phylo4-methods: Create a phylogenetic tree

In phylobase: Base Package for Phylogenetic Structures and Comparative Data

Create a phylogenetic tree

Description

phylo4 is a generic constructor that creates a phylogenetic tree object for use in phylobase methods. Phylobase contains functions for input of phylogenetic trees and data, manipulation of these objects including pruning and subsetting, and plotting. The phylobase package also contains translation functions to forms used in other comparative phylogenetic method packages.

Usage

phylo4(x, ...)

phylo4_orderings

## S4 method for signature 'matrix'
phylo4(
  x,
  edge.length = NULL,
  tip.label = NULL,
  node.label = NULL,
  edge.label = NULL,
  order = "unknown",
  annote = list()
)

## S4 method for signature 'phylo'
phylo4(x, check.node.labels = c("keep", "drop"), annote = list())

## S4 method for signature 'nexml'
phylo4(x)

Arguments

x	a matrix of edges or an object of class phylo (see above)
...	optional arguments (none used at present).
edge.length	Edge (branch) length. (Optional)
tip.label	A character vector of species names (names of "tip" nodes). (Optional)
node.label	A character vector of internal node names. (Optional)
edge.label	A character vector of edge (branch) names. (Optional)
order	character: tree ordering (allowable values are listed in phylo4_orderings, currently "unknown", "preorder" (="cladewise" in ape), and "postorder", with "cladewise" and "pruningwise" also allowed for compatibility with ape)
annote	any additional annotation data to be passed to the new object
check.node.labels	if x is of class phylo, either "keep" (the default) or "drop" node labels. This argument is useful if the phylo object has non-unique node labels.
edge	A numeric, two-column matrix with as many rows as branches in the phylogeny.

Format

An object of class character of length 5.

Details

The minimum information necessary to create a phylobase tree object is a valid edge matrix. The edge matrix describes the topology of the phylogeny. Each row describes a branch of the phylogeny, with the (descendant) node number in column 2 and its ancestor's node number in column 1. These numbers are used internally and must be unique for each node.

The labels designate either nodes or edges. The vector node.label names internal nodes, and together with tip.label, name all nodes in the tree. The vector edge.label names all branches in the tree. All label vectors are optional, and if they are not given, internally-generated labels will be assigned. The labels, whether user-specified or internally generated, must be unique as they are used to join species data with phylogenetic trees.

phylobase also allows to create phylo4 objects using the function phylo4() from objects of the classes: phylo (from ape), and nexml (from RNeXML).

Note

Translation functions are available from many valid tree formats. See coerce-methods.

Author(s)

phylobase team

See Also

coerce-methods for translation functions. The phylo4 class. See also the phylo4d-methods constructor, and phylo4d class.

Examples

# a three species tree:
mytree <- phylo4(x=matrix(data=c(4,1, 4,5, 5,2, 5,3, 0,4), ncol=2,
byrow=TRUE), tip.label=c("speciesA", "speciesB", "speciesC")) 
mytree
plot(mytree)

# another way to specify the same tree:
mytree <- phylo4(x=cbind(c(4, 4, 5, 5, 0), c(1, 5, 2, 3, 4)),
tip.label=c("speciesA", "speciesB", "speciesC")) 

# another way:
mytree <- phylo4(x=rbind(c(4, 1), c(4, 5), c(5, 2), c(5, 3), c(0, 4)),
tip.label=c("speciesA", "speciesB", "speciesC")) 

# with branch lengths:
mytree <- phylo4(x=rbind(c(4, 1), c(4, 5), c(5, 2), c(5, 3), c(0, 4)),
tip.label=c("speciesA", "speciesB", "speciesC"), edge.length=c(1, .2,
.8, .8, NA))
plot(mytree)

phylobase documentation built on May 29, 2024, 11:24 a.m.