hubbell: Hubbell community simulation

In gheysenemma/microsimR: A Simulator Package with a collection of basic community models that outputs count data of microbial communities

Description

Neutral species abundances simulation according to the Hubbell model.

Usage

hubbell(
  N,
  M,
  I = 1000,
  d = 10,
  m = 0.02,
  pbirth = runif(N, min = 0, max = 1),
  pmigr = runif(M, min = 0, max = 1),
  tskip = 0,
  tend,
  norm = FALSE
)

Arguments

N	Amount of different species initially in the local community
M	Amount of different species in the metacommunity, including those of the local community
I	Fixed amount of individuals in the local community
d	Fixed amount of deaths of local community individuals in each generation
m	Immigration rate: 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
pbirth	probabilities of birth to construct the initial abundances, will be updated in all next generations with previous abundances
pmigr	probabilities of migration
tskip	Nr of generations that should not be included in the outputted species abundance matrix.
tend	Nr of simulations to be simulated.
norm	logical to indicate whether the time series should be returned with the abundances as proportions (norm = TRUE) or the raw counts (norm = FALSE, default)

Value

matrix with species abundances as rows and time points as columns

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

hubbell(N = 8, M = 10, I = 1000, d = 50, m = 0.02, tend = 100)

gheysenemma/microsimR documentation built on Dec. 20, 2021, 10:46 a.m.