RUFAS.biophysical.animal.herd_factory module#

class RUFAS.biophysical.animal.herd_factory.HerdFactory(init_herd: bool = False, save_animals: bool = False, save_animals_path: Path = PosixPath('output'))#

Bases: object

Class to initialize herd for simulation.

Attributes#

breedstr: The breed of the animals in the simulation, retrieved from input data.
CIint: Calving interval from the animal configuration, retrieved from input data.
initial_animal_numint: The initial number of animals in the simulation, retrieved from input data.
simulation_daysint: The number of days the simulation will run to generate herd, retrieved from input data.
pre_animal_populationAnimalPopulation: An instance of AnimalPopulation representing the animal population before random sampling with replacement.
post_animal_populationAnimalPopulation: An instance of AnimalPopulation representing the animal population after random sampling with replacement.

post_animal_population: AnimalPopulation#

__init__(init_herd: bool = False, save_animals: bool = False, save_animals_path: Path = PosixPath('output')) → None#

Initializes HerdFactory.

Parameters#

init_herdbool, default=False: A flag to indicate whether to initialize through simulation or from input data.
save_animalsbool, default=False: Indicates whether to save the generated animals to JSON files.
save_animals_pathPath, default=Path(“output/”): The directory path where the animal data JSON files will be saved if save_animals is True.

classmethod set_post_animal_population(animal_population: AnimalPopulation) → None#

Sets the post-animal population for the class.

Parameters#

animal_populationAnimalPopulation: An instance of AnimalPopulation that represents the updated animal population.

Returns#

None

_calf_and_heiferI_update(animal: Animal) → DailyRoutinesOutput#

Updates the daily routines specific for calf and heiferI.

Parameters#

animalAnimal: The animal instance to update. Must be of type CALF or HEIFER_I.

Returns#

DailyRoutinesOutput: The updated daily routines output after processing the animal’s daily growth and life stage update.

Raises#

TypeError: If the animal type is not CALF or HEIFER_I.

_heiferII_update(animal: Animal) → DailyRoutinesOutput#

Updates the daily routines for heiferII.

Parameters#

animal: Animal: The animal instance to update. Must be of type AnimalType.HEIFER_II.

Returns#

DailyRoutinesOutput: The updated daily routines output containing the status of the animal.

Raises#

TypeError: If the animal type is not HEIFER_II.

_heiferIII_update(animal: Animal) → DailyRoutinesOutput#

Updates the daily routines for heiferIII.

Parameters#

animalAnimal: The animal instance to update. Must be of type AnimalType.HEIFER_III.

Returns#

DailyRoutinesOutput: The updated daily routines output containing the status of the animal.

Raises#

TypeError: If the provided animal is not of type AnimalType.HEIFER_III.

_cow_update(animal: Animal) → DailyRoutinesOutput#

Updates the daily routines of a cow.

Parameters#

animalAnimal: An instance of the Animal class representing the cow to be updated.

Returns#

DailyRoutinesOutput: An object that contains updates related to the cow’s daily routines such as reproduction outputs (newborn calf configuration) and animal life stage status.

Raises#

TypeError: If the provided animal is not of type cow.

_calves_update() → None#: Calves update for generating herd simulation

_heiferIs_update() → None#: heiferIs update for generating herd simulation

_heiferIIs_update() → None#: HeiferIIs update for generating herd simulation

_cow_give_birth(cow: Animal) → None#

Handles the birth process of a calf when a cow gives birth.

Parameters#

cowAnimal: The cow that is giving birth.

Returns#

None

_heiferIIIs_update(day: int) → None#: HeiferIIIs update for generating herd simulation

_cows_update() → None#: Cows update for generating herd simulation

_generate_animals() → AnimalPopulation#: Function to generate an AnimalPopulation object through simulation

_backtrack_animal_birth_date(days_born: int, time: RufasTime) → str#: Function to backtrack the birthdate of an animal loaded from data by subtracting the age of the animal from the simulation start date.

_init_animal_from_data(animal_type: str, animal_data: dict[str, Any]) → Animal#: Function to initialize an animal object from input data

_initialize_herd_from_data() → AnimalPopulation#: Function to initialize an AnimalPopulation object from input data

_random_sample_with_replacement() → AnimalPopulation#: Function to randomly sample the herd with replacement

_random_sample_with_replacement_by_type(animal_type: str) → list[Animal]#: Function to randomly sample a specific animal type with replacement

initialize_herd() → None#: Initialize an AnimalPopulation object for simulation, either from input data or generate from simulation. This function also optionally saves the generated herd data into a JSON file. The initialized herd with be randomly sampled with replacement, and set as the class attribute post_animal_population.