generate_series: Use a generalized stochastic Lotka-Volterra model to...

In kimberlyroche/rulesoflife:

Use a generalized stochastic Lotka-Volterra model to (mechanistically) simulate count data This code is adapted directly from Tredennick et al., 2017

Description

Use a generalized stochastic Lotka-Volterra model to (mechanistically) simulate count data This code is adapted directly from Tredennick et al., 2017

Usage

generate_series(
  S,
  NiTh,
  AsigE,
  rm,
  al,
  K,
  sigO,
  start_time,
  end_time,
  perturbations_global,
  perturbation_sd,
  alpha
)

Arguments

S	number of species to simulate
NiTh	parameter returned by generate_innate_params (near-steady state abundances?)
AsigE	parameter returned by generate_env_link (per-species response to environmental perturbation)
rm	parameter returned by generate_env_link (per-species growth rates)
al	parameter returned by generate_env_link (cooperative/competitive dynamics)
K	per-species carrying capacities
sigO	magnitude of observational noise
start_time	time point at which to begin "recording" the series (previous time points will be discarded as burn-in)
end_time	full length of series to simulate (including burn-in)
perturbations_global	global environmental perturbation matrix
alpha	proportion of perturbations_global in incorporate into the local perturbations matrix
perturbations_sd	standard deviation of zero-mean perturbations

Value

named list of simulated species series and generated parameters

kimberlyroche/rulesoflife documentation built on May 7, 2023, 11:08 a.m.