random_seed-
Number to seed the random number generation for stochasticity.
replicates-
Number of replicate simulation runs (default is 1).
time_steps-
Number of simulation time steps.
years_per_step-
Number of years per time step (default is 1).
populations-
Number of populations.
coordinates-
Data frame (or matrix) of X-Y population coordinates.
stages-
Number of lifecycle stages.
initial_abundance-
Array (or matrix) of initial abundances (at each stage in rows) for each population (in columns).
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).
demographic_stochasticity-
Boolean for choosing demographic stochasticity for transition, dispersal, harvest and/or other processes (default is TRUE).
standard_deviation-
Standard deviation matrix (or single value) for applying environmental stochasticity to transition rates.
correlation-
List containing either an environmental correlation matrix (correlation_matrix), a pre-calculated transposed (Cholesky) decomposition matrix (t_decomposition_matrix), or a compact transposed (Cholesky) decomposition matrix (t_decomposition_compact_matrix) and a corresponding map of population indices (t_decomposition_compact_map), as per SpatialCorrelation class attributes.
carrying_capacity-
Array (matrix) of carrying capacity values at each population cell (populations rows by time_steps columns when across time).
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 abundances 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 multipliers (when stages > 1) to the affected transition rates within a transition array (returns multiplied array).
simulator-
SimulatorReference object with dynamically accessible attached and results lists.
optional attributes-
Additional numeric attributes when density dependence is optionally nested in a list.
returns a transformed transition 3D array
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).
translocation-
An optional user-defined function (optionally nested in a list with additional attributes) for applying translocation or spatio-temporal management (to abundances): 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 lifecycle 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.
r-
Simulation replicate.
tm-
Simulation time step.
carrying_capacity-
Array of carrying capacity values for each population at time step.
stage_abundance-
Matrix of (current) abundance for each stage (rows) and population (columns) at time step.
occupied_indices-
Array of indices for populations occupied at (current) 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 a transformed stage abundance matrix (or a list with stage abundance and carrying capacity)
harvest-
An optional user-defined function (optionally nested in a list with additional attributes) for applying harvesting (to abundances): function(params) as per translocation.
mortality-
An optional user-defined function (optionally nested in a list with additional attributes) for applying mortality (to abundances): function(params) as per translocation.
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.
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.
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 (aliases: dispersal_n_k_cutoff & dispersal_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 (alias: dispersal_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 (aliases: dispersal_n_threshold & dispersal_n_cutoff).
abundance_threshold-
Abundance threshold (that needs to be exceeded) for each population to persist.
simulation_order-
A vector of simulation process names in configured order of execution (default is "transition", "translocation", "harvest" (plus harvested results), "mortality", "dispersal", "results" (except harvested).
additional transformation functions-
Additional user-defined abundance transformation functions (optionally nested in lists with additional attributes) are utilised when listed in simulation_order (function as per translocation).
results_selection-
List of results selection from: "abundance" (default), "ema", "extirpation", "extinction_location", "harvested", "occupancy"; "summarize" (default) or "replicate".
result_stages-
Array of booleans or numeric (0, 1, 2, ...) for each stage to indicate which stages are included/combined (each unique digit > 0; optionally named) in the results (default is 1 for all stages).