get_all_distances_to_tip: Get distances of all tips/nodes to a focal tip.

In castor: Efficient Phylogenetics on Large Trees

Get distances of all tips/nodes to a focal tip.

Description

Given a tree and a focal tip, calculate the phylogenetic ("patristic") distances between the focal tip and all other tips & nodes in the tree.

Usage

get_all_distances_to_tip(tree, focal_tip)

Arguments

tree	A rooted tree of class "phylo".
focal_tip	Either a character, specifying the name of the focal tip, or an integer between 1 and Ntips, specifying the focal tip's index.

Details

The "patristic distance" between two tips and/or nodes is the shortest cumulative branch length that must be traversed along the tree in order to reach one tip/node from the other. If tree$edge.length is missing, then each edge is assumed to be of length 1.

The tree may include multi-furcations as well as mono-furcations (i.e. nodes with only one child). The input tree must be rooted at some node for technical reasons (see function root_at_node), but the choice of the root node does not influence the result.

Value

A numeric vector of length Ntips+Nnodes, specifying the distances of all tips (entries 1,..,Ntips) and all nodes (entries Ntips+1,..,Ntips+Nnodes) to the focal tip.

Author(s)

Stilianos Louca

See Also

get_all_pairwise_distances, get_pairwise_distances

Examples

# generate a random tree
Ntips = 100
tree  = generate_random_tree(list(birth_rate_intercept=1),
                             max_tips = Ntips,
                             tip_basename="tip.")$tree

# calculate all distances to a focal tip
distances = get_all_distances_to_tip(tree, "tip.39")
print(distances)

castor documentation built on Aug. 18, 2023, 1:07 a.m.