RUFAS.routines.animal.life_cycle.heiferII module

RUFAS.routines.animal.life_cycle.heiferII.random() → x in the interval [0, 1).

class RUFAS.routines.animal.life_cycle.heiferII.HeiferII(args)

Bases: HeiferI

This class represents the attributes and activities that are characteristic of heifers in the second stage of their life cycle.

Class Attributes

statscollections.defaultdict[str, int]

A dictionary that stores statistics about all the heiferIIs instances that have been created. Currently, the following statistics are being tracked: - num_ai_performed: The number of times AI was performed across all heiferIIs. - num_successful_conceptions: The number of successful conceptions out of all AI performed. - num_ai_performed_in_ED: The number of times AI was performed in the ED protocol. - num_successful_conceptions_in_ED: The number of successful conceptions out of all AI performed in the ED. - num_ai_performed_in_TAI: The number of times AI was performed in the TAI protocol. - num_successful_conceptions_in_TAI: The number of successful conceptions out of all AI performed in the TAI. - num_ai_performed_in_SynchED: The number of times AI was performed in the SynchED protocol. - num_successful_conceptions_in_SynchED: The number of successful conceptions out of all AI performed in the SynchED.

stats = {}

__init__(args)

Description:

initialize the heifer in this stage from the first stage and

initialize or assigns the repro program parameters

Input:

args.id: id of the animal args.breed: breed of the animal args.birth_date: the date of the simulation when the calf was born args.daysBorn: age of the animal args.repro_program: reproduction program used in heifer,

three of them: ED, TAI, and synch-ED programs

args.repro_sub_protocol: string indicating the sub-type of the reproduction protocol being used. Can be

“5dCG2P”, “5dCGP”, “2P”, “CP” or “N/A”.

args.tai_method_h: timed-AI protocols used for

reproduction programs, three of them: 5dCG2P, 5dCGP, and user-defined

args.synch_ed_method_h: synch ed protocols used for

reproduction programs, two of them: 2P and CP

(optional: include the following to assign animal information) args.birth_weight: the birth weight of the animal args.body_weight: current body weight of the animal args.wean_weight: the wean weight of the animal args.mature_body_weight: the mature body weight of the animal args.events: events of the animal args.estrus_count : number of estrus during ED program args.estrus_day: the age when the heifer is estrus in ED program args.tai_program_start_day_h: start day for heifers in TAI program args.synch_ed_program_start_day_h: start day for heifers in synch_ED program args.synch_ed_estrus_day: the age when the heifer is estrus in synch_ED program args.synch_ed_stop_day: the age the the synch protocol stop for this round args.conception_rate: conception rate associated with repro programs and protocols args.ai_day: the age of animal for scheduled AI args.abortion_day: the age of the animal when abortion happens args.days_in_preg: days science pregnancy args.gestation_length: the prejected gestation args.p_gest_for_calf

get_bw_change()

Calculates the body weight change for a heifer, depending on if she is pregnant or not. If the gestation_length of the animal is equal to its days_in_preg, the difference is set to 1 (otherwise results in a division by 0 error).

Returns: the daily body weight change for a heifer

init_values(args)

Initialize repro program values

assign_heiferII_values(args)

Assign the repro program with given vales

get_heiferII_values()

Get current information from the heiferII

set_nutrient_rqmts(temperature: float, animal_grouping_scenario, nutrient_conc: Dict[str, float] = {}, metabolizable_energy: float = 15.625, previous_DMI: float = 10.0) → None

Calculates this heiferII’s nutrient requirements.

calc_manure_excretion(methane_model: str, nutrient_amount: Dict[str, float], nutrient_conc: Dict[str, float]) → None

Calculates and sets the manure excretion components.

Parameters

methane_modelstr

Methane model used for methane emission calculations, including Boadi, IPCC.

nutrient_amountDict[str, float]

Amounts of nutrients in pen ration, calculated per animal, see Notes section for units.

nutrient_concDict[str, float]

Concentrations of nutrients in pen ration, calculated per animal, percentages.

Notes

nutrient_amount_units = {

“dm”: “kg/animal”, “CP”: “percent of DM”, “ADF”: “percent of DM”, “NDF”: “percent of DM”, “lignin”: “percent of DM”, “ash”: “percent of DM”, “phosphorus”: “percent of DM”, “potassium”: “percent of DM”, “N”: “percent of DM”, }

phosphorus_rqmts(DMI: float) → None

Calculates and sets the animal’s phosphorus requirement.

Parameters

DMIfloat

Dry Matter Intake (kg).

update(sim_day)

Controls heifer’s grow with average daily gain based on user’s input until breeding start day. Here is the place to change growth rate with heifer feeding methods later when we have heifer nutrition from the ration formulation module. Breeding starts with assigned reproduction program. RufasTime to move to the 3rd stage – replacement stage determined based on gestion length and user input of replacement time. Culling for reproduction problem occur when heifer doesn’t get pregnant for a long time.

# TODO: Refactor this method. Git issue #1038.

Returns:

cull_stage: culling for reproduction failure third_stage: move to next stage – heiferIII stage when time comes

_simulate_estrus(start_day: int, sim_day: int, estrus_note: str, avg_estrus_cycle: float, std_estrus_cycle: float, max_cycle_length: float = inf) → None

Calculate and set the next estrus day for the animal.

Parameters

start_dayint

The start day plus the estrus cycle length is the day of the next estrus.

sim_dayint

The current day of the entire simulation.

estrus_notestr

A note that describes the reason for simulating estrus.

avg_estrus_cyclefloat

The average estrus cycle length.

std_estrus_cyclefloat

The standard deviation of the estrus cycle length.

max_cycle_lengthfloat

The maximum estrus cycle length.

Returns

None

static _compare_randomized_rate_less_than(reference_rate: float) → bool

Compare a randomized rate to a reference rate.

Parameters

reference_ratefloat

The reference rate to compare to.

Returns

bool

True if the randomized rate is less than the reference rate, False otherwise.

log_event(event_day: int, sim_day: int, event_note: str) → None

Log a specific event on a given day in the simulation.

Parameters

event_dayint

The day of the animal’s life when the event occurred.

sim_dayint

The current day of the entire simulation.

event_notestr

A note or description associated with the event.

static get_avg_estrus_cycle() → int

Get the average estrus cycle length for heifers (days).

Returns

int

The average estrus cycle length for heifers (days).

static get_std_estrus_cycle() → float

Get the standard deviation of the estrus cycle length for heifers (days).

Returns

float

The standard deviation of the estrus cycle length for heifers (days).

static get_avg_estrus_cycle_after_pgf() → int

Get the average estrus cycle length for heifers and cows after PGF (days).

Returns

int

The average estrus cycle length for heifers and cows after PGF (days).

static get_std_estrus_cycle_after_pgf() → float

Get the standard deviation of the estrus cycle length for heifers and cows after PGF (days).

Returns

float

The standard deviation of the estrus cycle length for heifers and cows after PGF (days).

get_general_estrus_detection_rate() → float

Get the general estrus detection rate for heifers.

Returns

float

The general estrus detection rate for heifers.

static _get_user_defined_synch_ed_estrus_detection_rate() → float

Get the user-defined estrus detection rate for heifers used in the SynchED protocol.

Returns

float

The user-defined estrus detection rate for heifers used in the SynchED protocol.

static _get_default_synch_ed_estrus_detection_rate() → float

Get the default estrus detection rate for heifers used in the SynchED protocol.

Returns

float

The default estrus detection rate for heifers used in the SynchED protocol.

_get_user_defined_or_default_synch_ed_estrus_detection_rate() → float

Get the estrus detection rate for heifers used in the SynchED protocol.

Returns

float

The estrus detection rate for heifers used in the SynchED protocol.

get_general_conception_rate() → float

Get the general conception rate for heifers.

Returns

float

The general conception rate for heifers.

static get_user_defined_tai_conception_rate() → float

Get the user-defined conception rate for heifers used in TAI protocols.

This is to contrast with the estrus conception rate used in the ED protocol.

Returns

float

The specific conception rate for heifers used in the TAI protocol.

static _get_default_TAI_conception_rate() → float

Get the default conception rate for heifers used in TAI protocols.

Notes

This is to contrast with the estrus conception rate used in the ED protocol.

Returns

float

The default conception rate for heifers used in the TAI protocol.

_get_user_defined_or_default_TAI_conception_rate() → float

Get the conception rate for heifers used in TAI protocols.

This is to contrast with the estrus conception rate used in the ED protocol.

Returns

float

The conception rate for heifers used in the TAI protocol.

_detect_estrus(detection_rate: float) → bool

Determine if estrus was detected.

Estrus is detected if a randomized rate is less than the estrus detection rate.

Parameters

detection_ratefloat

The reference estrus detection rate to compare to.

Returns

bool

True if estrus was detected, False otherwise.

execute_ed_protocol(sim_day: int) → None

Execute the ED protocol.

Notes

The two main differences between how estrus detection is handled in the ED protocol and the SynchED protocol are: 1. The estrus detection rate and conception rate are different. 2. Here, when estrus is not detected, another estrus is simulated. In the SynchED protocol,

when estrus is not detected, TAI will be performed next.

Parameters

sim_dayint

The current day of the entire simulation.

Returns

None

_handle_generic_estrus_detection(sim_day: int) → None

Perform a typical estrus detection used in the ED protocol.

Parameters

sim_day : int

Returns

_handle_estrus_detection(sim_day: int, on_estrus_detected: Callable[[int], None], on_estrus_not_detected: Callable[[int], None]) → None

A skeletal method for handling estrus detection that needs to be provided with the appropriate functions to call when estrus is detected and when estrus is not detected.

Parameters

sim_dayint

The current day of the entire simulation.

on_estrus_detectedCallable[[int], None]

A function to call when estrus is detected.

on_estrus_not_detectedCallable[[int], None]

A function to call when estrus is not detected.

Returns

None

_handle_estrus_detected(sim_day: int) → None

Perform the typical actions associated with estrus detection as used in the ED protocol.

Parameters

sim_dayint

The current day of the entire simulation.

Returns

None

_handle_estrus_not_detected(sim_day: int) → None

Perform the typical actions associated with estrus not being detected as used in the ED protocol.

Parameters

sim_dayint

The current day of the entire simulation.

Returns

None

_deliver_hormones(hormones: list[str], delivery_day: int, sim_day: int) → None

Deliver hormones to the heifer.

Parameters

hormoneslist[str]

A list of hormones to deliver. Supported options: ‘GnRH’, ‘PGF’, ‘CIDR’.

delivery_dayint

The day of the heifer’s life when the hormones were delivered.

sim_dayint

The current day of the entire simulation.

Returns

None

_execute_hormone_delivery_schedule(sim_day: int, schedule: dict[int, dict]) → None

Execute a hormone delivery schedule.

Parameters

sim_dayint

The current day of the entire simulation.

scheduledict[int, dict]

A dictionary of days and actions to perform on those days.

Returns

None

static _get_breeding_start_day() → int

Get the day of the heifer’s life when breeding starts.

Returns

int

The day of the heifer’s life when breeding starts.

static get_user_defined_repro_data(attribute: str) → Any

Get the reproduction data for heifers defined by the user.

Parameters

attributestr

The attribute to get from the reproduction data.

Returns

Any

The value of the attribute.

Raises

KeyError

If the attribute is not a valid attribute.

static get_user_defined_repro_protocol() → str

Get the reproduction protocol for heifers defined by the user.

Returns

str

The reproduction protocol for heifers defined by the user.

static get_user_defined_repro_sub_protocol() → str

Get the reproduction sub protocol for heifers defined by the user.

Returns

str

The reproduction sub protocol for heifers defined by the user.

static _get_default_repro_sub_protocol(protocol: str) → str

Get the default reproduction sub-protocol for heifers for a given reproduction protocol.

Notes

The default reproduction sub-protocol for heifers is defined in the InternalReproSettings class.

Parameters

protocolstr

The reproduction protocol to get the default sub protocol for.

Returns

str

The default reproduction sub protocol for heifers for the given reproduction protocol.

_get_user_defined_or_default_repro_sub_protocol() → str

Get the reproduction sub protocol for the heifer.

Notes

When the current reproduction protocol is the same as the user-defined protocol, the user-defined sub-protocol is used. Otherwise, the default sub-protocol for the current reproduction protocol is used.

Returns

str

The reproduction sub-protocol for the heifer.

static get_user_defined_repro_sub_properties() → dict

Get the reproduction sub properties for heifers defined by the user.

Returns

dict

The reproduction sub properties for heifers defined by the user.

execute_tai_protocol(sim_day: int) → None

Execute the timed artificial insemination (TAI) protocol.

Parameters

sim_dayint

The current day of the entire simulation.

Returns

None

execute_synch_ed_protocol(sim_day: int) → None

Execute the SynchED protocol.

This method may be called every day after the heifer enters the breeding phase. However, only on certain days will the heifer receive hormone injections or be checked for estrus.

Parameters

sim_dayint

The current day of the entire simulation.

Returns

None

_set_up_hormone_schedule(animal_category: Literal['heifers', 'cows'], repro_sub_protocol: str, start_from: int) → None

Set up the hormone delivery schedule for the heifer. Used in TAI and SynchED protocols.

Parameters

animal_categoryLiteral[‘heifers’, ‘cows’]

The animal category to use. Either ‘heifers’ or ‘cows’.

repro_sub_protocolstr

The reproduction sub protocol to use.

start_fromint

The day of the heifer’s life when the hormone delivery schedule starts.

Returns

None

Raises

Exception

If there is no hormone delivery schedule for the animal category.

_handle_synch_ed_hormone_delivery_and_set_estrus_day(sim_day: int) → None

Handle hormone delivery and set the estrus day for the heifers in the SynchED program.

Estrus day is calculated and set after the last hormone delivery.

Parameters

sim_dayint

The current day of the entire simulation.

Returns

None

_handle_synch_ed_estrus_detection(sim_day: int) → None

Handle estrus detection in the heifers in the SynchED program.

If estrus is detected, AI day is set to the next day.

Parameters

sim_dayint

The current day of the entire simulation.

Returns

None

_handle_estrus_not_detected_in_synch_ed(sim_day: int) → None

Handle the scenario where estrus is not detected in the heifers in the SynchED program.

Parameters

sim_dayint

The current day of the entire simulation.

Returns

None

_set_repro_program(sim_day: int, repro_program: str) → None

Set the reproduction program for the heifer.

Parameters

sim_dayint

The current day of the entire simulation.

repro_programstr

The reproduction program to set.

Returns

None

Raises

ValueError

If the reproduction program is not valid.

open(sim_day: int) → None

Open heifer after abortion or pregnancy loss.

Notes

Regardless of the reproduction program used for the first breeding, the rebreeding program is estrus detection (ED). The new estrus day will be the abortion day plus the estrus cycle length.

Parameters

sim_dayint

The current day of the entire simulation.

property is_pregnant

Determine if the heifer is pregnant.

Returns

bool

True if the heifer is pregnant, False otherwise.

_perform_ai(sim_day: int) → None

Perform artificial insemination on the heifer.

Parameters

sim_dayint

The current day of the entire simulation.

Returns

None

_increment_ai_counts() → None

Increment the performed AI counts across all heifers.

Notes

The following counts are incremented: - num_ai_performed: the total number of AIs performed - num_ai_performed_in_ED: the number of AIs performed in the ED protocol - num_ai_performed_in_TAI: the number of AIs performed in the TAI protocol - num_ai_performed_in_SynchED: the number of AIs performed in the SynchED protocol

Note that a heifer can go through multiple breeding programs in its lifetime. For example, a heifer can be bred using the TAI protocol, then open, then bred using the ED protocol.

Returns

None

_increment_successful_conceptions() → None

Increment the successful conception counts across all heifers.

The following counts are incremented: - num_successful_conceptions: the total number of successful conceptions - num_successful_conceptions_in_ED: the number of successful conceptions in the ED protocol - num_successful_conceptions_in_TAI: the number of successful conceptions in the TAI protocol - num_successful_conceptions_in_SynchED: the number of successful conceptions in the SynchED protocol

Note that a heifer can go through multiple breeding programs in its lifetime. For example, a heifer can be bred using the TAI protocol, then open, then bred using the ED protocol.

Returns

None

_handle_successful_conception(sim_day: int)

Handle a successful conception in the heifer by logging the event and initializing pregnancy parameters.

Parameters

sim_dayint

The current day of the entire simulation.

Returns

None

_handle_failed_conception(sim_day: int) → None

Handle a failed conception in the heifer by logging the event and simulating estrus.

Parameters

sim_dayint

The current day of the entire simulation.

Returns

None

static _calculate_gestation_length() → int

Calculate the gestation length of the heifer (days).

Returns

int

The gestation length of the heifer (days).

static _calculate_calf_birth_weight(breed: Literal['HO', 'JE']) → float

Calculate the birth weight of the calf.

Parameters

breedLiteral[‘HO’, ‘JE’]

The breed of the heifer.

Returns

float

The birth weight of the calf.

_initialize_pregnancy_parameters() → None

Initialize the pregnancy parameters for the heifer.

Returns

None

preg_update(sim_day: int) → None

Update the pregnancy status of the heifer.

Parameters

sim_dayint

The current day of the entire simulation.

Returns

None

_handle_preg_check(preg_check_config: PregCheckConfig, sim_day)

Handle a pregnancy check by logging the event and terminating the pregnancy if necessary.

Parameters

preg_check_configdict[str, str | int | float]

A dictionary of pregnancy check configuration values.

sim_dayint

The current day of the entire simulation.

Returns

None

_terminate_pregnancy(preg_loss_const: str, sim_day: int) → None

Terminate the pregnancy by logging the event and resetting the pregnancy parameters.

Parameters

preg_loss_conststr

The description of the pregnancy loss event.

sim_dayint

The current day of the entire simulation.

Returns

None