Print Summary of a Phylogeny

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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

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## 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

See Also

read.tree, summary for the generic R function, multiphylo, c.phylo

Examples

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

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