is_monophyletic: Determine if a set of tips is monophyletic.

Description

Given a rooted phylogenetic tree and a set of focal tips, this function determines whether the tips form a monophyletic group.

Usage

is_monophyletic(tree, focal_tips, check_input=TRUE)

Arguments

tree

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

focal_tips

Either an integer vector or a character vector, listing the tips to be checked for monophyly. If an integer vector, it should list tip indices (i.e. from 1 to Ntips). If a character vector, it should list tip names; in that case tree$tip.label must exist.

check_input

Logical, whether to perform basic validations of the input data. If you know for certain that your input is valid, you can set this to FALSE to reduce computation time.

Value

A logical, indicating whether the focal tips form a monophyletic set.

Details

This function first finds the most recent common ancestor (MRCA) of the focal tips, and then checks if all tips descending from that MRCA fall within the focal tip set.

Examples

Run this code

# NOT RUN {
# generate random tree
Ntips = 100
tree  = generate_random_tree(list(birth_rate_intercept=1),max_tips=Ntips)$tree

# pick a random subset of focal tips
focal_tips = which(sample.int(2,size=Ntips,replace=TRUE)==1)

# check if focal tips form a monophyletic group
is_monophyletic(tree, focal_tips)
# }