branch_matrix: Branch matrix

In prioritizr: Systematic Conservation Prioritization in R

Branch matrix

Description

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 both share that same period of evolutionary history. This function creates a matrix that shows which species are connected with branch. In other words, it creates a matrix that shows which periods of evolutionary history each species have experienced.

Usage

branch_matrix(x)

## Default S3 method:
branch_matrix(x)

## S3 method for class 'phylo'
branch_matrix(x)

Arguments

x	ape::phylo() tree object.

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 denoted with a one.

Examples

# load data
sim_phylogeny <- get_sim_phylogeny()

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

# plot data
## Not run: 
plot(sim_phylogeny, main = "phylogeny")
Matrix::image(m, main = "branch matrix")

## End(Not run)

prioritizr documentation built on April 3, 2025, 8:45 p.m.