hasSingle {phylobase}R Documentation

Test trees for polytomies, inline nodes, or reticulation

Description

checks to see whether trees have (structural) polytomies, inline nodes (i.e., nodes with a single descendant), or reticulation (i.e., nodes with more than one ancestor)

Usage

hasSingle(object)
hasPoly(object)
hasRetic(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

library(ape)
tree.owls.bis <- 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)

[Package phylobase version 0.5 Index]