randomE: Generate random efficiency matrix

In microbiome/miaSim: Microbiome Data Simulation

Generate random efficiency matrix

Description

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 scalar. Specifies the mean number of resources consumed by each species drawn from a poisson distribution (Default: n_resources/4)
mean_production	Numeric scalar. Specifies the mean number of resources produced by each species drawn from a poisson distribution (Default: n_resources/6)
maintenance	Numeric scalar. Specifies the 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: 0.5)
trophic_levels	Integer scalar. Indicates the number of species in microbial trophic levels. If NULL, by default, microbial trophic levels would not be considered. (Default: NULL)
trophic_preferences	List. Indicates the 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. (Default: NULL)
exact	Logical scalar. 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: 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)
)

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