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<Species>

Source: R/class-Species.R
Species-class.Rd

<Species> is an S4 class that comprises species-level properties of simulated agents. It includes attributes related to taxonomy, physiology, behavioural/activity states, responses to environmental and non-environmental drivers, and population size.

Slots

id

character string, a unique identifier for the species.

common_name

character string, the common name of the species.

scientific_name

character string, the scientific name of the species.

body_mass_distr

an object of class VarDist, defining the distribution of body mass for the species.

energy_to_mass_distr

a VarDist object, providing the energy-to-bodymass conversion rate for the species (e.g. g/kJ). Determines how gained or lost energy translates into changes in body mass.

states_profile

a list of State objects, defining the behavioural/activity states for the species to consider in the model.

driver_responses

list of DriverResponse objects, specifying the species’ responses to predefined model drivers, such as environmental pressures, biological influences, and human-induced impacts affecting movement and behaviour/activity states. See DriverResponse for details.

Each element in the driver_responses list must correspond to an existing object of class Driver. At the initialization phase of the Individual-Based Model (IBM), these driver_responses are matched with their respective Driver objects to ensure a consistent and well-defined set of species-driver interactions. Failure to provide a corresponding Driver object for each entry of driver_responses will result in missing or undefined driver effects during the simulation.

mortality_thresh_distr

an object of class VarDist, specifying the values of agent's condition (e.g. body mass), below which it is assumed to have died (Note: slot may require further generalization)

pop_size

numeric, the population size (i.e., number of individuals) within the area of calculation (AOC).

See also