simHubbell: Hubbell Simulation

In hallucigenia-sparsa/seqtime: Time Series Analysis of Sequencing Data

Hubbell Simulation

Description

Simulate species abundances with the basic Hubbell model.

Usage

simHubbell(N = 50, M = 500, I = 500, y = rep(1/N, N),
  m.vector = rep(1/M, M), m = 0.02, d = 10, tskip = 0,
  tend = 100, perturb = NULL)

Arguments

N	species number in the local community
M	species number in the metacommunity
I	number of individuals
y	initial species proportions in the local community, should sum to one
m.vector	species proportions in the metacommunity, should sum to one
m	immigration rate (probability that a dead individuum is replaced by an individuum from the metacommunity)
d	number of deaths at each time step
tskip	number of initial time points to be skipped when returning the result (to avoid the transient)
tend	number of time points (i.e. the number of generations)
perturb	a perturbation object

Details

For a recent review on the Hubbell model, see Rosindell, Hubbell and Etienne, 2011.

Value

a matrix with species abundances as rows and time points as columns

References

Rosindell, Hubbell and Etienne (2011). The Unified Neutral Theory of Biodiversity and Biogeography at Age Ten. Trends in Ecology and Evolution, vol. 26 (7), 340-348.

See Also

simUntb for the neutral model with the untb package

Examples

## Not run: 
  N <- 50
  M <- 500
  metapop <- generateAbundances(N = M, mode = 5, probabs = TRUE)
  tsplot(simHubbell(N = N, M = M, I = 3000, d = N, m.vector = metapop, tskip=500, tend=1000))

## End(Not run)

hallucigenia-sparsa/seqtime documentation built on Jan. 9, 2023, 11:53 p.m.