hasSingle {phylobase} | R Documentation |
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)
hasSingle(object) hasPoly(object) hasRetic(object)
object |
an object inheriting from class phylo4 |
Logical value
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.)
Ben Bolker
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)