find_farthest_tip_pair {castor}R Documentation

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.

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.

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.

Author(s)

Stilianos Louca

See Also

find_nearest_tips, find_farthest_tips

Examples

# 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))

[Package castor version 1.7.0 Index]