prioritizr: branch_matrix – R documentation

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branch_matrix

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

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
data(sim_phylogeny)

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

# plot data
## Not run: 
par(mfrow = c(1,2))
plot(sim_phylogeny, main = "phylogeny")
plot(raster(as.matrix(m)), main = "branch matrix", axes = FALSE,
     box = FALSE)

## End(Not run)

prioritizr

Systematic Conservation Prioritization in R

v7.0.1

GPL-3

Authors

Jeffrey O Hanson [aut] (<https://orcid.org/0000-0002-4716-6134>), Richard Schuster [aut, cre] (<https://orcid.org/0000-0003-3191-7869>), Nina Morrell [aut], Matthew Strimas-Mackey [aut] (<https://orcid.org/0000-0001-8929-7776>), Matthew E Watts [aut], Peter Arcese [aut] (<https://orcid.org/0000-0002-8097-482X>), Joseph Bennett [aut] (<https://orcid.org/0000-0002-3901-9513>), Hugh P Possingham [aut] (<https://orcid.org/0000-0001-7755-996X>)

Initial release