get_subtree_at_node: Extract a subtree descending from a specific node.

In castor: Efficient Phylogenetics on Large Trees

Extract a subtree descending from a specific node.

Description

Given a tree and a focal node, extract the subtree descending from the focal node and place the focal node as the root of the extracted subtree.

Usage

get_subtree_at_node(tree, node)

Arguments

tree	A tree of class "phylo".
node	Character or integer specifying the name or index, respectively, of the focal node at which to extract the subtree. If an integer, it must be between 1 and tree$Nnode. If a character, it must be a valid entry in tree$node.label.

Details

The input tree need not be rooted, however "descendance" from the focal node is inferred based on the direction of edges in tree$edge. The input tree may include multi-furcations (i.e. nodes with more than 2 children) as well as mono-furcations (i.e. nodes with only one child).

Value

A named list with the following elements:

subtree	A new tree of class "phylo", containing the subtree descending from the focal node. This tree will be rooted, with the new root being the focal node.
new2old_tip	Integer vector of length Ntips_kept (=number of tips in the extracted subtree) with values in 1,..,Ntips, mapping tip indices of the subtree to tip indices in the original tree. In particular, tree$tip.label[new2old_tip] will be equal to subtree$tip.label.
new2old_node	Integer vector of length Nnodes_kept (=number of nodes in the extracted subtree) with values in 1,..,Nnodes, mapping node indices of the subtree to node indices in the original tree. For example, new2old_node[1] is the index that the first node of the subtree had within the original tree. In particular, tree$node.label[new2old_node] will be equal to subtree$node.label (if node labels are available).
new2old_edge	Integer vector of length Nedges_kept (=number of edges in the extracted subtree), with values in 1,..,Nedges, mapping edge indices of the subtree to edge indices in the original tree. In particular, tree$edge.length[new2old_edge] will be equal to subtree$edge.length (if edge lengths are available).

Author(s)

Stilianos Louca

See Also

get_subtree_with_tips

Examples

# generate a random tree
Ntips = 1000
tree = generate_random_tree(list(birth_rate_intercept=1),Ntips)$tree

# extract subtree descending from a random node
node = sample.int(tree$Nnode,size=1)
subtree = get_subtree_at_node(tree, node)$subtree

# print summary of subtree
cat(sprintf("Subtree at %d-th node has %d tips\n",node,length(subtree$tip.label)))

castor documentation built on June 29, 2024, 9:08 a.m.