phylobase: treeStructure-methods – R documentation

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treeStructure-methods

Test trees for polytomies, inline nodes (singletons), or reticulation

Description

Methods to test whether trees have (structural) polytomies, inline nodes (i.e., nodes with a single descendant), or reticulation (i.e., nodes with more than one ancestor). hasPoly only check for structural polytomies (1 node has more than 2 descendants) and not polytomies that result from having edges with a length of 0.

Usage

hasSingle(object)

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

hasRetic(object)

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

hasPoly(object)

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

Arguments

object

an object inheriting from class phylo4

Value

Logical value

Note

Some algorithms are unhappy with structural polytomies (i.e., >2 descendants from a node), with single-descendant nodes, or with reticulation; these functions check those properties. We haven't bothered to check for zero branch lengths: the consensus is that it doesn't come up much, and that it's simple enough to test any(edgeLength(x) == 0) in these cases. (Single-descendant nodes are used e.g. in OUCH, or in other cases to represent events occurring along a branch.)

Author(s)

Ben Bolker

Examples

tree.owls.bis <- ape::read.tree(text="((Strix_aluco:4.2,Asio_otus:4.2):3.1,Athene_noctua:7.3);")
owls4 <- as(tree.owls.bis, "phylo4")
hasPoly(owls4)
hasSingle(owls4)

phylobase

Base Package for Phylogenetic Structures and Comparative Data

v0.8.10

GPL (>= 2)

Authors

R Hackathon et al. (alphabetically: Ben Bolker, Marguerite Butler, Peter Cowan, Damien de Vienne, Dirk Eddelbuettel, Mark Holder, Thibaut Jombart, Steve Kembel, Francois Michonneau, David Orme, Brian O'Meara, Emmanuel Paradis, Jim Regetz, Derrick Zwickl)

Initial release