bioregion (version 1.3.0)

mat_to_net: 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
)

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.

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.

Author

Maxime Lenormand ()
Pierre Denelle ()
Boris Leroy ()

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)