simulateSOI: Self-Organised Instability model (SOI) simulation

In microbiome/miaSim: Microbiome Data Simulation

Self-Organised Instability model (SOI) simulation

Description

Generate time-series with The Self-Organised Instability (SOI) model. Implements a K-leap method for accelerating stochastic simulation.

Usage

simulateSOI(
  n_species,
  x0 = NULL,
  names_species = NULL,
  carrying_capacity = 1000,
  A = NULL,
  k_events = 5,
  t_end = 1000,
  metacommunity_probability = runif(n_species, min = 0.1, max = 0.8),
  death_rates = runif(n_species, min = 0.01, max = 0.08),
  norm = FALSE
)

Arguments

n_species	Integer: number of species
x0	Numeric scalar. Specifies initial community abundances If NULL, based on migration rates. (Default: NULL)
names_species	Character: names of species. If NULL, paste0("sp", seq_len(n_species)) is used. (default: names_species = NULL)
carrying_capacity	Integer scalar. Indicates community size, number of available sites (individuals). (Default: 1000)
A	Matrix. Defines the positive and negative interactions between n_species. If NULL, powerlawA(n_species) is used. (Default: NULL)
k_events	Integer scalar. Indicates the number of transition events that are allowed to take place during one leap. Higher values reduce runtime, but also accuracy of the simulation. (Default: 5).
t_end	Numeric scalar. Specifies the end time of the simulation, defining the modeled time length of the community. (Default: 1000)
metacommunity_probability	Numeric scalar: Indicates the normalized probability distribution of the likelihood that species from the metacommunity can enter the community during the simulation. (Default: runif(n_species, min = 0.1, max = 0.8))
death_rates	Numeric scalar. Indicates the death rates of each species. (Default: runif(n_species, min = 0.01, max = 0.08))
norm	Logical scalar. Whether the time series should be returned with the abundances as proportions (norm = TRUE) or the raw counts. (Default: FALSE)

Value

simulateSOI returns a TreeSummarizedExperiment class object

Examples

# Generate interaction matrix
A <- miaSim::powerlawA(10, alpha = 1.2)
# Simulate data from the SOI model
tse <- simulateSOI(
    n_species = 10, carrying_capacity = 1000, A = A,
    k_events = 5, x0 = NULL, t_end = 150, norm = TRUE
)

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