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Load interspecific interaction settings (radius + matrix)

Source: R/config.R
load_interactions.Rd

Reads a separate interactions config file and returns a local-interaction radius along with an \(S \times S\) interaction matrix for \(S\) species (rows = focal, columns = neighbour). If the file is missing or incomplete, a neutral matrix of ones and radius 0 are returned.

Usage

load_interactions(interactions_file, n_species)

Arguments

interactions_file

Character scalar or NULL. Path to the interactions configuration file. If NULL or not found, the returned radius is 0 and all coefficients are 1.

n_species

Integer. Number of species; defines the size of the returned matrix and the expected label set LETTERS[1:n_species].

Value

A list with components:

radius

Numeric length-1; the interaction radius (0 disables interactions).

matrix

Numeric matrix of size \(S \times S\) with dimnames LETTERS[1:S]. Non-finite values are rejected.

Details

The interactions file is parsed as simple KEY = value pairs. The following keys are recognized:

  • INTERACTION_RADIUS: non-negative numeric; distance threshold within which neighbours influence assignment probabilities.

  • MATRIX_CSV: path to a CSV containing a (sub)matrix with row names and column names corresponding to species labels (e.g. A..Z). Any missing rows/columns are filled with 1.

  • EDGELIST_CSV: path to a CSV with columns focal, neighbor, value; entries are inserted into the appropriate cells of the full matrix.

  • AUTO: optional flag (TRUE/FALSE) enabling a simple built-in example structure if no CSV is provided.

If both MATRIX_CSV and EDGELIST_CSV are supplied, MATRIX_CSV takes precedence.

See also

load_config()

Examples

if (FALSE) { # \dontrun{
I <- load_interactions("config/interactions.txt", n_species = 10)
I$radius
I$matrix[1:3, 1:3]
} # }