find_root_of_monophyletic_tips: Find the node or tip that, as root, would make a set of...

In castor: Efficient Phylogenetics on Large Trees

Find the node or tip that, as root, would make a set of target tips monophyletic.

Description

Given a tree (rooted or unrooted) and a specific set of target tips, this function finds the tip or node that, if turned into root, would make a set of target tips a monophyletic group that either descends from a single child of the new root (if as_MRCA==FALSE) or whose MRCA is the new root (if as_MRCA==TRUE).

Usage

find_root_of_monophyletic_tips(tree, monophyletic_tips, as_MRCA=TRUE, is_rooted=FALSE)

Arguments

tree	A tree object of class "phylo". Can be unrooted or rooted.
monophyletic_tips	Character or integer vector, specifying the names or indices, respectively, of the target tips that should be turned monophyletic. If an integer vector, its elements must be between 1 and Ntips. If a character vector, its elements must be elements in tree$tip.label.
as_MRCA	Logical, specifying whether the new root should become the MRCA of the target tips. If FALSE, the new root is chosen such that the MRCA of the target tips is the child of the new root.
is_rooted	Logical, specifying whether the input tree can be assumed to be rooted. If you are sure that the input tree is rooted, set this to TRUE for computational efficiency, otherwise to be on the safe side set this to FALSE.

Details

The input tree may include an arbitrary number of incoming and outgoing edges per node (but only one edge per tip), and the direction of these edges can be arbitrary. Of course, the undirected graph defined by all edges must still be a valid tree (i.e. a connected acyclic graph). This function does not change the tree, it just determines which tip or node should be made root for the target tips to be a monophyletic group. If the target tips do not form a monophyletic group regardless of root placement (this is typical if the tips are simply chosen randomly), this function returns NA.

The asymptotic time complexity of this function is O(Nedges).

Value

A single integer between 1 and (Ntips+Nnodes), specifying the index of the tip or node that, if made root, would make the target tips monophyletic. If this was not possible, NA is returned.

Author(s)

Stilianos Louca

See Also

find_root

Examples

# generate a random tree
Ntips = 100
tree = generate_random_tree(list(birth_rate_intercept=1),max_tips=Ntips)$tree

# pick a random node and find all descending tips
MRCA = sample.int(tree$Nnode,size=1)
monophyletic_tips = get_subtree_at_node(tree, MRCA)$new2old_tip

# change root of tree (change edge directions)
tree = root_at_node(tree, new_root_node=10, update_indices=FALSE)

# determine root that would make target tips monophyletic
new_root = find_root_of_monophyletic_tips(tree, monophyletic_tips, as_MRCA=TRUE, is_rooted=FALSE)

# compare expectation with result
cat(sprintf("MRCA = %d, new root node=%d\n",MRCA,new_root-Ntips))

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