1 and farthest_tip2.

Details

If tree$edge.length is missing or NULL, then each edge is assumed to have length 1. The tree may include multi-furcations as well as mono-furcations (i.e. nodes with only one child).

The asymptotic time complexity of this function is O(Nedges), where Nedges is the number of edges in the tree.

Examples

Run this code

# NOT RUN {
# generate a random tree
Ntips = 1000
parameters = list(birth_rate_intercept=1,death_rate_intercept=0.9)
tree = generate_random_tree(parameters,Ntips,coalescent=FALSE)$tree

# find farthest pair of tips
results = find_farthest_tip_pair(tree)

# print results
cat(sprintf("Tip %d and %d have distance %g\n",
            results$tip1,results$tip2,results$distance))
# }