phylobase (version 0.6.8)

phylo4-accessors: Methods for S4 phylogeny classes

Description

Generic methods for phylogenetic trees represented as S4 classes

Usage

## S3 method for class 'phylo4':
nNodes(x)
## S3 method for class 'phylo4':
nTips(x)
## S3 method for class 'phylo4':
depthTips(x)
## S3 method for class 'phylo4':
edges(x, drop.root=FALSE, \dots)
## S3 method for class 'phylo4':
nEdges(x)
## S3 method for class 'phylo4':
edgeOrder(x, \dots)
## S3 method for class 'phylo4':
hasEdgeLength(x)
## S3 method for class 'phylo4':
edgeLength(x, node)
## S3 method for class 'phylo4':
edgeLength(x, use.names=TRUE) <- value
## S3 method for class 'phylo4':
nodeType(x)
## S3 method for class 'phylo4':
nodeDepth(x, node)
## S3 method for class 'phylo4':
isRooted(x)
## S3 method for class 'phylo4':
rootEdge(x)
## S3 method for class 'phylo4':
rootNode(x)
## S3 method for class 'phylo4':
rootNode(x) <- value
## S3 method for class 'phylo4':
isUltrametric(x, tol=.Machine$double.eps^0.5)

Arguments

x

a phylo4/phylo4d object

node

which edge 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?

tol

tolerance in rounding error to determine whether the tree is ultrametric

...

additional parameters passed (currently ignored)

Examples

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