branch_matrix: Branch matrix
In prioritizr/prioritizrutils: Utilities for prioritizr

Description Usage Arguments Value Examples

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 histroy. 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 experienced.

branch_matrix(x)

## Default S3 method:
branch_matrix(x)

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

`x`	`phylo` tree object.

dgCMatrix-class 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.

# load data
data(sim_phylogeny)

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

# plot data
if (requireNamespace("ape", quietly = TRUE)) {
  par(mfrow = c(1,2))
  plot(sim_phylogeny, main = "phylogeny")
  plot(raster(as.matrix(m)), main = "branch matrix")
} else {
  message("the \"ape\" package needs to be installed to plot phylogenies")
}