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 which branches. In other words, it creates a matrix that shows which periods of evolutionary history different species have experienced.
branch_matrix(x) # S3 method for default branch_matrix(x) # S3 method for phylo branch_matrix(x)
Arguments
| x |
|
|---|
Value
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 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")
