edges: Edges accessors

Description

Access or modify information about the edges.

Usage

edges(x, ...)
# S4 method for phylo4
edges(x, drop.root = FALSE)
edgeOrder(x, ...)
# S4 method for phylo4
edgeOrder(x)
internalEdges(x)
# S4 method for phylo4
internalEdges(x)
terminalEdges(x)
# S4 method for phylo4
terminalEdges(x)

Value

edges: returns the edge matrix that represent the ancestor-descendant relationships among the nodes of the tree.

edgeOrder

returns the order in which the edge matrix is in.

internalEdges

returns a logical vector indicating internal edges (edges that connect an internal node to another). This vector is named with the edgeId

terminalEdges

returns a logical vector indicating terminal edges (edges that connect an internal node to a tip). This vector is named with the edgeId

Arguments

x: a phylo4 or phylo4d object.
...: Optional arguments used by specific methods. (None used at present).
drop.root: logical (default FALSE), should the edge connecting the root be included in the edge matrix?

Author

Ben Bolker, Francois Michonneau, Thibaut Jombart

Examples

Run this code

   data(geospiza)
   edges(geospiza)
   edgeOrder(geospiza)
   geoPost <- reorder(geospiza, "postorder")
   edgeOrder(geoPost)
   ## with a binary tree this should always be true
   identical(!terminalEdges(geospiza), internalEdges(geospiza))