Modular functions for the population simulator for performing density dependent adjustments to transition rates.
population_density(
populations,
stage_matrix,
fecundity_mask,
fecundity_max,
density_dependence,
growth_rate_max,
density_affects,
density_stages,
density_precision,
simulator
)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_array3D array of transition rates: stages by stages by populations.
carrying_capacityArray of carrying capacity values for each population.
stage_abundanceMatrix of abundance for each stage (rows) and population (columns).
occupied_indicesArray of indices for populations occupied.
Number of populations.
Matrix of transition (fecundity & survival) rates between stages at each time step (Leslie/Lefkovitch matrix).
Matrix of 0-1 to indicate which (proportions) of transition rates refer to fecundity.
Maximum transition fecundity rate (in Leslie/Lefkovitch matrix).
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_array3D array of transition rates: stages by stages by populations.
fecundity_maskMatrix of 0-1 to indicate which (proportions) of transition rates refer to fecundity.
fecundity_maxMaximum transition fecundity rate (in Leslie/Lefkovitch matrix).
carrying_capacityArray of carrying capacity values for each population.
stage_abundanceMatrix of abundance for each stage (rows) and population (columns).
population_abundanceArray of summed population abundances for all stages.
density_abundanceArray of summed population abundances for stages affected by density.
growth_rate_maxMaximum growth rate value or array for populations.
occupied_indicesArray of indices for populations occupied at (current) time step.
calculate_multipliersFunction (function(growth_rates)) for finding multipliers (when stages > 1) to apply to affected transitions that result in target growth rates (dominant eigenvalues).
apply_multipliersFunction (function(transition_array, multipliers) for applying (when stages > 1) multipliers to the affected transition rates within a transition array (returns multiplied transition array).
simulatorSimulatorReference object with dynamically accessible attached and results lists.
additional attributesAdditional attributes when density dependence is optionally nested in a list.
returns an adjusted transition array for occupied populations
Maximum growth rate (utilized by density dependence processes).
Matrix of booleans or numeric (0-1) indicating the transition vital rates affected by density (default is all).
Array of booleans or numeric (0,1) for each stage to indicate which stages are affected by density (default is all).
Numeric precision of the calculated multipliers (used when stages > 1) applied to affected transition rates (default is 3 decimal places).
SimulatorReference object with dynamically accessible attached and results lists.