phylobase: phylo4-methods – R documentation

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phylo4-methods

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

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

Base Package for Phylogenetic Structures and Comparative Data

v0.8.10

GPL (>= 2)

Authors

R Hackathon et al. (alphabetically: Ben Bolker, Marguerite Butler, Peter Cowan, Damien de Vienne, Dirk Eddelbuettel, Mark Holder, Thibaut Jombart, Steve Kembel, Francois Michonneau, David Orme, Brian O'Meara, Emmanuel Paradis, Jim Regetz, Derrick Zwickl)

Initial release