find_root {castor}R Documentation

Find the root of a tree.

Description

Find the root of a phylogenetic tree. The root is defined as the unique node with no parent.

Usage

find_root(tree)

Arguments

tree

A tree of class "phylo". If the tree is not rooted, the function will return NA.

Details

By convention, the root of a "phylo" tree is typically the first node (i.e. with index Ntips+1), however this is not always guaranteed. This function finds the root of a tree by searching for the node with no parent. If no such node exists, NA is returned. If multiple such nodes exist, NA is returned. If any node has more than 1 parent, NA is returned. Hence, this function can be used to test if a tree is rooted purely based on the edge structure, assuming that the tree is connected (i.e. not a forest).

The asymptotic time complexity of this function is O(Nedges), where Nedges is the number of edges in the tree.

Value

Index of the tree's root, as listed in tree$edge. An integer ranging from Ntips+1 to Ntips+Nnodes, where Ntips and Nnodes is the number of tips and nodes in the tree, respectively. By convention, the root will typically be Ntips+1 but this is not guaranteed.

Author(s)

Stilianos Louca

See Also

find_root_of_monophyletic_tips, root_at_node, root_at_midpoint

Examples

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

# reroot the tree at the 20-th node
new_root_node = 20
tree = root_at_node(tree, new_root_node, update_indices=FALSE)

# find new root index and compare with expectation
cat(sprintf("New root is %d, expected at %d\n",find_root(tree),new_root_node+Ntips))

[Package castor version 1.7.0 Index]