Create a data.frame from a contingency table

This function creates a two- or three-columns data.frame where each row represents the interaction between two nodes (site and species for example) and an optional third column indicating the weight of the interaction (if weight = TRUE) from a contingency table (sites as rows and species as columns for example).

Usage

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

Arguments

mat: a contingency table (i.e. matrix).
weight: a boolean indicating if the value are weights.
remove_zeroes: a boolean determining whether interactions with weight equal to 0 should be removed from the output.
include_diag: a boolean indicating whether the diagonal should be included in the output. Only for squared matrix.
include_lower: a boolean indicating whether the lower triangular matrix should be included in the output. Only for squared matrix.

Value

A data.frame where each row represents the interaction between two nodes and an optional third column indicating the weight of the interaction.

Author

Maxime Lenormand (maxime.lenormand@inrae.fr), Pierre Denelle (pierre.denelle@gmail.com) and 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)