ape: as.matching – R documentation

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ape

as.matching

Conversion Between Phylo and Matching Objects

Description

These functions convert objects between the classes "phylo" and "matching".

Usage

as.matching(x, ...)
## S3 method for class 'phylo'
as.matching(x, labels = TRUE, ...)
## S3 method for class 'matching'
as.phylo(x, ...)

Arguments

`x`	an object to convert as an object of class `"matching"` or of class `"phylo"`.
`labels`	a logical specifying whether the tip and node labels should be included in the returned matching.
`...`	further arguments to be passed to or from other methods.

Details

A matching is a representation where each tip and each node are given a number, and sibling groups are grouped in a “matching pair” (see Diaconis and Holmes 1998, for details). This coding system can be used only for binary (fully dichotomous) trees.

Diaconis and Holmes (1998) gave some conventions to insure that a given tree has a unique representation as a matching. I have tried to follow them in the present functions.

Value

as.matching returns an object of class "matching" with the following component:

`matching`	a two-column numeric matrix where the columns represent the sibling pairs.
`tip.label`	(optional) a character vector giving the tip labels where the ith element is the label of the tip numbered i in `matching`.
`node.label`	(optional) a character vector giving the node labels in the same order than in `matching` (i.e. the ith element is the label of the node numbered i + n in `matching`, with n the number of tips).

as.phylo.matching returns an object of class "phylo".

Note

Branch lengths are not supported in the present version.

Author(s)

Emmanuel Paradis

References

Diaconis, P. W. and Holmes, S. P. (1998) Matchings and phylogenetic trees. Proceedings of the National Academy of Sciences USA, 95, 14600–14602.

Examples

data(bird.orders)
m <- as.matching(bird.orders)
str(m)
m
tr <- as.phylo(m)
all.equal(tr, bird.orders, use.edge.length = 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