View source: R/branch_matrix.R
branch_matrix  R Documentation 
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.
branch_matrix(x, ...) ## Default S3 method: branch_matrix(x, ...) ## S3 method for class 'phylo' branch_matrix(x, assert_validity = TRUE, ...)
x 

... 
not used. 
assert_validity 

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.
# 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")
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