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Generate random efficiency matrix

Source: R/randomE.R
randomE.Rd

Generate random efficiency matrix for consumer resource model from Dirichlet distribution, where positive efficiencies indicate the consumption of resources, whilst negatives indicate that the species would produce the resource.

Usage

randomE(
  n_species,
  n_resources,
  names_species = NULL,
  names_resources = NULL,
  mean_consumption = n_resources/4,
  mean_production = n_resources/6,
  maintenance = 0.5,
  trophic_levels = NULL,
  trophic_preferences = NULL,
  exact = FALSE
)

Arguments

n_species

Integer: number of species

n_resources

Integer: number of resources

names_species

Character: names of species. If NULL, paste0("sp", seq_len(n_species)) is used. (default: names_species = NULL)

names_resources

Character: names of resources. If NULL, paste0("res", seq_len(n_resources)) is used.

mean_consumption

Numeric: mean number of resources consumed by each species drawn from a poisson distribution (default: mean_consumption = n_resources/4)

mean_production

Numeric: mean number of resources produced by each species drawn from a poisson distribution (default: mean_production = n_resources/6)

maintenance

Numeric: proportion of resources that cannot be converted into products between 0~1 the proportion of resources used to maintain the living of microorganisms. 0 means all the resources will be used for the reproduction of microorganisms, and 1 means all the resources would be used to maintain the living of organisms and no resources would be left for their growth(reproduction). (default: maintenance = 0.5)

trophic_levels

Integer: number of species in microbial trophic levels. If NULL, by default, microbial trophic levels would not be considered. (default: trophic_levels = NULL)

trophic_preferences

List: preferred resources and productions of each trophic level. Positive values indicate the consumption of resources, whilst negatives indicate that the species would produce the resource.

exact

Logical: whether to set the number of consumption/production to be exact as mean_consumption/mean_production or to set them using a Poisson distribution. (default: exact = FALSE) If length(trophic_preferences) is smaller than length(trophic_levels), then NULL values would be appended to lower trophic levels. If NULL, by default, the consumption preference will be defined randomly. (default: trophic_preferences = NULL)

Value

randomE returns a matrix E with dimensions (n_species x n_resources), and each row represents a species.

Examples

# example with minimum parameters
ExampleEfficiencyMatrix <- randomE(n_species = 5, n_resources = 12)

# examples with specific parameters
ExampleEfficiencyMatrix <- randomE(
    n_species = 3, n_resources = 6,
    names_species = letters[1:3],
    names_resources = paste0("res", LETTERS[1:6]),
    mean_consumption = 3, mean_production = 1
)
ExampleEfficiencyMatrix <- randomE(
    n_species = 3, n_resources = 6,
    maintenance = 0.4
)
ExampleEfficiencyMatrix <- randomE(
    n_species = 3, n_resources = 6,
    mean_consumption = 3, mean_production = 1, maintenance = 0.4
)

# examples with microbial trophic levels
ExampleEfficiencyMatrix <- randomE(
    n_species = 10, n_resources = 15,
    trophic_levels = c(6, 3, 1),
    trophic_preferences = list(
        c(rep(1, 5), rep(-1, 5), rep(0, 5)),
        c(rep(0, 5), rep(1, 5), rep(-1, 5)),
        c(rep(0, 10), rep(1, 5))
    )
)
ExampleEfficiencyMatrix <- randomE(
    n_species = 10, n_resources = 15,
    trophic_levels = c(6, 3, 1),
    trophic_preferences = list(c(rep(1, 5), rep(-1, 5), rep(0, 5)), NULL, NULL)
)
ExampleEfficiencyMatrix <- randomE(
    n_species = 10, n_resources = 15,
    trophic_levels = c(6, 3, 1)
)