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Create a contingency table from a data.frame

Source: R/net_to_mat.R
net_to_mat.Rd

This function generates a contingency table from 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).

Usage

net_to_mat(
  net,
  weight = FALSE,
  squared = FALSE,
  symmetrical = FALSE,
  missing_value = 0
)

Arguments

net

A two- or three-column data.frame where each row represents the interaction between two nodes (e.g., site and species), with an optional third column indicating the weight of the interaction.

weight

A logical value indicating whether the weight column should be considered.

squared

A logical value indicating whether the output matrix should be square (i.e., containing the same nodes in rows and columns).

symmetrical

A logical value indicating whether the resulting matrix should be symmetrical. This applies only if squared = TRUE. Note that different weights associated with opposite pairs already present in net will be preserved.

missing_value

The value to assign to pairs of nodes not present in net. Defaults to 0.

Value

A matrix with the first nodes (from the first column of net) as rows and the second nodes (from the second column of net) as columns. If squared = TRUE, the rows and columns will have the same number of elements, corresponding to the unique union of objects in the first and second columns of net. If squared = TRUE and symmetrical = TRUE, the matrix will be forced to be symmetrical based on the upper triangular part of the matrix.

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: mat_to_net

Author

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

Examples

net <- data.frame(
  Site = c(rep("A", 2), rep("B", 3), rep("C", 2)),
  Species = c("a", "b", "a", "c", "d", "b", "d"),
  Weight = c(10, 100, 1, 20, 50, 10, 20)
)

mat <- net_to_mat(net, weight = TRUE)