DescendantEdges: Identify descendant edges

In TreeTools: Create, Modify and Analyse Phylogenetic Trees

Identify descendant edges

Description

DescendantEdges() efficiently identifies edges that are "descended" from edges in a tree.

DescendantTips() efficiently identifies leaves (external nodes) that are "descended" from edges in a tree.

Usage

DescendantEdges(
  parent,
  child,
  edge = NULL,
  node = NULL,
  nEdge = length(parent),
  includeSelf = TRUE
)

DescendantTips(parent, child, edge = NULL, node = NULL, nEdge = length(parent))

AllDescendantEdges(parent, child, nEdge = length(parent))

Arguments

parent	Integer vector corresponding to the first column of the edge matrix of a tree of class phylo, i.e. tree[["edge"]][, 1]
child	Integer vector corresponding to the second column of the edge matrix of a tree of class phylo, i.e. tree[["edge"]][, 2].
edge	Integer specifying the number of the edge whose children are required (see edgelabels()).
node	Integer specifying the number(s) of nodes whose children are required. Specify 0 to return all nodes. If NULL (the default), the edge parameter will be used instead.
nEdge	number of edges (calculated from length(parent) if not supplied).
includeSelf	Logical specifying whether to mark edge as its own descendant.

Value

DescendantEdges() returns a logical vector stating whether each edge in turn is the specified edge (if includeSelf = TRUE) or one of its descendants.

DescendantTips() returns a logical vector stating whether each leaf in turn is a descendant of the specified edge.

AllDescendantEdges() is deprecated; use DescendantEdges() instead. It returns a matrix of class logical, with row N specifying whether each edge is a descendant of edge N (or the edge itself).

See Also

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

Examples

tree <- as.phylo(0, 6)
plot(tree)
desc <- DescendantEdges(tree$edge[, 1], tree$edge[, 2], edge = 5)
which(desc)
ape::edgelabels(bg = 3 + desc)
tips <- DescendantTips(tree$edge[, 1], tree$edge[, 2], edge = 5)
which(tips)
tiplabels(bg = 3 + tips)

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