ape: as.bitsplits – R documentation

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as.bitsplits

Split Frequencies and Conversion Among Split Classes

Description

bitsplits returns the bipartitions (aka splits) for a single tree or a list of trees. If at least one tree is rooted, an error is returned.

countBipartitions returns the frequencies of the bipartitions from a reference tree (phy) observed in a list of trees (X), all unrooted.

as.bitsplits and as.prop.part are generic functions for converting between the "bitsplits" and "prop.part" classes.

Usage

bitsplits(x)
countBipartitions(phy, X)
as.bitsplits(x)
## S3 method for class 'prop.part'
as.bitsplits(x)
## S3 method for class 'bitsplits'
print(x, ...)
## S3 method for class 'bitsplits'
sort(x, decreasing = FALSE, ...)
as.prop.part(x, ...)
## S3 method for class 'bitsplits'
as.prop.part(x, include.trivial = FALSE, ...)

Arguments

`x`	an object of the appropriate class.
`phy`	an object of class `"phylo"`.
`X`	an object of class `"multiPhylo"`.
`decreasing`	a logical value to sort the bipartitions in increasing (the default) or decreasing order of their frequency.
`include.trivial`	a logical value specifying whether to include the trivial split with all tips in the returned object.
`...`	further arguments passed to or from other methods.

Details

These functions count bipartitions as defined by internal branches, so they not work only with unrooted trees. The structure of the class "bitsplits" is described in a separate document on ape's web site.

Value

bitsplits, as.bitsplits, and sort return an object of class "bitsplits".

countBipartitions returns a vector of integers.

as.prop.part returns an object of class "prop.part".

Author(s)

Emmanuel Paradis

Examples

tr <- rtree(20)
pp <- prop.part(tr)
as.bitsplits(pp)
## works only with unrooted trees (ape 5.5):
countBipartitions(rtree(10, rooted = FALSE), rmtree(100, 10, rooted = FALSE))

ape

Analyses of Phylogenetics and Evolution

v5.5

GPL-2 | GPL-3

Authors

Emmanuel Paradis [aut, cre, cph] (<https://orcid.org/0000-0003-3092-2199>), Simon Blomberg [aut, cph] (<https://orcid.org/0000-0003-1062-0839>), Ben Bolker [aut, cph] (<https://orcid.org/0000-0002-2127-0443>), Joseph Brown [aut, cph] (<https://orcid.org/0000-0002-3835-8062>), Santiago Claramunt [aut, cph] (<https://orcid.org/0000-0002-8926-5974>), Julien Claude [aut, cph] (<https://orcid.org/0000-0002-9267-1228>), Hoa Sien Cuong [aut, cph], Richard Desper [aut, cph], Gilles Didier [aut, cph] (<https://orcid.org/0000-0003-0596-9112>), Benoit Durand [aut, cph], Julien Dutheil [aut, cph] (<https://orcid.org/0000-0001-7753-4121>), RJ Ewing [aut, cph], Olivier Gascuel [aut, cph], Thomas Guillerme [aut, cph] (<https://orcid.org/0000-0003-4325-1275>), Christoph Heibl [aut, cph] (<https://orcid.org/0000-0002-7655-3299>), Anthony Ives [aut, cph] (<https://orcid.org/0000-0001-9375-9523>), Bradley Jones [aut, cph] (<https://orcid.org/0000-0003-4498-1069>), Franz Krah [aut, cph] (<https://orcid.org/0000-0001-7866-7508>), Daniel Lawson [aut, cph] (<https://orcid.org/0000-0002-5311-6213>), Vincent Lefort [aut, cph], Pierre Legendre [aut, cph] (<https://orcid.org/0000-0002-3838-3305>), Jim Lemon [aut, cph], Guillaume Louvel [aut, cph] (<https://orcid.org/0000-0002-7745-0785>), Eric Marcon [aut, cph] (<https://orcid.org/0000-0002-5249-321X>), Rosemary McCloskey [aut, cph] (<https://orcid.org/0000-0002-9772-8553>), Johan Nylander [aut, cph], Rainer Opgen-Rhein [aut, cph], Andrei-Alin Popescu [aut, cph], Manuela Royer-Carenzi [aut, cph], Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>), Korbinian Strimmer [aut, cph] (<https://orcid.org/0000-0001-7917-2056>), Damien de Vienne [aut, cph] (<https://orcid.org/0000-0001-9532-5251>)

Initial release

2021-04-24