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Create a data.frame from a contingency table

Source: R/mat_to_net.R
mat_to_net.Rd

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.

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

Author

Maxime Lenormand (maxime.lenormand@inrae.fr)
Pierre Denelle (pierre.denelle@gmail.com)
Boris Leroy (leroy.boris@gmail.com)

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)