phylobase (version 0.8.12)

phylo4-labels: Labels for phylo4/phylo4d objects

Description

Methods for creating, accessing and updating labels in phylo4/phylo4d objects

Usage

labels(object, ...)
# S4 method for phylo4
labels(object, type = c("all", "tip", "internal"))
labels(x, type, use.names, ...) <- value
# S4 method for phylo4
labels(x, type = c("all", "tip", "internal"), use.names, ...) <- value
hasDuplicatedLabels(x, type)
# S4 method for phylo4
hasDuplicatedLabels(x, type = c("all", "tip", "internal"))
hasNodeLabels(x)
# S4 method for phylo4
hasNodeLabels(x)
nodeLabels(x)
# S4 method for phylo4
nodeLabels(x)
nodeLabels(x, ...) <- value
# S4 method for phylo4
nodeLabels(x, ...) <- value
tipLabels(x)
# S4 method for phylo4
tipLabels(x)
tipLabels(x, ...) <- value
# S4 method for phylo4
tipLabels(x, ...) <- value
hasEdgeLabels(x)
# S4 method for phylo4
hasEdgeLabels(x)
edgeLabels(x)
# S4 method for phylo4
edgeLabels(x)
edgeLabels(x, ...) <- value
# S4 method for phylo4
edgeLabels(x, ...) <- value

Value

labels in ascending order.

Arguments

object

a phylo4 or phylo4d object.

...

additional optional arguments (not in use)

type

which type of labels: all (tips and internal nodes), tip (tips only), internal (internal nodes only).

x

a phylo4 or phylo4d object.

use.names

should the names of the vector used to create/update labels be used to match the labels? See Details for more information.

value

a vector of class character, see Details for more information.

Methods

labels

signature(object = "phylo4"): tip and/or internal node labels, ordered by node ID

hasDuplicatedLabels

signature(object = "phylo4"): are any labels duplicated?

tipLabels

signature(object = "phylo4"): tip labels, ordered by node ID

hasNodeLabels

signature(object = "phylo4"): whether tree has (internal) node labels

nodeLabels

signature(object = "phylo4"): internal node labels, ordered by node ID

hasEdgeLabels

signature(object = "phylo4"): whether tree has (internal) edge labels

edgeLabels

signature(object = "phylo4"): internal edge labels, ordered according to the edge matrix

Author

Ben Bolker, Peter Cowan, Steve Kembel, Francois Michonneau

Details

In phylo4/phylo4d objects, tips must have labels (that's why there is no method for hasTipLabels), internal nodes and edges can have labels.

Labels must be provided as a vector of class character. The length of the vector must match the number of elements they label.

The option use.names allows the user to match a label to a particular node. In this case, the vector must have names that match the node numbers.

The function labels is mostly intended to be used internally.

Examples

data(geospiza)

## Return labels from geospiza
tipLabels(geospiza)

## Internal node labels in geospiza are empty
nodeLabels(geospiza)

## Creating internal node labels
ndLbl <- paste("n", 1:nNodes(geospiza), sep="")
nodeLabels(geospiza) <- ndLbl
nodeLabels(geospiza)

## naming the labels
names(ndLbl) <- nodeId(geospiza, "internal")

## shuffling the labels
(ndLbl <- sample(ndLbl))

## by default, the labels are attributed in the order
## they are given:
nodeLabels(geospiza) <- ndLbl
nodeLabels(geospiza)

## but use.names puts them in the correct order
labels(geospiza, "internal", use.names=TRUE) <- ndLbl
nodeLabels(geospiza)