igpsim: Simulate meta-food web dynamics with intraguild predation
In aterui/mcbrnet: Ecological simulation in spatial networks

igpsim

R Documentation

Simulate meta-food web dynamics with intraguild predation

Description

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.