Metacommunity dynamics from growth rates — mc

The engine of simulate_metacommunity(), for users who want to supply their own growth rates (e.g. responses to several environmental variables).

Usage

mc_dynamics(
  r,
  alpha,
  dispersal,
  n_steps = 1000,
  seed_steps = seq(10, 100, 10),
  seed_mean = 0.5,
  disp_matrix = NULL,
  record_steps = NULL,
  sites = NULL,
  species = NULL,
  extirpation = 0
)

Arguments

r: Sites x species matrix of density-independent growth rates, or a function of the time step that returns such a matrix.
alpha: Competition matrix from competition_matrix(), with species in the same order as the rows of traits.
dispersal: Emigration probability, one value or one per species.
n_steps: Number of time steps.
seed_steps: Steps at which individuals are added during colonisation.
seed_mean: Mean number of individuals of each species added to each site at each seeding step (and at the start).
disp_matrix: Row-stochastic dispersal matrix (sites x sites), or NULL for uniform dispersal.
record_steps: Optional steps at which abundances are recorded.
sites, species: Optional names of sites and species.
extirpation: Probability that a population is lost at each time step, one value or one per species.

Value

List with abundance and history, as in simulate_metacommunity().

Examples

set.seed(1)
# one species alone converges to (r - 1) / alpha = (5 - 1) / 0.05 = 80
out <- mc_dynamics(matrix(5, 20, 1), matrix(0.05), dispersal = 0, n_steps = 200)
mean(out$abundance)
#> [1] 78.05