phylobase (version 0.6.8)

treewalk: tree traversal and utility functions

Description

Functions for describing relationships among phylogenetic nodes (i.e. internal nodes or tips).

Usage

ancestors(phy, node, type=c("all","parent","ALL"))
ancestor(phy, node)
siblings(phy,node,include.self=FALSE)
children(phy, node)
descendants(phy, node, type=c("tips","children","all"))
MRCA(phy, ...)
shortestPath(phy, node1, node2)
## S3 method for class 'phylo4':
sumEdgeLength(x, node)

Arguments

phy

a phylo4 object (or one inheriting from phylo4, e.g. a phylo4d object)

x

a phylo4 object (or one inheriting from phylo4, e.g. a phylo4d object)

node

either an integer corresponding to a node ID number, or a character corresponding to a node label; for ancestors and descendants, this may be a vector of multiple node numbers or names

type

(ancestors) specify whether to return just direct ancestor ("parent"), all ancestor nodes ("all"), or all ancestor nodes including self ("ALL"); (descendants) specify whether to return just direct descendants ("ch

include.self

whether to include self in list of siblings

...

a list of node numbers or names, or a vector of node numbers or names

node1

a node number (or name)

node2

a node number (or name)

Value

• ancestors and descendants
  return a named vector (or a list of such vectors in the case of multiple input nodes) of the ancestors and descendants of a node
• ancestor and children
  ancestor is analogous to ancestors(..., type="parent") (i.e. direct ancestor only), but returns a single concatenated vector in the case of multiple input nodes; children is analogous to descendants(..., type="children") (i.e. direct descendants only), but is not currently intended to be used with multiple input nodes
• siblings
  returns sibling nodes (children of the same parent)
• MRCA
  returns the most recent common ancestor of two or more nodes
• shortestPath
  returns the nodes of the shortest path from one node to another (excluding node1 and node2)
• sumEdgeLength
  returns the sum of branch length for branches starting at nodes provided

Details

ancestors and descendants can take node vectors of arbitrary length, returning a list of output vectors if the number of valid input nodes is greater than one. List element names are taken directly from the input node vector.

If any supplied nodes are not found in the tree, the behavior currently varies across functions. Invalid nodes are automatically omitted by ancestors and descendants, with a warning. ancestor will return NA for any invalid nodes, with a warning. Both children and siblings will return an empty vector, again with a warning. In contrast, MRCA and shortestPath will throw an immediate error if any input nodes are invalid.

See Also

mrca, in the ape package, gives a list of all subtrees

Examples

data(geospiza)
  nodeLabels(geospiza) <- LETTERS[1:nNodes(geospiza)]
  plot(as(geospiza, "phylo4"), show.node.label=TRUE)
  ancestor(geospiza, "E")
  children(geospiza, "C")
  descendants(geospiza, "D", type="tips")
  descendants(geospiza, "D", type="all")
  ancestors(geospiza, "D")
  MRCA(geospiza, "conirostris", "difficilis", "fuliginosa")
  MRCA(geospiza, "olivacea", "conirostris")

  ## shortest path between 2 nodes
  shortestPath(geospiza, "fortis", "fuliginosa")
  shortestPath(geospiza, "F", "L")

  ## branch length from a tip to the root
  sumEdgeLength(geospiza, ancestors(geospiza, "fortis", type="ALL"))