find_minimum_spanning_edges {Claddis}

Get edges of minimum spanning tree

Description

Returns edges of a minimum spanning tree given a distance matrix.

Usage

find_minimum_spanning_edges(distance_matrix)

Arguments

distance_matrix

A square matrix of distances between objects.

Details

This function is a wrapper for mst in the ape package, but returns a vector of edges rather than a square matrix of links.

Value

A vector of named edges (X->Y) with their distances. The sum of this vector is the length of the minimum spanning tree.

Author(s)

Graeme T. Lloyd [e-mail]

Examples

# Create a simple square matrix of distances:
distance_matrix <- matrix(c(0, 1, 2, 3, 1, 0, 1, 2, 2, 1, 0, 1, 3, 2, 1, 0),
  nrow = 4,
  dimnames = list(LETTERS[1:4], LETTERS[1:4])
)

# Show matrix to confirm that the off diagonal has the shortest
# distances:
distance_matrix

# Use find_minimum_spanning_edges to get the edges for the minimum spanning
# tree:
find_minimum_spanning_edges(distance_matrix)

# Use sum of find_minimum_spanning_edges to get the length of the minimum
# spanning tree:
sum(find_minimum_spanning_edges(distance_matrix))