R6 class representing a nested container for dispersal generator attributes

R6 class representing a nested container for DispersalGenerator attributes that are maintained when new model clones are created. The container maintains input and output attribute names, file, function and distribution templates, correlation parameters (for distribution generation), rounding decimals, occupancy mask, and other DispersalGenerator attributes that need to be maintained when cloning.

Super class

poems::GenerativeTemplate -> DispersalTemplate

Public fields

attached: A list of dynamically attached attributes (name-value pairs).

Active bindings

description: A brief description of what the generator generates.
inputs: An array of input attribute names for the generator.
outputs: An array of output attribute names for the generator.
file_templates: A nested list of file template attributes.
function_templates: A nested list of function template attributes.
distribution_templates: A list of distribution template attributes.
uses_correlations: A boolean to indicate that a SpatialCorrelation (or inherited class) object is used for generating correlated random deviates.
spatial_correlation: A SpatialCorrelation (or inherited class) object for generating correlated random deviates.
temporal_correlation: Absolute correlation coefficient between simulation time steps for all grid cells (0-1; default = 1).
time_steps: Number of simulation time steps.
decimals: Number of decimal places applied to generated data outputs (default: NULL = no rounding).
occupancy_mask: Optional binary mask array (matrix), data frame, or raster (stack) for generated (time-series) data outputs.
dispersal_friction: A DispersalFriction (or inherited class) object for dispersal distance multiplier data.
distance_classes: Vector of distance interval boundaries (in km) for calculating discrete dispersal rates.
max_distance_classes: The maximum number of distance classes when they are calculated automatically via the maximum distance (default: 1000).
distance_scale: Scale of distance values in meters (default = 1). Usage: set to 1 for values in meters, or to 1000 for values in kilometers.
distance_data: Data frame of distance classes including indices for the construction of compact matrices (columns: target_pop, source_pop, compact_row, distance_class).
dispersal_function_data: Data frame of discrete dispersal function values. Optional first column may provide distance intervals (non-inclusive lower bounds).
dispersal_proportion: Dispersal function: p*exp(-distance/b) p parameter. Represents the proportion and limit of dispersers between model cells.
dispersal_breadth: Dispersal function: p*exp(-distance/b) b parameter. Represents the breadth of the dispersal between model cells. Typically estimated via average migration distance.
dispersal_max_distance: Dispersal maximum distance or range (r) parameter limits the use of the dispersal function: p*exp(-distance/b). The function is utilized when distance <= r otherwise the dispersal rate is set to zero.

Methods

Public methods

DispersalTemplate$clone()

Inherited methods

poems::GenerativeTemplate$initialize()

Method `clone()`

The objects of this class are cloneable with this method.

Usage

DispersalTemplate$clone(deep = FALSE)

Arguments

deep: Whether to make a deep clone.

Examples

dispersal_template <- DispersalTemplate$new()
dispersal_template$dispersal_breadth <- 130
dispersal_template$dispersal_proportion <- 0.4
coordinates <- data.frame(x = rep(1:4, 4), y = rep(1:4, each = 4))
dispersal_gen <- DispersalGenerator$new(
  coordinates = coordinates, inputs = c("dispersal_r"),
  generative_template = dispersal_template
)
dispersal_gen$dispersal_breadth
#> [1] 130
dispersal_gen$dispersal_proportion
#> [1] 0.4