cdynsim: Community dynamics simulation with stock enhancement
In aterui/cdyns: Community Dynamics Simulation with Stock Enhancement

View source: R/cdynsim.R

cdynsim

R Documentation

Community dynamics simulation with stock enhancement

Description

Community dynamics simulation with stock enhancement

Usage

cdynsim(
  n_timestep = 1000,
  n_warmup = 100,
  n_burnin = 100,
  n_stock_start = NULL,
  n_species = 10,
  k = 100,
  r_type = "constant",
  r = 1.5,
  r_min = 1,
  r_max = 3.5,
  sd_env = 0.1,
  stochastic = FALSE,
  stock = 0,
  phi = 1,
  int_type = "constant",
  alpha = 0.5,
  alpha_scale = TRUE,
  inv_sign = TRUE,
  immigration = 0,
  sd_immigration = 0,
  p_immigration = 0,
  model = "ricker",
  seed = 5,
  seed_interval = 10,
  extinct = 0
)

Arguments

`n_timestep`	Number of simulation time steps to be saved
`n_warmup`	Number of warm-up time steps. Species are randomly seeded during this period with no stock enhancement.
`n_burnin`	Number of burn-in time steps. Stock enhancement operates.
`n_stock_start`	Time step at which stocking starts.
`n_species`	Number of species in a simulated community.
`k`	Carrying capacity.
`r_type`	Generation method for intrinsic population growth rates. Either `"constant"` or `"random"`.
`r`	Intrinsic population growth rate. Disabled if `r_type = "random"`.
`r_min`	Minimum value of intrinsic population growth rate. Disabled if `r_type = "constant"`.
`r_max`	Maximum value of intrinsic population growth rate. Disabled if `r_type = "constant"`.
`sd_env`	SD of environmental stochasticity in a log scale.
`stochastic`	Whether demographic stochasticity is induced or not. If `TRUE`, population & immigration outcomes will be a random draws from a Poisson distribution with the expected value of population density or immigration.
`stock`	Number of released individuals.
`phi`	Fitness of released individuals relative to wild individuals.
`int_type`	Generation method for an interaction matrix. Either `"constant"` or `"random"`. If `"random"`, competition coefficients are randomly generated with an exponential distribution Exp(1/alpha). If `"constant"`, competition coefficients are constant or supplied as a full matrix.
`alpha`	Competition coefficient. If `int_type = "constant"`, constant or a full matrix . If `int_type = "random"`, alpha represents the expected value of an exponential distribution. Provide a full matrix if `int_type = "manual"`.
`alpha_scale`	Logical. If `TRUE`, competition coefficients are scaled by carrying capacity.
`inv_sign`	Logical. Indicate whether the sign of competition coefficients is multiplied by minus one. If `TRUE`, values in `alpha` will become `-alpha` internally. For example, with a Ricker model, the equation will be `x * exp(r - alpha * x)` (`x * exp(r + alpha * x)` if `inv_sign = FALSE`)
`immigration`	Mean immigration per generation. Immigration is determined as `m ~ N(log(immigration), sd_immigration^2)`
`sd_immigration`	SD immigration over time in a log scale.
`p_immigration`	Probability of immigration.
`model`	Model for community dynamics. Either `"ricker"` (multi-species Ricker model) or `"bh"` (multi-species Beverton-Holt model).
`seed`	Expected number of seeds.
`seed_interval`	Time interval for seeding.
`extinct`	Absorbing condition. Species with density < extinct will be removed from the simulation.