summary-methods: Summary for phylo4/phylo4d objects

Description

Summary of information for the tree (phylo4 only) and/or the associated data (phylo4d).

Usage

summary(object, ...)
# S4 method for phylo4
summary(object, quiet = FALSE)
# S4 method for phylo4d
summary(object, quiet = FALSE)
nodeType(object)
# S4 method for phylo4
nodeType(object)

Value

The nodeType method returns named vector which has the type of node (internal, tip, root) for value, and the node number for name

The summary method invisibly returns a list with the following components:

list("name"): the name of the object
list("nb.tips"): the number of tips
list("nb.nodes"): the number of nodes
list("mean.el"): mean of edge lengths
list("var.el"): variance of edge lengths (estimate for population)
list("sumry.el"): summary (i.e. range and quartiles) of the edge lengths
list("degree"): (optional) type of polytomy for each node: ‘node’, ‘terminal’ (all descendants are tips) or ‘internal’ (at least one descendant is an internal node); displayed only when there are polytomies
list("sumry.tips"): (optional) summary for the data associated with the tips
list("sumry.nodes"): (optional) summary for the data associated with the internal nodes

Arguments

object: a phylo4d object
...: optional additional elements (not in use)
quiet: Should the summary be displayed on screen?

Author

Ben Bolker, Thibaut Jombart, Francois Michonneau

Examples

Run this code

  tOwls <- "(((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3):6.3,Tyto_alba:13.5);"
  tree.owls <- ape::read.tree(text=tOwls)
  P1 <- as(tree.owls, "phylo4")
  P1
  summary(P1)
  nodeType(P1)

  ## summary of a polytomous tree
  E <- matrix(c(
      8,  9,
      9, 10,
     10,  1,
     10,  2,
      9,  3,
      9,  4,
      8, 11,
     11,  5,
     11,  6,
     11,  7,
      0,  8), ncol=2, byrow=TRUE)

  P2 <- phylo4(E)
  nodeLabels(P2) <- as.character(nodeId(P2, "internal"))
  plot(P2, show.node.label=TRUE)
  sumryP2 <- summary(P2)
  sumryP2