get_ancestral_nodes: Compute ancestral nodes.

In castor: Efficient Phylogenetics on Large Trees

Compute ancestral nodes.

Description

Given a rooted phylogenetic tree and a set of tips and/or nodes ("descendants"), determine their ancestral node indices, traveling a specific number of splits back in time (i.e., towards the root).

Usage

get_ancestral_nodes(tree, descendants, Nsplits)

Arguments

tree	A rooted tree of class "phylo".
descendants	An integer vector or character vector, specifying the tips/nodes for each of which to determine the ancestral node. If an integer vector, it must list indices of tips (from 1 to Ntips) and/or nodes (from Ntips+1 to Ntips+Nnodes), where Ntips and Nnodes is the number of tips and nodes in the tree, respectively. If a character vector, it must list tip and/or node names. In this case tree must include tip.label, as well as node.label if nodes are included in descendants.
Nsplits	Either a single integer or an integer vector of the same length as descendants, with values >=1, specifying how many splits to travel backward. For example, Nsplits=1 will yield the parent node of each tip/node in descendants.

Details

The 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

An integer vector of the same length as descendants, with values in 1,..,Nnodes, listing the node indices representing the ancestors of descendants traveling backward Nsplits.

Author(s)

Stilianos Louca

See Also

get_pairwise_mrcas, get_mrca_of_set

Examples

# generate a random tree
tree = generate_random_tree(list(birth_rate_intercept=1),
                            max_tips = 50,
                            tip_basename = "tip.",
                            node_basename = "node.")$tree

# pick 3 tips
descendants=c("tip.5", "tip.7","tip.10")

# determine the immediate parent node of each tip
ancestors = castor::get_ancestral_nodes(tree, descendants, Nsplits=1)
print(tree$node.label[ancestors])

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