population_dispersal: Nested functions for population dispersal.

In poems: Pattern-Oriented Ensemble Modeling System

Nested functions for population dispersal.

Description

Modular functions for the population simulator for performing dispersal of stage abundance at a specified time step via dispersal rates provided.

Usage

population_dispersal(
  replicates,
  time_steps,
  years_per_step,
  populations,
  demographic_stochasticity,
  density_stages,
  dispersal,
  dispersal_stages,
  dispersal_source_n_k,
  dispersal_target_k,
  dispersal_target_n,
  dispersal_target_n_k = NULL,
  simulator
)

Arguments

replicates	Number of replicate simulation runs.
time_steps	Number of simulation time steps.
years_per_step	Number of years per time step.
populations	Number of populations.
demographic_stochasticity	Boolean for optionally choosing demographic stochasticity for the transformation.
density_stages	Array of booleans or numeric (0,1) for each stage to indicate which stages are affected by density.
dispersal	Either a matrix of dispersal rates between populations (source columns to target rows) or a list of data frames of non-zero dispersal rates and indices for constructing a compact dispersal matrix, and optional changing rates over time (as per class DispersalGenerator dispersal_data attribute). Alternatively a user-defined function (optionally nested in a list with additional attributes) may be used: function(params), where params is a list passed to the function containing: replicates Number of replicate simulation runs. time_steps Number of simulation time steps. years_per_step Number of years per time step. populations Number of populations. stages Number of life cycle stages. demographic_stochasticity Boolean for optionally choosing demographic stochasticity for the transformation. density_stages Array of booleans or numeric (0,1) for each stage to indicate which stages are affected by density. dispersal_stages Array of relative dispersal (0-1) for each stage to indicate the degree to which each stage participates in dispersal. dispersal_source_n_k Dispersal proportion (p) density dependence via source population abundance divided by carrying capacity (n/k), where p is reduced via a linear slope (defined by two list items) from n/k <= cutoff (p = 0) to n/k >= threshold. dispersal_target_k Dispersal rate (r) density dependence via target population carrying capacity (k), where r is reduced via a linear slope (through the origin) when k <= threshold. dispersal_target_n Dispersal rate (r) density dependence via target population abundance (n), where r is reduced via a linear slope (defined by two list items) from n >= threshold to n <= cutoff (r = 0) or visa-versa. dispersal_target_n_k Dispersal rate (r) density dependence via target population abundance divided by carrying capacity (n/k), where r is reduced via a linear slope (defined by two list items) from n/k >= threshold to n/k <= cutoff (r = 0) or visa-versa. r Simulation replicate. tm Simulation time step. carrying_capacity Array of carrying capacity values for each population at time step. stage_abundance Matrix of abundance for each stage (rows) and population (columns) at time step. occupied_indices Array of indices for populations occupied at time step. simulator SimulatorReference object with dynamically accessible attached and results lists. additional attributes Additional attributes when the transformation is optionally nested in a list. returns the post-dispersal abundance matrix
dispersal_stages	Array of relative dispersal (0-1) for each stage to indicate the degree to which each stage participates in dispersal (default is 1 for all stages).
dispersal_source_n_k	Dispersal proportion (p) density dependence via source population abundance divided by carrying capacity (n/k), where p is reduced via a linear slope (defined by two list items) from n/k <= cutoff (p = 0) to n/k >= threshold or visa-versa.
dispersal_target_k	Dispersal rate (r) density dependence via target population carrying capacity (k), where r is reduced via a linear slope (through the origin) when k <= threshold.
dispersal_target_n	Dispersal rate (r) density dependence via target population abundance (n), where r is reduced via a linear slope (defined by two list items) from n >= threshold to n <= cutoff (r = 0) or visa-versa.
dispersal_target_n_k	Dispersal rate (r) density dependence via target population abundance divided by carrying capacity (n/k), where r is reduced via a linear slope (defined by two list items) from n/k >= threshold to n/k <= cutoff (r = 0) or visa-versa.
simulator	SimulatorReference object with dynamically accessible attached and results lists.

Value

Dispersal function: function(r, tm, carrying_capacity, stage_abundance, occupied_indices), where:

r

Simulation replicate.

tm

Simulation time step.

carrying_capacity

Array of carrying capacity values for each population at time step.

stage_abundance

Matrix of abundance for each stage (rows) and population (columns) at time step.

occupied_indices

Array of indices for populations occupied at time step.

returns

New stage abundance matrix with dispersal applied.

poems documentation built on Oct. 7, 2023, 9:06 a.m.