ape: summary.phylo – R documentation

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summary.phylo

Print Summary of a Phylogeny

Description

The first function prints a compact summary of a phylogenetic tree (an object of class "phylo"). The three other functions return the number of tips, nodes, or edges, respectively.

Usage

## S3 method for class 'phylo'
summary(object, ...)

Ntip(phy)
## S3 method for class 'phylo'
Ntip(phy)
## S3 method for class 'multiPhylo'
Ntip(phy)

Nnode(phy, ...)
## S3 method for class 'phylo'
Nnode(phy, internal.only = TRUE, ...)
## S3 method for class 'multiPhylo'
Nnode(phy, internal.only = TRUE, ...)

Nedge(phy)
## S3 method for class 'phylo'
Nedge(phy)
## S3 method for class 'multiPhylo'
Nedge(phy)

Arguments

`object, phy`	an object of class `"phylo"` or `"multiPhylo"`.
`...`	further arguments passed to or from other methods.
`internal.only`	a logical indicating whether to return the number of internal nodes only (the default), or of internal and terminal (tips) nodes (if `FALSE`).

Details

The summary includes the numbers of tips and of nodes, summary statistics of the branch lengths (if they are available) with mean, variance, minimum, first quartile, median, third quartile, and maximum, listing of the first ten tip labels, and (if available) of the first ten node labels. It is also printed whether some of these optional elements (branch lengths, node labels, and root edge) are not found in the tree.

summary simply prints its results on the standard output and is not meant for programming.

Value

A NULL value in the case of summary, a single numeric value for the three other functions.

Author(s)

Emmanuel Paradis

Examples

data(bird.families)
summary(bird.families)
Ntip(bird.families)
Nnode(bird.families)
Nedge(bird.families)

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