RUFAS.biophysical.animal.animal_config module

class RUFAS.biophysical.animal.animal_config.AnimalConfig

Bases: object

AnimalConfig class that holds all the animal configuration parameters from user input.

Attributes

wean_dayint

The number of days after birth when a calf is weaned, (simulation days).

wean_lengthint

The duration required for weaning, (simulation days).

target_heifer_pregnant_dayint

The target day for heifers to become pregnant, (simulation days).

heifer_breed_start_dayint

The day heifer breeding starts, , (simulation days).

heifer_prefresh_dayint

The number of days for prefresh heifer preparation , (simulation days).

calving_intervalint

The targeted interval between calvings, (simulation days).

dry_off_day_of_pregnancyint

The day of pregnancy when a cow is dried off, (simulation days).

heifer_reproduction_cull_dayint

Maximum day at which a heifer is culled if not pregnant, (simulation days).

do_not_breed_timeint

The duration after which breeding is stopped, (simulation days).

cull_milk_productionint

The threshold milk production below which cows are culled, (simulation days).

semen_typestr

Types of semen used for reproduction, e.g., “conventional”, (unitless).

male_calf_rate_conventional_semenfloat

Proportion of male calves when conventional semen is used, (unitless).

male_calf_rate_sexed_semenfloat

Proportion of male calves when sexed semen is used, (unitless).

keep_female_calf_ratefloat

Rate at which female calves are kept, (unitless).

still_birth_ratefloat

Probability of stillbirth occurring during calving, (unitless).

average_gestation_lengthint

The average gestation length, (simulation days).

std_gestation_lengthfloat

The standard deviation for gestation length, (simulation days).

cow_times_milked_per_dayint

Number of times a cow is milked per day, (unitless).

milk_fat_percentfloat

Percentage of milk fat in cow’s milk, (unitless).

true_protein_percentfloat

Percentage of true protein in cow’s milk, (unitless).

heifer_reproduction_programHeiferReproductionProtocol

Heifer reproduction program used.

heifer_reproduction_sub_programHeiferTAISubProtocol | HeiferSynchEDSubProtocol

Sub-program for heifer reproduction.

heifer_estrus_detection_ratefloat

Probability of detecting estrus in heifers, (unitless).

heifer_estrus_conception_ratefloat

Conception rate during detected estrus for heifers, (unitless).

heifer_reproduction_sub_program_conception_ratefloat

Conception rate for the heifer sub-program, (unitless).

heifer_reproduction_sub_program_estrus_detection_ratefloat

Estrus detection rate for the heifer sub-program, (unitless).

cow_reproduction_programCowReproductionProtocol

Main reproduction program used for cows.

cow_estrus_conception_ratefloat

Conception rate during detected estrus in cows, (unitless).

cow_presynch_methodCowPreSynchSubProtocol

Presynchronization method for cows.

cow_tai_methodCowTAISubProtocol

Timed artificial insemination (TAI) protocol for cows.

cow_ovsynch_methodCowTAISubProtocol

Ovsynch protocol for use in reproduction schedules.

cow_resynch_methodCowReSynchSubProtocol

Resynchronization protocol for cows.

cow_estrus_detection_ratefloat

Probability of detecting estrus in cows.

ovsynch_program_start_dayint

The starting day for the Ovsynch program, (simulation days).

ovsynch_program_conception_ratefloat

Conception rate associated with the Ovsynch program, (unitless).

presynch_program_start_dayint

The starting day for the presynchronization program, (simulation days).

voluntary_waiting_periodint

The voluntary waiting period before breeding is resumed after calving, (simulation days).

birth_weight_avg_hofloat

Average Holstein birth weight, (kg).

birth_weight_std_hofloat

Standard deviation for Holstein birth weight, (kg).

birth_weight_avg_jefloat

Average Jersey birth weight, (kg).

birth_weight_std_jefloat

Standard deviation for Jersey birth weight, (kg).

average_mature_body_weightfloat

Average weight of a mature cow, (kg).

std_mature_body_weightfloat

Standard deviation for mature cow body weight, (kg).

conception_rate_decreasefloat

Proportional decrease in conception rate with each unsuccessful breeding attempt, (unitless).

should_decrease_conception_rate_in_rebreedingbool

Whether to adjust conception rates for subsequent breeding cycles, (unitless).

should_decrease_conception_rate_by_paritybool

Whether to adjust conception rates based on parity number, (unitless).

average_estrus_cycle_returnint

Average number of days before an estrus cycle returns, (simulation days).

std_estrus_cycle_returnfloat

Standard deviation for estrus cycle return time, (simulation days).

average_estrus_cycle_heiferint

Average estrus cycle length for heifers, (simulation days).

std_estrus_cycle_heiferfloat

Standard deviation for heifer estrus cycle length, (simulation days).

average_estrus_cycle_cowint

Average estrus cycle length for cows, (simulation days).

std_estrus_cycle_cowfloat

Standard deviation for cow estrus cycle length, (simulation days).

average_estrus_cycle_after_pgfint

Average estrus cycle length after prostaglandin injection, (simulation days).

std_estrus_cycle_after_pgffloat

Standard deviation for estrus cycle length after prostaglandin injection, (simulation days).

first_pregnancy_check_dayint

First pregnancy check day post-breeding, (simulation days).

first_pregnancy_check_loss_ratefloat

Pregnancy loss probability during the first pregnancy check, (unitless).

second_pregnancy_check_dayint

Second pregnancy check day post-breeding, (simulation days).

second_pregnancy_check_loss_ratefloat

Pregnancy loss probability during the second pregnancy check, (unitless).

third_pregnancy_check_dayint

Third pregnancy check day post-breeding, (simulation days).

third_pregnancy_check_loss_ratefloat

Pregnancy loss probability during the third pregnancy check, (unitless).

parity_death_probabilitylist[float]

List of probabilities of death based on parity number, (unitless).

death_day_probabilitylist[float]

Cumulative probability of cow death as a function of days in production, (unitless).

parity_cull_probabilitylist[float]

List of culling probabilities based on parity number, (unitless).

cull_day_countlist[int]

List of day intervals for culling analysis, (simulation days).

feet_leg_cull_probabilityfloat

Probability of feet and leg-related culling, (unitless).

feet_leg_cull_day_probabilitylist[float]

Feet and leg-related culling probability over time, (unitless).

injury_cull_probabilityfloat

Probability of culling due to injuries, (unitless).

injury_cull_day_probabilitylist[float]

Cumulative distribution for injury-related culling over time, (unitless).

mastitis_cull_probabilityfloat

Probability of culling due to mastitis, (unitless).

mastitis_cull_day_probabilitylist[float]

Cumulative distribution for mastitis-related culling over time, (unitless).

disease_cull_probabilityfloat

Probability of culling due to diseases, (unitless).

disease_cull_day_probabilitylist[float]

Cumulative distribution for disease-related culling over time, (unitless).

udder_cull_probabilityfloat

Probability of culling due to udder-related issues, (unitless).

udder_cull_day_probabilitylist[float]

Cumulative distribution for udder-related culling over time, (unitless).

unknown_cull_probabilityfloat

Probability of culling for unknown reasons, (unitless).

unknown_cull_day_probabilitylist[float]

Cumulative distribution for unknown reasons of culling over time, (unitless).

methane_modelstr

The methane emission model being used, e.g., “IPCC”, (unitless).

methane_mitigation_methodstr

The mitigation method applied for methane reduction, e.g., “None”, (unitless).

methane_mitigation_additive_amountfloat

The amount of additive used for methane mitigation, (kg).

milk_reduction_maximumfloat

Maximum possible milk production reduction from a given cause, (kg).

wean_day: int = 60

wean_length: int = 7

target_heifer_pregnant_day: int = 399

heifer_breed_start_day: int = 380

heifer_prefresh_day: int = 21

calving_interval: int = 400

dry_off_day_of_pregnancy: int = 218

heifer_reproduction_cull_day: int = 500

do_not_breed_time: int = 185

cull_milk_production: int = 30

semen_type: str = 'conventional'

male_calf_rate_conventional_semen: float = 0.53

male_calf_rate_sexed_semen: float = 0.1

keep_female_calf_rate: float = 1

still_birth_rate: float = 0.065

average_gestation_length: int = 276

std_gestation_length: float = 6

cow_times_milked_per_day: int = 3

milk_fat_percent: float = 4

true_protein_percent: float = 3.2

heifer_reproduction_program: HeiferReproductionProtocol = 'ED'

heifer_reproduction_sub_program: HeiferTAISubProtocol | HeiferSynchEDSubProtocol = '5dCG2P'

heifer_estrus_detection_rate: float = 0.9

heifer_estrus_conception_rate: float = 0.6

heifer_reproduction_sub_program_conception_rate: float = 0.6

heifer_reproduction_sub_program_estrus_detection_rate: float = 0.9

cow_reproduction_program: CowReproductionProtocol = 'ED-TAI'

cow_estrus_conception_rate: float = 0.6

cow_presynch_method: CowPreSynchSubProtocol = 'Double OvSynch'

cow_tai_method: CowTAISubProtocol = 'OvSynch 56'

cow_ovsynch_method: CowTAISubProtocol = 'OvSynch 56'

cow_resynch_method: CowReSynchSubProtocol = 'TAIafterPD'

cow_estrus_detection_rate: float = 0.5

ovsynch_program_start_day: int = 64

ovsynch_program_conception_rate: float = 0.6

presynch_program_start_day: int = 50

voluntary_waiting_period: int = 50

birth_weight_avg_ho: float = 43.9

birth_weight_std_ho: float = 1

birth_weight_avg_je: float = 27.2

birth_weight_std_je: float = 1

average_mature_body_weight: float = 740.1

std_mature_body_weight: float = 73.5

conception_rate_decrease: float = 0.026

should_decrease_conception_rate_in_rebreeding: bool = False

should_decrease_conception_rate_by_parity: bool = False

average_estrus_cycle_return: int = 23

std_estrus_cycle_return: float = 6

average_estrus_cycle_heifer: int = 21

std_estrus_cycle_heifer: float = 2.5

average_estrus_cycle_cow: int = 21

std_estrus_cycle_cow: float = 4

average_estrus_cycle_after_pgf: int = 5

std_estrus_cycle_after_pgf: float = 2

first_pregnancy_check_day: int = 32

first_pregnancy_check_loss_rate: float = 0.02

second_pregnancy_check_day: int = 60

second_pregnancy_check_loss_rate: float = 0.096

third_pregnancy_check_day: int = 200

third_pregnancy_check_loss_rate: float = 0.017

parity_death_probability: list[float] = [0.039, 0.056, 0.085, 0.117]

death_day_probability: list[float] = [0, 0.18, 0.32, 0.42, 0.48, 0.54, 0.6, 0.65, 0.7, 0.77, 0.83, 0.89, 0.95, 1]

parity_cull_probability: list[float] = [0.169, 0.233, 0.301, 0.408]

cull_day_count: list[int] = [0, 5, 15, 45, 90, 135, 180, 225, 270, 330, 380, 430, 480, 530]

feet_leg_cull_probability: float = 0.1633

feet_leg_cull_day_probability: list[float] = [0, 0.03, 0.08, 0.16, 0.25, 0.36, 0.48, 0.59, 0.69, 0.78, 0.85, 0.9, 0.95, 1]

injury_cull_probability: float = 0.2883

injury_cull_day_probability: list[float] = [0, 0.08, 0.18, 0.28, 0.38, 0.47, 0.56, 0.64, 0.71, 0.78, 0.85, 0.9, 0.95, 1]

mastitis_cull_probability: float = 0.2439

mastitis_cull_day_probability: list[float] = [0, 0.06, 0.12, 0.19, 0.3, 0.43, 0.56, 0.68, 0.78, 0.85, 0.9, 0.94, 0.97, 1]

disease_cull_probability: float = 0.1391

disease_cull_day_probability: list[float] = [0, 0.04, 0.12, 0.24, 0.34, 0.42, 0.5, 0.57, 0.64, 0.72, 0.81, 0.89, 0.95, 1]

udder_cull_probability: float = 0.0645

udder_cull_day_probability: list[float] = [0, 0.12, 0.24, 0.33, 0.41, 0.48, 0.55, 0.62, 0.68, 0.76, 0.82, 0.89, 0.95, 1]

unknown_cull_probability: float = 0.1009

unknown_cull_day_probability: list[float] = [0, 0.05, 0.11, 0.18, 0.27, 0.37, 0.45, 0.54, 0.62, 0.7, 0.77, 0.84, 0.92, 1]

methane_model: str = 'IPCC'

methane_mitigation_method: str = 'None'

methane_mitigation_additive_amount: float = 0.0

milk_reduction_maximum: float

classmethod initialize_animal_config() → None

Initialize the animal config from the input manager user input data.