as.matrix.multiPhylo: Vectorize a Set of Phylognetic Trees

In HoujieWang/Rtropical: Data Analysis Tools over Space of Phylogenetic Trees Using Tropical Geometry

Vectorize a Set of Phylognetic Trees

Description

Unifies tip labels of all phylogenetic trees in multiPhylo object the same as the first tree and returns the cophenetic distance of their corresponding chronogram.

Usage

## S3 method for class 'multiPhylo'
as.matrix(x, tipOrder = x[[1]]$tip.label, parallel = FALSE, ncores = 2, ...)

Arguments

x	an object of class multiPhylo
tipOrder	a numeric vector of order of leaf names to which all trees in the multiPhylo object will unified. If not specified on purpose, the tip order of the first tree will be used.
parallel	a logical value indicating if parallel computing should be used. (default: FALSE)
ncores	a numeric value indicating the number of threads utilized for multi-cored CPUs. (default: 2)
...	Not used. Other arguments to as.vector

Value

A data matrix with each row a vector representation of a chronogram. Each element of the vector is the distance between two leaves.

Examples

data(apicomplexa)
data <- as.matrix(apicomplexa[1: 10]) # matrixize first ten trees

HoujieWang/Rtropical documentation built on May 18, 2022, 11:56 a.m.