NodeDepth: Distance of each node from tree exterior

In TreeTools: Create, Modify and Analyse Phylogenetic Trees

Distance of each node from tree exterior

Description

NodeDepth() evaluates how "deep" each node is within a tree.

Usage

NodeDepth(x, shortest = FALSE, includeTips = TRUE)

Arguments

x	A tree of class phylo, its ⁠$edge⁠ property, or a list thereof.
shortest	Logical specifying whether to calculate the length of the shortest away-from-root path to a leaf. If FALSE, the length of the longest such route will be returned.
includeTips	Logical specifying whether to include leaves (each of depth zero) in return value.

Details

For a rooted tree, the depth of a node is the minimum (if shortest = TRUE) or maximum (shortest = FALSE) number of edges that must be traversed, moving away from the root, to reach a leaf.

Unrooted trees are treated as if a root node occurs in the "middle" of the tree, meaning the position that will minimise the maximum node depth.

Value

NodeDepth() returns an integer vector specifying the depth of each external and internal node in x.

Author(s)

Martin R. Smith ([e-mail])

See Also

ape::node.depth returns the number of tips descended from a node.

Other tree navigation: AncestorEdge(), CladeSizes(), DescendantEdges(), EdgeAncestry(), EdgeDistances(), ListAncestors(), MRCA(), MatchEdges(), NDescendants(), NodeNumbers(), NodeOrder(), RootNode()

Examples

tree <- CollapseNode(BalancedTree(10), c(12:13, 19))
plot(tree)
nodelabels(NodeDepth(tree, includeTips = FALSE))

TreeTools documentation built on Sept. 11, 2024, 8:27 p.m.