randomA: Generate random interaction matrix for GLV model

In microbiome/miaSim: Microbiome Data Simulation

Generate random interaction matrix for GLV model

Description

Generates a random interaction matrix for Generalized Lotka-Volterra (GLV) model.

Usage

randomA(
  n_species,
  names_species = NULL,
  diagonal = -0.5,
  connectance = 0.2,
  scale_off_diagonal = 0.1,
  mutualism = 1,
  commensalism = 1,
  parasitism = 1,
  amensalism = 1,
  competition = 1,
  interactions = NULL,
  symmetric = FALSE,
  list_A = NULL
)

Arguments

n_species	Integer: number of species
names_species	Character: names of species. If NULL, paste0("sp", seq_len(n_species)) is used. (default: names_species = NULL)
diagonal	Numeric vector. Defines the strength of self-interactions. Input can be a number (will be applied to all species) or a vector of length n_species. Positive self-interaction values lead to exponential growth. (Default: -0.5)
connectance	Numeric scalar. Specifies the frequency of inter-species interactions. i.e. proportion of non-zero off-diagonal terms. Between 0 and 1. (Default: 0.2)
scale_off_diagonal	Numeric scalar. Indicates the scale of the off-diagonal elements compared to the diagonal. (Default: 0.1)
mutualism	Numerical scalar. Specifies the relative proportion of interactions terms consistent with mutualism (positive <-> positive). (Default: 1)
commensalism	Numeric scalar. Indicates the relative proportion of interactions terms consistent with commensalism (positive <-> neutral). (Default: 1)
parasitism	Numeric scalar. Indicates the relative proportion of interactions terms consistent with parasitism (positive <-> negative). (Default: 1)
amensalism	Numeric scalar. Indicates the relative proportion of interactions terms consistent with amensalism (neutral <-> negative). (Default: 1)
competition	Numeric scalar. Indicates the relative proportion of interactions terms consistent with competition (negative <-> negative). (Default: 1)
interactions	Numeric scalar. Indicates the values of the n_species^2 pairwise interaction strengths. Diagonal terms will be replaced by the 'diagonal' parameter. If NULL, interactions are drawn from runif(n_species^2, min=0, max=abs(diagonal)). Negative values are first converted to positive then the signs are defined by the relative weights of the biological interactions (i.e. mutualism, commensalism, parasitism, amensalism, competition). (Default: NULL)
symmetric	Logical scalar. whether the strength of mutualistic and competitive interactions are symmetric. This is implemented by overwrite a half of the matrix, so the proportions of interactions might deviate from expectations. (Default: FALSE)
list_A	List. A list of matrices generated by randomA. Used to support different groups of interactions. If NULL (by default), no group is considered. Otherwise the given list of matrices will overwrite values around the diagonal. (Default: NULL)

Value

randomA returns a matrix A with dimensions (n_species x n_species)

Examples

dense_A <- randomA(
    n_species = 10,
    scale_off_diagonal = 1,
    diagonal = -1.0,
    connectance = 0.9
)

sparse_A <- randomA(
    n_species = 10,
    diagonal = -1.0,
    connectance = 0.09
)

user_interactions <- rbeta(n = 10^2, .5, .5)
user_A <- randomA(n_species = 10, interactions = user_interactions)

competitive_A <- randomA(
    n_species = 10,
    mutualism = 0,
    commensalism = 0,
    parasitism = 0,
    amensalism = 0,
    competition = 1,
    connectance = 1,
    scale_off_diagonal = 1
)

parasitism_A <- randomA(
    n_species = 10,
    mutualism = 0,
    commensalism = 0,
    parasitism = 1,
    amensalism = 0,
    competition = 0,
    connectance = 1,
    scale_off_diagonal = 1,
    symmetric = TRUE
)

list_A <- list(dense_A, sparse_A, competitive_A, parasitism_A)
groupA <- randomA(n_species = 40, list_A = list_A)

microbiome/miaSim documentation built on Oct. 25, 2024, 7:16 p.m.