Simulate population dynamics

Given a set of parameters, simulate population dynamics.

Usage

pop_dyn(
  n_patches,
  n_time,
  n_ages,
  x_rec,
  ar_time,
  f_a_t,
  x_sv = NULL,
  m = 0.25,
  pars,
  init,
  init_type,
  movement = FALSE,
  adj_mat = NULL,
  mov_age = NULL
)

Arguments

n_patches

number of patches

n_time

number of timepoints

n_ages

a integer indicating the number of (assumed) age-classes.

x_rec

matrix of environmental factors affecting recruitment

ar_time

a boolean indicating whether an AR(1) term should be included to the log-recruitment.

f_a_t

fishing mortality

x_sv

matrix of environmental factors affecting survival

m

a numeric value indicating the natural mortality instantaneous rate.

pars

a named list of model parameters.

init

initialization vector of length n_ages - 1

init_type

type of initialization (integer between 0 and 5)

movement

a boolean indicating whether movement should be applied or not. If TRUE, than pars must have an element called zeta indicating the probability of staying at a given patch between two timepoints.

adj_mat

a n_patches by n_patches row-standardized adjacency matrix.

mov_age

a vector of ages at which movement starts.

Value

an array of expected densities per age-group, patch, and timepoint.

Author

lcgodoy