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Create <Species> objects

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

Helper function to construct instances of Species objects, representing species-level properties of simulated agents. These include attributes related to taxonomy, physiology, behavioural/activity states, responses to environmental and non-environmental drivers, and population size.

Usage

Species(
  id = NA_character_,
  common_name = NA_character_,
  scientific_name = NA_character_,
  body_mass_distr = VarDist(),
  energy_to_mass_distr = VarDist(),
  mortality_thresh_distr = VarDist(),
  states_profile = list(),
  driver_responses = list(),
  pop_size = NA_real_
)

Arguments

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.

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: parameter may require further generalization)

states_profile

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

driver_responses

a 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 the Details section below and DriverResponse for further information.

pop_size

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

Details

Each element in the driver_responses list must correspond to an existing object of class Driver. At the initialization phase of {roamR}s IBM, these driver_responses are matched with their respective Driver objects to ensure a consistent 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.

See also

Helper functions VarDist(), DriverResponse() and State()

Examples


library(distributional)
#> 
#> Attaching package: ‘distributional’
#> The following objects are masked from ‘package:roamR’:
#> 
#>     generate, parameters

# 1. Start by setting the state profile
states <- list(
 flight = State(
    id = "flying",
    energy_cost = VarDist(dist_uniform(1, 2), units = "kJ/hour/gram"),
    time_budget = VarDist(dist_uniform(1, 3), "hours/day"),
    speed = VarDist(dist_uniform(10, 20), "m/s")
    ),
 dive = State(
    id = "diving",
    energy_cost = VarDist(dist_uniform(1, 2), units = "kJ/hour/gram"),
    time_budget = VarDist(dist_uniform(1, 3), "hours/day"),
    speed = VarDist(dist_uniform(10, 20), "m/s")
  )
)

# 2. Then the list of driver responses
driver_resp <- list(
  coast = DriverResponse(
    driver_id = "land",
    movement = MoveInfluence(
      prob = VarDist(distributional::dist_degenerate(1)),
      fn = function(x, slope = 1/2) exp(-slope * x),
      type = "repulsion"
    )),
  owf = DriverResponse(
    driver_id = "owf_foot",
    movement = MoveInfluence(
      prob = VarDist(dist_beta(2, 8)),
      fn = function(x, slope = 1/2) exp(-slope * x),
      type = "repulsion"
    ),
    states = list(
      StateInfluence(
        state_id = "flying",
        prob = VarDist(dist_beta(1, 5)),
        extent = VarDist(dist_lognormal(2, 1), "hr/day")
      )))
  )

# 3. specify <Species>
guill <- Species(
     id = "guill",
     common_name = "guillemot",
     scientific_name = "Uria Aalge",
     pop_size = 10000,
     body_mass_distr = VarDist(dist_uniform(850, 1130), "g"),
     mortality_thresh_distr = VarDist(dist_normal(500, 20), "g"),
     states_profile = states,
     driver_responses = driver_resp
   )