phylo4-accessors {phylobase}R Documentation

Methods for S4 phylogeny classes

Description

Generic methods for phylogenetic trees represented as S4 classes

Usage

## S4 method for signature 'phylo4':
nNodes(x)
## S4 method for signature 'phylo4':
nTips(x)
## S4 method for signature 'phylo4':
edges(x, drop.root=FALSE, ...)
## S4 method for signature 'phylo4':
nEdges(x)
## S4 method for signature 'phylo4':
edgeOrder(x, ...)
## S4 method for signature 'phylo4':
hasEdgeLength(x)
## S4 method for signature 'phylo4':
edgeLength(x, node)
## S4 method for signature 'phylo4':
edgeLength(x, use.names=TRUE) <- value
## S4 method for signature 'phylo4':
nodeType(x)
## S4 method for signature 'phylo4':
isRooted(x)
## S4 method for signature 'phylo4':
rootEdge(x)
## S4 method for signature 'phylo4':
rootNode(x)
## S4 method for signature 'phylo4':
rootNode(x) <- value

Arguments

x a phylo4/phylo4d object
node which edge lengths to extract (indexed by descendant node)
value a vector of edge lengths or a node number
use.names Should the names of value be used to match edge lengths provided?
drop.root logical: drop root row from edge matrix?
... additional parameters passed (currently ignored)

Methods

nTips
signature(object="phylo4"): number of tips
nNodes
signature(object="phylo4"): number of internal nodes
nEdges
signature(object = "phylo4"): number of edges
edges
signature(object = "phylo4"): returns the edge matrix
edgeOrder
signature(object = "phylo4"): returns the order in which the edges are stored
hasEdgeLength
signature(object = "phylo4"): whether tree has edge (branch) lengths
edgeLength
signature(object = "phylo4"): edge (branch) lengths (or NAs if missing) ordered according to the edge matrix
nodeType
signature(object = "phylo4"): named vector which has the type of node (internal, tip, root) for value, and the node number for name
isRooted
signature(object = "phylo4"): whether tree is rooted (i.e. has explicit root edge defined or root node has <= 2 descendants)
rootEdge
signature(object = "phylo4"): root edge

Examples

data(geospiza)
edgeLength(geospiza,5)
edgeLength(geospiza,"olivacea")
edgeLength(geospiza,5:7)

[Package phylobase version 0.5 Index]