Simulate metacommunity dynamics

Usage

mcsim(
  n_species = 5,
  n_patch = 5,
  n_warmup = 200,
  n_burnin = 200,
  n_timestep = 1000,
  propagule_interval = NULL,
  propagule_seed = 0.5,
  carrying_capacity = 100,
  xi = 1,
  interaction_type = "constant",
  alpha = 0,
  min_alpha = NULL,
  max_alpha = NULL,
  r0 = 4,
  niche_optim = NULL,
  min_optim = -1,
  max_optim = 1,
  sd_niche_width = NULL,
  min_niche_width = 0.1,
  max_niche_width = 1,
  niche_cost = 1,
  xy_coord = NULL,
  distance_matrix = NULL,
  dispersal_matrix = NULL,
  p_disturb = 0,
  i_disturb = 0,
  landscape_size = 10,
  mean_env = 0,
  sd_env = 0.1,
  spatial_env_cor = FALSE,
  phi = 1,
  p_dispersal = 0.1,
  theta = 1,
  zeta = 0,
  impact = 0,
  plot = FALSE
)

Arguments

n_species: Integer. Number of species in a metacommunity.
n_patch: Integer. Number of patches in a metacommunity.
n_warmup: Integer. Number of time-steps for warm-up. Default 200.
n_burnin: Integer. Number of time-steps for burn-in. Default 200.
n_timestep: Integer. Number of time-steps to be saved. Default 1000.
propagule_interval: Integer. Time interval for propagule introduction during warm-up. If NULL, a value of ceiling(n_warmup / 10) will be used.
propagule_seed: Numeric. Propagule mean density (intensity parameter in a Poisson distribution). Default 0.5.
carrying_capacity: Numeric. Carrying capacities of individual patches. Length must be one or equal to n_patch. Default 100.
xi: Numeric. Hassell exponent. Undercompensation (xi < 1), no compensation (xi = 1; reduced to Beverton-Holt), and overcompensation (xi > 1).
interaction_type: Character. "constant" or "random". "constant" assumes the unique interaction strength of alpha for all pairs of species. "random" draws random numbers from a uniform distribution with min_alpha and max_alpha.
alpha: Numeric matrix. Species interaction strength. Enabled if interaction_type = "constant". Default 0.
min_alpha: Numeric. Minimum value of a uniform distribution generating interaction strength. Enabled if interaction_type = "random". Default NULL.
max_alpha: Numeric. Maximum value of a uniform distribution generating interaction strength. Enabled if interaction_type = "random". Default NULL.
r0: Numeric. Maximum reproductive number of the Beverton-Holt model. Length must be one or equal to n_species.
niche_optim: Numeric. Niche optimum of species (the environmental value at which the reproductive number is maximized). Length must be one or equal to n_species. Default NULL.
min_optim: Numeric. Minimum value of a uniform distribution generating the optimal environmental values of simulated species. Values are randomly assigned to species. Enabled if niche_optim = NULL.
max_optim: Numeric. Maximum value of a uniform distribution generating the optimal environmental values of simulated species. Values are randomly assigned to species. Enabled if niche_optim = NULL.
sd_niche_width: Numeric. Niche width of species. Higher values indicate greater niche width. Length must be one or equal to n_species.
min_niche_width: Numeric. Minimum value of a uniform distribution generating the niche width values of simulated species. Values are randomly assigned to species. Enabled if sd_niche_width = NULL.
max_niche_width: Numeric. Maximum value of a uniform distribution generating the niche width values of simulated species. Values are randomly assigned to species. Enabled if sd_niche_width = NULL.
niche_cost: Numeric. This parameter determines the cost of wide niche. Smaller values imply greater costs of wider niche. Default 1.
xy_coord: Site coordinates. Must be provided as a data frame, in which each row corresponds to an individual site with x and y coordinates (columns). Defualt NULL.
distance_matrix: Distance matrix. Each element must indicate distance between a given pair of habitat patches. If provided, the distance matrix will be used to generate dispersal matrix and distance decay of environmental correlations. Default NULL.
dispersal_matrix: Dispersal matrix. If provided, this matrix overrides distance_matrix to simulate dispersal process. Default NULL.
p_disturb: Numeric. Disturbance probability.
i_disturb: Numeric. Disturbance intensity expressed as proportional mortality (0 to 1). Length must be one or equal to n_patch.
landscape_size: Length of a landscape on a side. Enabled if distance_matrix = NULL and dispersal_matrix = NULL.
mean_env: Numeric. Mean environmental values of patches. Length must be one or equal to n_patch.
sd_env: Numeric. Standard deviation of temporal environmental variation at each patch.
spatial_env_cor: Numeric. If TRUE, spatial autocorrelation in temporal environmental fluctuation is considered. Default FALSE.
phi: Numeric. This parameter describes the distance decay of spatial autocorrelation in temporal environmental fluctuation. Enabled if spatial_env_cor = TRUE.
p_dispersal: Numeric. This parameter describes dispersal probability. Length must be one or equal to n_species.
theta: Numeric. Rate parameter of exponential dispersal kernel.
zeta: Numeric. Species sensitivity to environmental pollutants.
impact: Numeric. Concentration of environmental pollutants.
plot: Logical. If TRUE, five sample patches and species of df_dynamics are plotted.

Reference

see package webpage for details

Author

Akira Terui, hanabi0111@gmail.com

Examples

if (FALSE) { # \dontrun{
# not run
mcsim(n_patch = 5, n_species = 5)
} # }