extract_tip_radius: Extract a subtree spanning tips within a certain radius.

In castor: Efficient Phylogenetics on Large Trees

Extract a subtree spanning tips within a certain radius.

Description

Given a rooted tree, a focal tip and a phylogenetic (patristic) distance radius, extract a subtree comprising all tips located within the provided radius from the focal tip.

Usage

extract_tip_radius(tree, 
                   focal_tip,
                   radius,
                   include_subtree = TRUE)

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.
radius	Non-negative numeric, specifying the patristic distance radius to consider around the focal tip.
include_subtree	Logical, whether to actually extract the subtree, rather than just returning the inferred within-radius tips.

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 which tips are extracted.

Value

A named list with the following elements:

radius_tips	Integer vector with values in 1,..,Ntips, specifying which tips were found to be within the specified radius of the focal tip.
subtree	A new tree of class "phylo", containing only the tips within the specified radius from the focal tip, and the nodes & edges connecting those tips to the root. Only returned if include_subtree=TRUE.
new2old_tip	Integer vector of length Ntips_extracted (=number of tips in the extracted subtree, i.e., within the specified distance radius from the focal tip) with values in 1,..,Ntips, mapping tip indices of the extracted subtree to tip indices in the original tree. In particular, tree$tip.label[new2old_tip] will be equal to subtree$tip.label. Only returned if include_subtree=TRUE.

Author(s)

Stilianos Louca

See Also

get_all_distances_to_tip

Examples

# generate a random tree
Ntips = 50
tree  = generate_random_tree(list(birth_rate_factor=0.1),
                             max_tips = Ntips,
                             tip_basename="tip.")$tree

# extract all tips within radius 50 from a focal tip
subtree = extract_tip_radius(tree, 
                             focal_tip="tip.39",
                             radius=50)$subtree

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