Branch matrix — branch

Phylogenetic trees depict the evolutionary relationships between different species. Each branch in a phylogenetic tree represents a period of evolutionary history. Species that are connected to the same branch share the same period of evolutionary history represented by the branch. This function creates a matrix that shows which species are connected with which branches. In other words, it creates a matrix that shows which periods of evolutionary history each species has experienced.

Usage

branch_matrix(x, ...)

# Default S3 method
branch_matrix(x, ...)

# S3 method for class 'phylo'
branch_matrix(x, assert_validity = TRUE, ...)

Arguments

x: ape::phylo() tree object.
...: not used.
assert_validity: logical value (i.e., TRUE or FALSE indicating if the argument to x should be checked for validity. Defaults to TRUE.

Value

A Matrix::dgCMatrix sparse matrix object. Each row corresponds to a different species. Each column corresponds to a different branch. Species that inherit from a given branch are indicated with a one.

Examples

# load Matrix package to plot matrices
library(Matrix)

# load data
data(sim_tree)

# generate species by branch matrix
m <- branch_matrix(sim_tree)

# plot data
par(mfrow = c(1, 2))
plot(sim_tree, main = "phylogeny")
image(m, main = "branch matrix")