as.matrix.multiPhylo {Rtropical} | R Documentation |
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 |
tipOrder |
a numeric vector of order of leaf names to which all trees
in the |
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
[Package Rtropical version 1.2.1 Index]