RUFAS.routines.animal.pen module#

class RUFAS.routines.animal.pen.Pen(pen_id: int, pen_name: str, vertical_dist_to_milking_parlor: float, horizontal_dist_to_milking_parlor: float, number_of_stalls: int, housing_type: str, bedding_type: str, pen_type: str, manure_handling: str, manure_separator: str, manure_separator_after_digestion: str, manure_storage: str, animal_combination: AnimalCombination, max_stocking_density: float)#

Bases: object

Manages a pen’s operation. Stores the characteristics of the pen and the animals that are housed in it any point in the simulation. This class also keeps track of some key characteristics of the average animal in the pen.

Attributes#

pen_idint: The pen’s unique pen ID. Obtained from the input file.
vertical_dist_to_milking_parlorfloat: The vertical distance to milking parlor, measured in kilometers. Obtained from the input file.
horizontal_dist_to_milking_parlorfloat: The horizontal distance to milking parlor, measured in kilometers. Obtained from the input file.
number_of_stallsint: The number of stalls. Obtained from the input file.
housing_typestring: The housing type of the pen. Obtained from the input file.
bedding_typestring: The bedding type of the pen. Obtained from the input file.
pen_typestring: The pen type (freestall or tiestall). Obtained from the input file.
manure_handlingstring: The manure handling method used to clean the pen.
manure_separatorstring: The type of manure separator that processes manure excreted in the pen.
manure_separator_after_digestionstring: The type of manure separator that processes manure from the pen after it’s been in a digestor.
manure_storagestring: The type of manure storage receptacle that stores manure excreted in the pen.
avg_p_intakefloat: The average phosphorus intake of the animals in the pen.
avg_p_reqfloat: The average phosphorus requirements of the animals in the pen.
avg_p_animalfloat: The average phosphorus content/mass of the animals in the pen.
animals_in_pendictionary: A dictionary of all animals in this pen that maps animal id to animal object.
classes_in_penset: The set (no repeats) of all the classes to which the animals in the pen belong.
avg_DBWfloat: The average daily change in (delta) body weight of the animals in the pen. Used for ration formulation.
avg_BWfloat: The average body weight of the animals in the pen. Used for ration formulation.
avg_DMIestfloat: The average dry matter intake estimation of the animals in the pen. Used for ration formulation
avg_nutrient_rqmtsdict: Contains the average nutrient requirements of the animals in the pen. Used for ration formulation
avg_milkfloat: The average milk production of the animals in the pen. Used for (lactating cow) ration formulation
avg_CP_milkfloat: The average milk crude protein content of the animals in the pen. Used for (lactating cow) ration formulation
rationdict: Contains the ration for all the animals in the pen.
ration_nutrient_amountdict: Contains the total amount of different nutrients in the current ration.
ration_nutrient_concdict: Contains the concentration of different nutrients in the current ration.
dry_matter_intakefloat: The dry matter intake value of the animals in the pen.
avg_growthfloat: The average growth of the animals in the pen.
MEdietfloat: The metabolizable energy concentration of the diet fed to the pen.
_manure_dict_templatedict: The dictionary template for the manure attributes (manure, calf_total, etc)
manuredict: Contains the total manure excretion of all animals in the pen.
calf_totaldict: Contains the total manure excretion of the calves in the pen.
heifer_totaldict: Contains the total manure excretion of the heifers in the pen.
dry_totaldict: Contains the total manure excretion of the dry cows in the pen.
lactating_totaldict: Contains the total manure excretion of the lactating cows in the pen.
animal_combinationAnimalCombination: Represents the valid animal type combinations in the pen.

__init__(pen_id: int, pen_name: str, vertical_dist_to_milking_parlor: float, horizontal_dist_to_milking_parlor: float, number_of_stalls: int, housing_type: str, bedding_type: str, pen_type: str, manure_handling: str, manure_separator: str, manure_separator_after_digestion: str, manure_storage: str, animal_combination: AnimalCombination, max_stocking_density: float) → None#

Initializes a pen with the given arguments.

Parameters#

pen_idint
the unique id number of the pen

vertical_dist_to_milking_parlorfloat
vertical distance to milking parlor, km

horizontal_dist_to_milking_parlor: float
horizontal distance to milking parlor, km

number_of_stallsint
number of stalls in the pen

housing_typestr
housing type of the pen

bedding_typestr
bedding type of the pen

pen_typestr
freestall or tiestall

manure_handlingstr
the manure handling method used to clean the pen

manure_separatorstr
the manure separator that processes manure excreted in this pen

manure_separator_after_digestionstr
the second manure separator that processes manure excreted in this pen post-digestor

manure_storagestr
the manure storage receptacle that stores manure excreted in this pen

animal_combinationAnimalCombination
the valid animal combinations inside this pen, an instance of the AnimalCombination Enum

max_stocking_densityfloat
maximum stocking density allowed for pen

property current_stocking_density: float#

Returns the current stocking density of the pen.

Returns#

float: the current stocking density of the pen.

property is_populated: bool#

Returns whether the pen is populated.

Returns#

bool: True if the pen is populated, False otherwise.

property needs_ration_formulation: bool#

Returns whether pen needs a ration formulated.

This is currently written to cover the case in which a ration was not formulated due to the pen being empty,: but was populated in subsequent days.

Returns#

bool: True if pen needs ration formulation.

set_avg_nutrient_rqmts(avg_nutrient_rqmts: Dict[str, float | EssentialAminoAcidRequirements]) → None#

Sets the pen’s average nutrient requirements

Parameters#

avg_nutrient_rqmts: Dict[str, float]: The new average nutrient requirements

set_milk_avgs(avg_milk: float, avg_CP_milk: float, avg_milk_production_reduction: float) → None#

Sets the pen’s average milk and average CP milk.

Parameters#

avg_milk: float: The new average nutrient requirements
avg_CP_milk: float: The new average CP milk

add_new_animals(new_animals: List[Calf | HeiferI | HeiferII | HeiferIII | Cow]) → None#

Adds all animals in new_animals to the pen.

Parameters#

new_animals: List[Calf | Cow | HeiferI | HeiferII | HeiferIII]: list of new animals to be added to the pen

update_animal_combination(animal_combination: AnimalCombination) → None#

Sets the pen’s animal combination to animal_combination

Parameters#

animal_combination: AnimalCombination: the new AnimalCombination

update_classes_in_pen() → None#: Updates the classes contained within the pen

update_animals(new_animals: List[Any], animal_combination: AnimalCombination) → None#

Calls functions that will add new animals to the pen and update associated attributes.

Parameters#

new_animals: List[Calf | Cow | HeiferI | HeiferII | HeiferIII]: list of new animals to be added to the pen
animal_combination: AnimalCombination: an AnimalCombination Enum representing the type of the new animals

manure_sums(manure: Dict[float, int], curr_manure: AnimalManureExcretions, animal_dict: Dict[float, int]) → Tuple[Dict[float, int], Dict[float, int]]#

Accumulator helper function for calc_manure. The function finds sums of manure components for each animal in the pen and the total manure for each animal type.

Parameters#

manure: Dict[float, int]: A dictionary that contains the the accumulated manure excretion values for all animals
curr_manure: AnimalManureExcretions: A dictionary that contains the manure excretion values used to update the manure and animal dictionaries in the AnimalManureExcretions class definition.
animal_dict: Dict[float, int]: A dictionary that contains the manure excretion values for specific animals in the pen

Returns#

Tuple[Dict[float, int], Dict[float, int]]: A tuple containing the updated manure dictionary and the updated animal dictionary.

calc_manure(feed, methane_model: str)#

Calculates the manure excretion of the animals in the pen.

Parameters#

feed: Feed: An object of the Feed class containing information about the feed.
methane_modelstr: Methane model used for calculations.

_copy_manure_template()#

reset_manure()#

calc_avg_growth() → None#: Calculates the average growth of the animals in the pen.

calc_daily_walking_dist()#: Sets the daily walking distance for the cows in the pen (if any).

call_p_rqmts()#: Calls each animal’s method to calculate phosphorus requirements.

daily_p_update()#: Calls each animal’s method to calculate daily phosphorus update.

remove_animals_by_ids(animal_ids: List[int]) → None#

Removes animals from the pen by their ids.

Notes#

Because this method takes O(n) time, it is recommended that the caller of this method should prepare a list of animal ids to be removed from the pen first, and then call this method with that list once.

Parameters#

animal_idsList[int]: List of animals that match the given ids to be removed from the pen.

clear()#: Clears the pen attributes for re-allocation.

subset_class_feeds(feed) → None#

Subsets the feed_ids list to appropriately include the feeds necessary for that pen object, based on the animal type(s) that are currently in the pen.

Parameters#

feedFeed: An object of the Feed class.

static _get_prefix_and_default_manure_excretion(animal: Calf | HeiferI | HeiferII | HeiferIII | Cow, is_lactating_cow=False) → Tuple[str, AnimalManureExcretions]#

Get the prefix and default manure value for a given animal.

Parameters#

animal: Calf | HeiferI | HeiferII | HeiferIII | Cow: The animal instance for which to get the prefix and manure.
is_lactating_cow: bool, optional: True if the animal is a lactating cow, False otherwise. Default is set to False.

Returns#

Tuple[str, AnimalManureExcretions]: A tuple containing the prefix and default manure value for the animal.

Raises#

ValueError: If prefix for animal type is not found.

_calc_animal_manure_excretion(animal: Calf | HeiferI | HeiferII | HeiferIII | Cow, methane_model: str, methane_mitigation_method: str, methane_mitigation_additive_amount: float) → Tuple[str, AnimalManureExcretions]#

Calculate the manure excretion for a given animal and return the prefix and excretions.

Parameters#

animal: Calf | HeiferI | HeiferII | HeiferIII | Cow: The animal instance for which to calculate manure excretion.
feed: Feed: An object of the Feed class containing information about the feed.
methane_model: str: Methane model used for calculations.
methane_mitigation_method: str: Methane mitigation method used.
methane_mitigation_additive_amount: float: Amount of methane mitigation additive, mg/kg dry matter intake (DMI).

Returns#

Tuple[str, AnimalManureExcretions]: A tuple containing the prefix and calculated manure excretion for the animal.

Update the manure excretion dictionaries and the self.manure variable.

Parameters#

manure_excretions_output_data: dict[str, dict[str, str | AnimalManureExcretions]]: Dictionary mapping prefixes to animal manure data.
prefix: str: Prefix related to the animal type.
manure: AnimalManureExcretions: Manure excretions data for the animal.
animal: Calf | HeiferI | HeiferII | HeiferIII | Cow: The animal instance for which to update the manure excretion data.

Returns#

None

calc_total_manure(methane_model: str, methane_mitigation_method: str, methane_mitigation_additive_amount: float, manure_excretions_output_data: dict[str, dict[str | AnimalManureExcretions]]) → None#

Calculate the total manure excreted by all animals in the pen.

Parameters#

feed: Feed: An object of the Feed class that stores the feed information managed by the farm
methane_model: str: Methane model used for methane emission calculations, including “Mutian”, “Mills”, “IPCC”.
methane_mitigation_method: str: Methane mitigation method used to reduce enteric methane emissions, including “3-NOP”, “Monensin”, “Essential Oils”, and “Seaweed”.
methane_mitigation_additive_amount: float: The amount of methane mitigation feed additive that is added, mg/kg dry matter intake (DMI). The recommended dose for 3-NOP is between 40 and 100 mg/kg DMI, while that for monensin is between 16 and 36 mg/kg DMI.
manure_excretions_output_datadict[str, dict[str | AnimalManureExcretions]]: Dictionary mapping prefixes to animal manure data.

Returns#

None

_set_animal_nutrient_values(animal, animal_grouping_scenario, feed, temp, phosphorus_concentration) → None#

Set the nutrient values for the animal.

Parameters#

animalUnion[Calf, HeiferI, HeiferII, HeiferIII, Cow]: The animal to set the nutrient values for.

animal_grouping_scenario feed temp phosphorus_concentration : float

Returns#

None

_calc_new_ration(num_animals: int)#

Calculate the new ration for the pen based on the number of animals in the pen.

Parameters#

num_animalsint: The number of animals in the pen.

Returns#

rationDict[str, Union[float, str]]: The new ration for the pen.

add_animal(animal, animal_grouping_scenario, feed, temp, phosphorus_concentration: float) → None#

Add an animal to the pen and adjust the ration accordingly.

Parameters#

animalUnion[Calf, HeiferI, HeiferII, HeiferIII, Cow]: The animal to be added to the pen.

animal_grouping_scenario feed temp phosphorus_concentration : float

Returns#

None

remove_animal(animal_id: int) → None#

Remove an animal from the pen by its id and adjust the ration accordingly.

Parameters#

animal_idint: The id of the animal to be removed from the pen.

Returns#

None

_count_lactating_cows() → int#: Returns the count of lactating cows currently held in this pen.

get_manure_data() → PenManureData#: Packages manure data from this pen.