caper (version 0.4)

clade.members: Identify tips descended from a node

Description

Obtains a vector of the tips subtending from either one node or all nodes in a phylogeny.

Usage

clade.members(x, phy, tip.labels = FALSE, include.nodes=FALSE)
clade.members.list(phy, tips = FALSE, tip.labels = FALSE, include.nodes=FALSE)

Arguments

x

A integer identifying the node for which a list of tips is required.

phy

An object of class 'phylo'.

tips

A logical indicating whether to include external node membership in the list.

tip.labels

A logical flag indicating whether to return the node numbers of the tips or their tip labels.

include.nodes

A logical flag indicating whether to return the node number of descendent internal nodes

Value

• A numeric vector of external node (i.e. tip) numbers or a character vector of tip labels for a single internal node or, for clade.members.list, a list of such vector for all nodes in the phylogeny. If include.nodes is TRUE then clade.members returns a list of length two containing a vector of the descendent tips and a vector of the descendent internal nodes - clade.members.list then contains a list of such lists.

Details

The function clade.members.list runs clade.members over each node in the phylogeny, possibly including the external nodes as indicated by the tips argument, and returns a list of vectors showing the members of the clade defined by each node.

Examples

data(perissodactyla)
# use comparative.data to add node labels
perisso <- comparative.data(perissodactyla.tree, perissodactyla.data, Binomial, na.omit=FALSE)
plot(perisso$phy, show.node.label=TRUE)
clade.members(22, perisso$phy, tip.labels=TRUE)
clade.members.list(perisso$phy, tip.labels=FALSE)