Genetics Implementation

README.md

@@ -1,7 +1,7 @@
 [![Flake8](https://img.shields.io/badge/Flake8-passed-brightgreen)](https://github.com/RuminantFarmSystems/MASM/actions/workflows/combined_format_lint_test_mypy.yml)
 [![Pytest](https://img.shields.io/badge/Pytest-passed-brightgreen)](https://github.com/RuminantFarmSystems/MASM/actions/workflows/combined_format_lint_test_mypy.yml)
 [![Coverage](https://img.shields.io/badge/Coverage-99%25-brightgreen)](https://github.com/RuminantFarmSystems/MASM/actions/workflows/combined_format_lint_test_mypy.yml)
-[![Mypy](https://img.shields.io/badge/Mypy-1190%20errors-red)](https://github.com/RuminantFarmSystems/MASM/actions/workflows/combined_format_lint_test_mypy.yml)
+[![Mypy](https://img.shields.io/badge/Mypy-1180%20errors-red)](https://github.com/RuminantFarmSystems/MASM/actions/workflows/combined_format_lint_test_mypy.yml)
 
 
 # RuFaS: Ruminant Farm Systems

RUFAS/biophysical/animal/animal_config.py

@@ -373,6 +373,10 @@ class AnimalConfig:
 
     milk_reduction_maximum: float
 
+    average_phenotype: dict[str, dict[int, float]] = {}
+    top_listing_semen: dict[str, dict[str, float]] = {}
+    simulate_genetics: bool = False
+
     @classmethod
     def initialize_animal_config(cls) -> None:
         """Initialize the animal config from the input manager user input data."""
@@ -527,3 +531,18 @@ def initialize_animal_config(cls) -> None:
                     "function": "initialize_animal_config",
                 },
             )
+
+        average_phenotype = im.get_data("animal_mean_phenotype")
+        cls.average_phenotype = {
+            trait: dict(zip(average_phenotype["birth_year"], values))
+            for trait, values in average_phenotype.items()
+            if trait != "birth_year"
+        }
+
+        top_listing_semen = im.get_data("animal_top_listing_semen")
+        cls.top_listing_semen = {
+            trait: dict(zip(top_listing_semen["year_month"], values))
+            for trait, values in top_listing_semen.items()
+            if trait != "year_month"
+        }
+        cls.simulate_genetics = animal_data["herd_information"]["simulate_genetics"]

RUFAS/biophysical/animal/animal_module_reporter.py

@@ -2,6 +2,8 @@
 from dataclasses import asdict
 from typing import Any
 
+from RUFAS.biophysical.animal.animal_config import AnimalConfig
+from RUFAS.biophysical.animal.animal_genetics.animal_genetics import UNITS as genetics_units
 from RUFAS.biophysical.animal.data_types.animal_events import AnimalEvents
 from RUFAS.biophysical.animal.data_types.animal_population import AnimalPopulationStatistics
 from RUFAS.biophysical.animal.data_types.animal_typed_dicts import SoldAnimalTypedDict, StillbornCalfTypedDict
@@ -160,22 +162,77 @@ def report_milk(cls, milk_reports: list[MilkProductionStatistics], simulation_da
             "class": AnimalModuleReporter.__name__,
             "function": AnimalModuleReporter.report_milk.__name__,
             "data_origin": [("MilkProduction", "perform_daily_milking_update")],
-            "units": MilkProductionStatistics.UNITS,
+            "units": (
+                (MilkProductionStatistics.UNITS | MilkProductionStatistics.GENETIC_UNITS)
+                if AnimalConfig.simulate_genetics
+                else MilkProductionStatistics.UNITS
+            ),
         }
 
         for milk_stats in milk_reports:
-            updated_milk_data: dict[str, int | float] = asdict(milk_stats)
-            updated_milk_data["is_milking"] = milk_stats.is_milking
-            updated_milk_data["estimated_daily_milk_produced"] = milk_stats.estimated_daily_milk_produced
-            updated_milk_data["milk_protein"] = milk_stats.milk_protein
-            updated_milk_data["milk_fat"] = milk_stats.milk_fat
-            updated_milk_data["milk_lactose"] = milk_stats.milk_lactose
-            updated_milk_data["parity"] = milk_stats.parity
-            updated_milk_data["cow_id"] = milk_stats.cow_id
-            updated_milk_data["pen_id"] = milk_stats.pen_id
-            updated_milk_data["simulation_day"] = simulation_day
+            updated_milk_data: dict[str, int | float | str] = {
+                "cow_id": milk_stats.cow_id,
+                "pen_id": milk_stats.pen_id,
+                "is_milking": milk_stats.is_milking,
+                "days_in_milk": milk_stats.days_in_milk,
+                "estimated_daily_milk_produced": milk_stats.estimated_daily_milk_produced,
+                "milk_protein": milk_stats.milk_protein,
+                "milk_fat": milk_stats.milk_fat,
+                "milk_lactose": milk_stats.milk_lactose,
+                "parity": milk_stats.parity,
+                "simulation_day": simulation_day,
+            }
+            if AnimalConfig.simulate_genetics:
+                updated_milk_data["days_born"] = milk_stats.days_born
+                updated_milk_data["days_in_pregnancy"] = milk_stats.days_in_pregnancy
+                updated_milk_data["animal_type"] = milk_stats.animal_type.name
+                updated_milk_data["TBV_fat"] = milk_stats.TBV_fat
+                updated_milk_data["TBV_protein"] = milk_stats.TBV_protein
+                updated_milk_data["E_permanent_fat"] = milk_stats.E_permanent_fat
+                updated_milk_data["E_permanent_protein"] = milk_stats.E_permanent_protein
+                updated_milk_data["E_temporary_fat"] = milk_stats.E_temporary_fat
+                updated_milk_data["E_temporary_protein"] = milk_stats.E_temporary_protein
+                updated_milk_data["phenotype_fat"] = milk_stats.phenotype_fat
+                updated_milk_data["phenotype_protein"] = milk_stats.phenotype_protein
+                updated_milk_data["EBV_fat"] = milk_stats.EBV_fat
+                updated_milk_data["EBV_protein"] = milk_stats.EBV_protein
+                updated_milk_data["ranking_index"] = milk_stats.ranking_index
+
             om.add_variable("milk_data_at_milk_update", updated_milk_data, info_map)
 
+    @classmethod
+    def report_average_genetics(
+        cls, average_genetics: dict[str, float | None], variable_name_prefix: str, simulation_day: int
+    ) -> None:
+        """
+        Reports the average genetics data with associated simulation metadata. The
+        method adds the given genetics data to a managed output variable, using
+        a specific variable name prefix and simulation day.
+
+        Parameters
+        ----------
+        average_genetics : dict[str, float | None]
+            A dictionary containing genetic measurements, where the key is
+            the measurement name and the value is the averaged measurement.
+        variable_name_prefix : str
+            A prefix to be appended to the variable name for distinguishing
+            the reported data in the output.
+        simulation_day : int
+            The specific day in the simulation timeline, used to annotate the
+            reported data for temporal tracking.
+
+        Returns
+        -------
+        None
+        """
+        info_map = {
+            "class": AnimalModuleReporter.__name__,
+            "function": AnimalModuleReporter.report_average_genetics.__name__,
+            "units": genetics_units,
+            "simulation_day": simulation_day,
+        }
+        om.add_variable(f"{variable_name_prefix}_average_genetics", average_genetics, info_map)
+
     @classmethod
     def report_ration_per_animal(
         cls,
@@ -929,6 +986,9 @@ def report_sold_animal_information(cls, herd_statistics: HerdStatistics) -> None
             )
             om.add_variable("days_in_milk", animal["days_in_milk"], dict(info_map, **{"units": MeasurementUnits.DAYS}))
             om.add_variable("parity", animal["parity"], dict(info_map, **{"units": MeasurementUnits.UNITLESS}))
+            om.add_variable(
+                "genetic_history", animal["genetic_history"], dict(info_map, **{"units": MeasurementUnits.UNITLESS})
+            )
 
     @classmethod
     def report_stillborn_calves_information(
@@ -1094,6 +1154,7 @@ def report_end_of_simulation(
         time: RufasTime,
         heiferII_events_by_id: dict[str, AnimalEvents],
         cow_events_by_id: dict[str, AnimalEvents],
+        all_animals_genetic_history: dict[int, str],
     ) -> None:
         """
         Calls all reporter methods that should happen at the end of the simulation.
@@ -1110,8 +1171,21 @@ def report_end_of_simulation(
             The dictionary of HeiferII events.
         cow_events_by_id : dict[str, AnimalEvents]
             The dictionary of Cow events.
+        all_animals_genetic_history : dict[int, str]
+            The dict of genetic histories for all animals in the herd by their IDs.
         """
-        empty_sold_animals: list[SoldAnimalTypedDict] = [{"sold_at_day": 0, "body_weight": 0}]
+        empty_sold_animals: list[SoldAnimalTypedDict] = [
+            {
+                "id": 0,
+                "animal_type": "",
+                "sold_at_day": 0,
+                "body_weight": 0.0,
+                "cull_reason": None,
+                "days_in_milk": 0,
+                "parity": 0,
+                "genetic_history": "",
+            }
+        ]
         AnimalModuleReporter.report_sold_animal_information(herd_statistics)
         if herd_statistics.sold_calves_info:
             AnimalModuleReporter.report_sold_animal_information_sort_by_sell_day(
@@ -1184,15 +1258,17 @@ def report_end_of_simulation(
 
         AnimalModuleReporter._record_heiferIIs_conception_rate(herd_reproduction_statistics)
         AnimalModuleReporter._record_cows_conception_rate(herd_reproduction_statistics)
+        if AnimalConfig.simulate_genetics:
+            AnimalModuleReporter._report_all_animals_genetic_history(all_animals_genetic_history)
 
     @classmethod
-    def _record_animal_events(cls, animal_events_by_id: dict[str, str], simulation_day: int) -> None:
+    def _record_animal_events(cls, animal_events_by_id: dict[str, AnimalEvents], simulation_day: int) -> None:
         """
         Record the events of the animals.
 
         Parameters
         ----------
-        animal_events_by_id : dict[str, str]
+        animal_events_by_id : dict[str, AnimalEvents]
             A dictionary of animal events, where the key is a string containing the animal id and the animal type,
             and the value is the string representation of the events of the animal.
         simulation_day : int
@@ -1308,6 +1384,16 @@ def _record_cows_conception_rate(cls, herd_reproduction_statistics: HerdReproduc
             dict(info_map, **{"units": MeasurementUnits.CONCEPTIONS_PER_SERVICE}),
         )
 
+    @classmethod
+    def _report_all_animals_genetic_history(cls, all_animals_genetic_history: dict[int, str]) -> None:
+        """Report all animals genetic history."""
+        info_map = {
+            "class": AnimalModuleReporter.__name__,
+            "function": AnimalModuleReporter._report_all_animals_genetic_history.__name__,
+            "units": MeasurementUnits.UNITLESS,
+        }
+        om.add_variable("animals_genetic_history", all_animals_genetic_history, info_map)
+
     @classmethod
     def report_animal_population_statistics(cls, prefix: str, herd_summary: AnimalPopulationStatistics) -> None:
         """Reports the herd summary statistics for the starting animal population."""

RUFAS/biophysical/animal/data_types/animal_typed_dicts.py

@@ -18,7 +18,6 @@ class CalfValuesTypedDict(TypedDict):
     wean_weight: float
     mature_body_weight: float
     events: str
-    net_merit: float
     initial_phosphorus: NotRequired[float]
     body_weight_history: NotRequired[list[BodyWeightHistory]]
     pen_history: NotRequired[list[PenHistory]]
@@ -36,7 +35,8 @@ class NewBornCalfValuesTypedDict(TypedDict):
     days_born: int
     birth_weight: float
     initial_phosphorus: float
-    net_merit: float
+    dam_tbv_fat: NotRequired[float]
+    dam_tbv_protein: NotRequired[float]
     body_weight_history: NotRequired[list[BodyWeightHistory]]
     pen_history: NotRequired[list[PenHistory]]
     conceptus_weight: NotRequired[float]
@@ -55,7 +55,6 @@ class HeiferIValuesTypedDict(TypedDict):
     wean_weight: float
     mature_body_weight: float
     events: str
-    net_merit: float
     body_weight_history: NotRequired[list[BodyWeightHistory]]
     pen_history: NotRequired[list[PenHistory]]
     conceptus_weight: NotRequired[float]
@@ -74,7 +73,6 @@ class HeiferIIValuesTypedDict(TypedDict):
     wean_weight: float
     mature_body_weight: float
     events: str
-    net_merit: float
     body_weight_history: NotRequired[list[BodyWeightHistory]]
     pen_history: NotRequired[list[PenHistory]]
     conceptus_weight: NotRequired[float]
@@ -109,7 +107,6 @@ class HeiferIIIValuesTypedDict(TypedDict):
     wean_weight: float
     mature_body_weight: float
     events: str
-    net_merit: float
     body_weight_history: NotRequired[list[BodyWeightHistory]]
     pen_history: NotRequired[list[PenHistory]]
     conceptus_weight: NotRequired[float]
@@ -144,7 +141,6 @@ class CowValuesTypedDict(TypedDict):
     wean_weight: float
     mature_body_weight: float
     events: str
-    net_merit: float
     body_weight_history: NotRequired[list[BodyWeightHistory]]
     pen_history: NotRequired[list[PenHistory]]
     conceptus_weight: NotRequired[float]
@@ -186,6 +182,7 @@ class SoldAnimalTypedDict(TypedDict):
     cull_reason: str | None
     days_in_milk: int | str
     parity: int | str
+    genetic_history: str
 
 
 class StillbornCalfTypedDict(TypedDict):

RUFAS/biophysical/animal/data_types/genetic_history.py

@@ -0,0 +1,33 @@
+from typing import TypedDict
+
+from RUFAS.biophysical.animal.data_types.animal_types import AnimalType
+
+
+class GeneticHistory(TypedDict):
+    """
+    A class to represent the genetic history of an individual animal on a farm.
+
+    This class is used to track the genetic attributes of an animal over the course of a simulation.
+    It contains information about the simulation day, the age of the animal in days, and its genetic attributes.
+
+    Attributes
+    ----------
+    start_day : int
+        The simulation day corresponding to the start of the genetic record of the animal.
+    end_day : int
+        The simulation day corresponding to the end of the genetic record of the animal.
+    id : int
+        The unique identifier of the animal.
+    animal_type : AnimalType
+        The type of animal.
+    genetics: dict[str, float]
+        Dictionary containing the genetic attributes of the animal.
+    """
+
+    start_day: int
+    end_day: int
+
+    id: int
+    animal_type: AnimalType
+
+    genetics: dict[str, float]

RUFAS/biophysical/animal/data_types/milk_production.py

@@ -1,6 +1,7 @@
 from dataclasses import dataclass
 
 from RUFAS.biophysical.animal.data_types.animal_events import AnimalEvents
+from RUFAS.biophysical.animal.data_types.animal_types import AnimalType
 from RUFAS.units import MeasurementUnits
 
 
@@ -76,6 +77,34 @@ class MilkProductionStatistics:
         The daily lactose content in the milk produced by the animal, (kg/day).
     parity : int
         The number of claves the cow has given birth, (unitless).
+    days_born : int
+        The number of days since the birth of the animal, (days).
+    days_in_pregnancy : int
+        The number of days since the animal has been pregnant, (days).
+    animal_type : AnimalType
+        The type of animal, (unitless).
+    TBV_fat : float or None
+        The True Breed Value for fat of the animal, (kg). Defaults to None.
+    TBV_protein : float or None
+        The True Breed Value for protein of the animal, (kg). Defaults to None.
+    E_permanent_fat : float or None
+        The Permanent Environment Effect for fat of the animal, (kg). Defaults to None.
+    E_permanent_protein : float or None
+        The Permanent Environment Effect for protein of the animal, (kg). Defaults to None.
+    E_temporary_fat : float or None
+        The Temporary Environment Effect for fat of the animal, (kg). Defaults to None.
+    E_temporary_protein : float or None
+        The Temporary Environment Effect for protein of the animal, (kg). Defaults to None.
+    phenotype_fat : float or None
+        The fat phenotype of the animal, (kg). Defaults to None.
+    phenotype_protein : float or None
+        The protein phenotype of the animal, (kg). Defaults to None.
+    EBV_fat : float or None
+        The Estimated Breeding Value for fat of the animal, (kg). Defaults to None.
+    EBV_protein : float or None
+        The Estimated Breeding Value for protein of the animal, (kg). Defaults to None.
+    ranking_index : float or None
+        The ranking index of the animal, (unitless). Defaults to None.
     """
 
     cow_id: int
@@ -86,6 +115,22 @@ class MilkProductionStatistics:
     milk_fat: float
     milk_lactose: float
     parity: int
+    days_born: int
+    days_in_pregnancy: int
+    animal_type: AnimalType
+
+    TBV_fat: float | None = None
+    TBV_protein: float | None = None
+    E_permanent_fat: float | None = None
+    E_permanent_protein: float | None = None
+
+    E_temporary_fat: float | None = None
+    E_temporary_protein: float | None = None
+    phenotype_fat: float | None = None
+    phenotype_protein: float | None = None
+    EBV_fat: float | None = None
+    EBV_protein: float | None = None
+    ranking_index: float | None = None
 
     UNITS = {
         "cow_id": MeasurementUnits.UNITLESS,
@@ -99,6 +144,22 @@ class MilkProductionStatistics:
         "is_milking": MeasurementUnits.UNITLESS,
         "simulation_day": MeasurementUnits.SIMULATION_DAY,
     }
+    GENETIC_UNITS = {
+        "days_born": MeasurementUnits.DAYS,
+        "days_in_pregnancy": MeasurementUnits.DAYS,
+        "animal_type": MeasurementUnits.UNITLESS,
+        "TBV_fat": MeasurementUnits.KILOGRAMS,
+        "TBV_protein": MeasurementUnits.KILOGRAMS,
+        "E_permanent_fat": MeasurementUnits.KILOGRAMS,
+        "E_permanent_protein": MeasurementUnits.KILOGRAMS,
+        "E_temporary_fat": MeasurementUnits.KILOGRAMS,
+        "E_temporary_protein": MeasurementUnits.KILOGRAMS,
+        "phenotype_fat": MeasurementUnits.KILOGRAMS,
+        "phenotype_protein": MeasurementUnits.KILOGRAMS,
+        "EBV_fat": MeasurementUnits.KILOGRAMS,
+        "EBV_protein": MeasurementUnits.KILOGRAMS,
+        "ranking_index": MeasurementUnits.UNITLESS,
+    }
 
     @property
     def is_milking(self) -> bool: