mat_to_net: Create a data.frame from a contingency table

In bioregion: Comparison of Bioregionalisation Methods

Create a data.frame from a contingency table

Description

This function generates a two- or three-column data.frame, where each row represents the interaction between two nodes (e.g., site and species) and an optional third column indicates the weight of the interaction (if weight = TRUE). The input is a contingency table, with rows representing one set of entities (e.g., site) and columns representing another set (e.g., species).

Usage

mat_to_net(
  mat,
  weight = FALSE,
  remove_zeroes = TRUE,
  include_diag = TRUE,
  include_lower = TRUE
)

Arguments

mat	A contingency table (i.e., a matrix).
weight	A logical value indicating whether the values in the matrix should be interpreted as interaction weights.
remove_zeroes	A logical value determining whether interactions with a weight equal to 0 should be excluded from the output.
include_diag	A logical value indicating whether the diagonal (self-interactions) should be included in the output. This applies only to square matrices.
include_lower	A logical value indicating whether the lower triangular part of the matrix should be included in the output. This applies only to square matrices.

Value

A data.frame where each row represents the interaction between two nodes. If weight = TRUE, the data.frame includes a third column representing the weight of each interaction.

Author(s)

Maxime Lenormand ([e-mail])
Pierre Denelle ([e-mail])
Boris Leroy ([e-mail])

See Also

For more details illustrated with a practical example, see the vignette: https://biorgeo.github.io/bioregion/articles/a2_matrix_and_network_formats.html.

Associated functions: net_to_mat

Examples

mat <- matrix(sample(1000, 50), 5, 10)
rownames(mat) <- paste0("Site", 1:5)
colnames(mat) <- paste0("Species", 1:10)

net <- mat_to_net(mat, weight = TRUE)

bioregion documentation built on April 12, 2025, 9:13 a.m.