Simulate meta-food web dynamics with intraguild predation

Usage

igpsim(
  n_patch = 5,
  n_warmup = 200,
  n_burnin = 200,
  n_timestep = 1000,
  r_b = 10,
  conv_eff = 0.9,
  attack_rate = 0.05,
  handling_time = 0.5,
  s = 0,
  propagule_interval = NULL,
  propagule_seed = c(100, 10, 1),
  carrying_capacity = 100,
  xy_coord = NULL,
  distance_matrix = NULL,
  dispersal_matrix = NULL,
  p_disturb = 0,
  i_disturb = 0,
  phi_disturb = Inf,
  landscape_size = 10,
  p_dispersal = 0.1,
  theta = 1,
  plot = FALSE
)

Arguments

n_patch: Number of patches in a metacommunity.
n_warmup: Number of time-steps for warm-up. Default 200.
n_burnin: Number of time-steps for burn-in. Default 200.
n_timestep: Number of time-steps to be saved. Default 1000.
r_b: Maximum reproductive rate of basal species
conv_eff: Energetic conversion efficiency; must be given by the order of basal to ig-prey, basal to ig-predator, and ig-prey to ig-predator
attack_rate: Attack rate. Must be given by the order of basal to ig_prey, basal to ig-predator, and ig-prey to ig-predator
handling_time: Handling time. Must be given by the order of basal to ig_prey, basal to ig-predator, and ig-prey to ig-predator
s: Strength of switching between basal and ig-prey (confined to 0 - 1). Switching to basal species is more likely to occur with higher values.
propagule_interval: Time interval for propagule introduction during warm-up. If NULL, a value of ceiling(n_warmup / 10) will be used.
propagule_seed: Propagule mean density (intensity parameter in a Poisson distribution). Should be given as a scalar or vector. If given as a vector, the elements should appear in order of basal, intra-guild prey, and intra-guild predator.
carrying_capacity: Carrying capacities of individual patches. Length must be one or equal to n_patch. Default 100.
xy_coord: Data frame for site coordinates. Each row should correspond to an individual patch, with x and y coordinates (columns). Defualt NULL.
distance_matrix: Distance matrix indicating distance between habitat patches. If provided, the distance matrix will be used to generate dispersal matrix and to calculate distance decay of environmental correlations. Default NULL.
dispersal_matrix: Dispersal matrix to be used to simulate dispersal process. Override distance_matrix. Default NULL.
p_disturb: Disturbance probability.
i_disturb: Disturbance-induced proportional mortality.
phi_disturb: Temporal precision of disturbance-induced proportional mortality. Set Inf to assume no temporal variability.
landscape_size: Length of a landscape on a side. Enabled if dispersal_matrix = NULL.
p_dispersal: Probability of dispersal. Length must be one or equal to n_species.
theta: Dispersal parameter describing dispersal capability of species.
plot: If TRUE, five sample patches and species of df_dynamics are plotted.

Reference

see package webpage for instruction

Author

Akira Terui, hanabi0111@gmail.com