get_mrca_of_set: Most recent common ancestor of a set of tips/nodes.

In castor: Efficient Phylogenetics on Large Trees

Most recent common ancestor of a set of tips/nodes.

Description

Given a rooted phylogenetic tree and a set of tips and/or nodes ("descendants"), calculate the most recent common ancestor (MRCA) of those descendants.

Usage

get_mrca_of_set(tree, descendants)

Arguments

tree

A rooted tree of class "phylo". The root is assumed to be the unique node with no incoming edge.

descendants

An integer vector or character vector, specifying the tips/nodes for which to find the MRCA. 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.

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). Duplicate entries in descendants are ignored.

Value

An integer in 1,..,(Ntips+Nnodes), representing the MRCA using the same index as in tree$edge. If the MRCA is a tip, then this index will be in 1,..,Ntips. If the MRCA is a node, then this index will be in (Ntips+1),..,(Ntips+Nnodes).

Author(s)

Stilianos Louca

See Also

get_pairwise_mrcas, get_tips_for_mrcas

Examples

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

# pick 3 random tips or nodes
descendants = sample.int(n=(Ntips+tree$Nnode), size=3, replace=FALSE)

# calculate MRCA of picked descendants
mrca = get_mrca_of_set(tree, descendants)

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