simulateHubbell: Hubbell's neutral model simulation

In microbiome/miaSim: Microbiome Data Simulation

Hubbell's neutral model simulation

Description

Neutral species abundances simulation according to the Hubbell model.

Usage

simulateHubbell(
  n_species,
  M,
  carrying_capacity = 1000,
  k_events = 10,
  migration_p = 0.02,
  t_skip = 0,
  t_end,
  norm = FALSE
)

Arguments

n_species	Integer scalar. Specifies the amount of different species initially in the local community.
M	Integer scalar. Specifies the amount of different species in the metacommunity, including those of the local community
carrying_capacity	Integer scalar. Indicates the fixed amount of individuals in the local community. (Default: 1000)
k_events	Inteer scalar. Indicates the fixed amount of deaths of local community individuals in each generation (Default: 10)
migration_p	Numeric scalar. The immigration rate; specifies the probability that a death in the local community is replaced by a migrant of the metacommunity rather than by the birth of a local community member (Default: 0.02)
t_skip	Integer scalar. Indicates the number of generations that should not be included in the outputted species abundance matrix. (Default: 0)
t_end	Integer scalar. Indicates the number of simulations to be simulated
norm	Logical scalar. Whether the time series should be returned with the abundances as proportions (norm = TRUE) or the raw counts. (Default: FALSE)

Value

simulateHubbell returns a TreeSummarizedExperiment class object

References

Rosindell, James et al. "The unified neutral theory of biodiversity and biogeography at age ten." Trends in ecology & evolution vol. 26,7 (2011).

Examples

tse <- simulateHubbell(
    n_species = 8, M = 10, carrying_capacity = 1000, k_events = 50,
    migration_p = 0.02, t_end = 100
)

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