population_transformation: Nested functions for a user-defined population abundance (and...

In poems: Pattern-Oriented Ensemble Modeling System

Nested functions for a user-defined population abundance (and capacity) transformation.

Description

Modular functions for the population simulator for performing a transformation of the stage abundance (and optionally carrying capacity) at a specified time step via a user-defined function.

Usage

population_transformation(
  replicates,
  time_steps,
  years_per_step,
  populations,
  demographic_stochasticity,
  density_stages,
  transformation,
  simulator,
  name = "transformation"
)

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.
transformation	A user-defined function (optionally nested in a list with additional attributes) for performing transformation: 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. 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)
simulator	SimulatorReference object with dynamically accessible attached and results lists.
name	Optional name for the transformation (default is "transformation").

Value

Abundance (and capacity) transformation 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

List with transformed stage abundance matrix (and optionally carrying capacity).

Examples

simulator <- SimulatorReference$new()
# Example transformation: a random population is chosen for a severe disturbance event
# (only life cycle stage 3 individuals survive)
disturbance_function <- function(params) {
  params$simulator$attached$params <- params # attach to reference object
  random_population <- sample(params$occupied_indices, 1)
  new_stage_abundance <- params$stage_abundance
  new_stage_abundance[1:2, random_population] <- 0
  return(new_stage_abundance)
}
transformation_function <- population_transformation(
  replicates = 4, time_steps = 10, years_per_step = 1,
  populations = 7, demographic_stochasticity = TRUE,
  density_stages = c(0, 1, 1), transformation = disturbance_function,
  simulator
)
carrying_capacity <- rep(10, 7)
carrying_capacity <- rep(10, 7)
stage_abundance <- matrix(c(
 7, 13, 0, 26, 0, 39, 47,
 2, 0, 6, 8, 0, 12, 13,
 0, 3, 4, 6, 0, 9, 10
), nrow = 3, ncol = 7, byrow = TRUE)
occupied_indices <- (1:7)[-5]
transformation_function(r = 2, tm = 6, carrying_capacity, stage_abundance,
                        occupied_indices)

poems documentation built on April 4, 2025, 5:07 a.m.