summary-methods: Summary for phylo4/phylo4d objects
In phylobase: Base Package for Phylogenetic Structures and Comparative Data

summary-methods

R Documentation

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 signature 'phylo4'
summary(object, quiet = FALSE)

## S4 method for signature 'phylo4d'
summary(object, quiet = FALSE)

nodeType(object)

## S4 method for signature 'phylo4'
nodeType(object)

Arguments

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

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

Author(s)

Ben Bolker, Thibaut Jombart, Francois Michonneau

Examples

  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

phylobase documentation built on May 29, 2024, 11:24 a.m.