population_density: Nested functions for population density dependence.
In poems: Pattern-Oriented Ensemble Modeling System

population_density

R Documentation

Nested functions for population density dependence.

Description

Modular functions for the population simulator for performing density dependent adjustments to transition rates.

Usage

population_density(
  populations,
  stage_matrix,
  fecundity_mask,
  fecundity_max,
  density_dependence,
  growth_rate_max,
  density_affects,
  density_stages,
  density_precision,
  simulator
)

Arguments

`populations`	Number of populations.
`stage_matrix`	Matrix of transition (fecundity & survival) rates between stages at each time step (Leslie/Lefkovitch matrix).
`fecundity_mask`	Matrix of 0-1 to indicate which (proportions) of transition rates refer to fecundity.
`fecundity_max`	Maximum transition fecundity rate (in Leslie/Lefkovitch matrix).
`density_dependence`	Density dependence can be "ceiling" (default), "logistic" (Ricker), or a user-defined function (optionally nested in a list with additional attributes) for adjusting transition rates: `function(params)`, where params is a list passed to the function containing: `transition_array` 3D array of transition rates: stages by stages by populations. `fecundity_mask` Matrix of 0-1 to indicate which (proportions) of transition rates refer to fecundity. `fecundity_max` Maximum transition fecundity rate (in Leslie/Lefkovitch matrix). `carrying_capacity` Array of carrying capacity values for each population. `stage_abundance` Matrix of abundance for each stage (rows) and population (columns). `population_abundance` Array of summed population abundances for all stages. `density_abundance` Array of summed population abundances for stages affected by density. `growth_rate_max` Maximum growth rate value or array for populations. `occupied_indices` Array of indices for populations occupied at (current) time step. `calculate_multipliers` Function (`function(growth_rates)`) for finding multipliers (when stages > 1) to apply to affected transitions that result in target growth rates (dominant eigenvalues). `apply_multipliers` Function (`function(transition_array, multipliers`) for applying (when stages > 1) multipliers to the affected transition rates within a transition array (returns multiplied transition array). `simulator` `SimulatorReference` object with dynamically accessible attached and results lists. `additional attributes` Additional attributes when density dependence is optionally nested in a list. returns an adjusted transition array for occupied populations
`growth_rate_max`	Maximum growth rate (utilized by density dependence processes).
`density_affects`	Matrix of booleans or numeric (0-1) indicating the transition vital rates affected by density (default is all).
`density_stages`	Array of booleans or numeric (0,1) for each stage to indicate which stages are affected by density (default is all).
`density_precision`	Numeric precision of the calculated multipliers (used when stages > 1) applied to affected transition rates (default is 3 decimal places).
`simulator`	`SimulatorReference` object with dynamically accessible attached and results lists.

Value

Density dependent calculation function, either:

function(carrying_capacity, stage_abundance)

For ceiling density dependence function, OR

function(transition_array, carrying_capacity, stage_abundance, occupied_indices)

For user-defined density dependence function, where:

transition_array: 3D array of transition rates: stages by stages by populations.
carrying_capacity: Array of carrying capacity values for each population.
stage_abundance: Matrix of abundance for each stage (rows) and population (columns).
occupied_indices: Array of indices for populations occupied.