[Animal] Streamline Animal Culling Inputs

RUFAS/biophysical/animal/animal.py

@@ -1767,9 +1767,6 @@ def daily_reproduction_update(
                 self.milk_production.set_wood_parameters(
                     wood_parameters["l"], wood_parameters["m"], wood_parameters["n"]
                 )
-                self.future_death_date = self.determine_future_death_date()
-                self._future_death_reason = animal_constants.DEATH_CULL
-                self.future_cull_date, self.cull_reason = self.determine_future_cull_date()
 
         self.events += reproduction_outputs.events
 
@@ -2422,110 +2419,73 @@ def _get_cow_values(self) -> CowValuesTypedDict:
             parity=self.calves,
         )
 
-    def determine_future_death_date(self) -> int:
+    def assess_removal_risk(self, percent_fresh: float, time: RufasTime) -> None:
         """
-        Determine the future death date of the animal based on its parity.
+        Roll a cow's daily mortality and acute-sale risk and schedule any resulting removal.
 
-        Returns
-        -------
-        int
-            Calculated future death date in simulation days.
+        Parameters
+        ----------
+        percent_fresh : float
+            Fraction of the herd currently fresh, used to scale the daily death and
+            acute-sale selection probabilities.
+        time : RufasTime
+            Current simulation time, used to record the day of death or sale.
 
-        Notes
+        Returns
         -------
-        [AN.ANM.1]
-
+        None
         """
-        if self.calves >= 4:
-            death_rate = AnimalConfig.parity_death_probability[3]
-        else:
-            death_rate = AnimalConfig.parity_death_probability[self.calves - 1]
-        death_rand = random()
-        if death_rand <= death_rate:
-            death_probability_upper_limit = death_probability_lower_limit = 0.0
-            death_time_upper_limit = death_time_lower_limit = 0.0
-            death_date_random = random()
-            for i in range(len(AnimalConfig.death_day_probability) - 1):
-                if (
-                    AnimalConfig.death_day_probability[i]
-                    <= death_date_random
-                    < AnimalConfig.death_day_probability[i + 1]
-                ):
-                    death_probability_lower_limit = AnimalConfig.death_day_probability[i]
-                    death_probability_upper_limit = AnimalConfig.death_day_probability[i + 1]
-                    death_time_lower_limit = AnimalConfig.cull_day_count[i]
-                    death_time_upper_limit = AnimalConfig.cull_day_count[i + 1]
-            n = (death_time_upper_limit - death_time_lower_limit) / (
-                death_probability_upper_limit - death_probability_lower_limit
-            )
-            return round(
-                death_time_lower_limit + n * (death_date_random - death_probability_lower_limit) + self.days_born
-            )
-        return sys.maxsize
+        if self.future_cull_date == sys.maxsize:
+            if self.is_selected_for_acute_sale(percent_fresh):
+                self.future_cull_date = self.days_born
+                self.cull_reason = animal_constants.ACUTE_SALE_CULL
+                self.sold_at_day = time.simulation_day
+                return
+        if self.future_death_date == sys.maxsize:
+            if self.is_selected_for_death(percent_fresh):
+                self.future_death_date = self.days_born
+                self.cull_reason = self._future_death_reason = animal_constants.DEATH_CULL
+                self.dead_at_day = time.simulation_day
+
+    def _parity_index(self) -> int:
+        """Return the 0-based index into a by-parity array, capping parity 4+ at the last entry."""
+        return 3 if self.calves >= 4 else self.calves - 1
 
-    def determine_future_cull_date(self) -> tuple[int, str]:
+    def is_selected_for_death(self, percent_fresh: float) -> bool:
         """
-        Determine the future cull date and reason for the animal based on parity-specific probabilities.
+        Roll the cow's daily mortality risk.
 
         Returns
         -------
-        tuple[int, str]
-            - Future cull date in simulation days.
-            - Reason for culling.
+        bool
+            ``True`` if the cow is selected to die, ``False`` otherwise.
+        """
+        average_daily_death_rate = AnimalConfig.parity_death_probability[self._parity_index()] / 365
+        percent_other = 1 - percent_fresh
 
-        Notes
-        -------
-        [AN.ANM.2]
+        daily_death_risk_other = average_daily_death_rate / (2.55 * percent_fresh + percent_other)
+        daily_death_risk_fresh = 2.55 * daily_death_risk_other
 
+        daily_death_risk = daily_death_risk_fresh if self.days_in_milk < 50 else daily_death_risk_other
+        return random() <= daily_death_risk
+
+    def is_selected_for_acute_sale(self, percent_fresh: float) -> bool:
         """
-        cull_reason = ""
-        future_cull_date = sys.maxsize
-        if self.calves >= 4:
-            inv_cull_rate = AnimalConfig.parity_cull_probability[3]
-        else:
-            inv_cull_rate = AnimalConfig.parity_cull_probability[self.calves - 1]
-        cull_rand = random()
-        if cull_rand <= inv_cull_rate:
-            cull_reason_rand = random()
-            cull_prob = 0.0
-            if cull_reason_rand <= (cull_prob := cull_prob + AnimalConfig.feet_leg_cull_probability):
-                cull_reason_cull_prob = AnimalConfig.feet_leg_cull_day_probability
-                cull_reason = animal_constants.LAMENESS_CULL
-
-            elif cull_reason_rand <= (cull_prob := cull_prob + AnimalConfig.injury_cull_probability):
-                cull_reason_cull_prob = AnimalConfig.injury_cull_day_probability
-                cull_reason = animal_constants.INJURY_CULL
-
-            elif cull_reason_rand <= (cull_prob := cull_prob + AnimalConfig.mastitis_cull_probability):
-                cull_reason_cull_prob = AnimalConfig.mastitis_cull_day_probability
-                cull_reason = animal_constants.MASTITIS_CULL
-
-            elif cull_reason_rand <= (cull_prob := cull_prob + AnimalConfig.disease_cull_probability):
-                cull_reason_cull_prob = AnimalConfig.disease_cull_day_probability
-                cull_reason = animal_constants.DISEASE_CULL
-
-            elif cull_reason_rand <= (cull_prob + AnimalConfig.udder_cull_probability):
-                cull_reason_cull_prob = AnimalConfig.udder_cull_day_probability
-                cull_reason = animal_constants.UDDER_CULL
+        Roll the cow's daily acute-sale (forced / involuntary) risk.
 
-            else:
-                cull_reason_cull_prob = AnimalConfig.unknown_cull_day_probability
-                cull_reason = animal_constants.UNKNOWN_CULL
-
-            cull_time_rand = random()
-            cull_reason_upper_limit = cull_reason_lower_limit = cull_time_upper_limit = cull_time_lower_limit = 0.0
-            for i in range(len(cull_reason_cull_prob) - 1):
-                if cull_reason_cull_prob[i] <= cull_time_rand < cull_reason_cull_prob[i + 1]:
-                    cull_reason_lower_limit = cull_reason_cull_prob[i]
-                    cull_reason_upper_limit = cull_reason_cull_prob[i + 1]
-                    cull_time_lower_limit = AnimalConfig.cull_day_count[i]
-                    cull_time_upper_limit = AnimalConfig.cull_day_count[i + 1]
-            x = (cull_time_upper_limit - cull_time_lower_limit) / (cull_reason_upper_limit - cull_reason_lower_limit)
-            future_cull_date = round(
-                cull_time_lower_limit + x * (cull_time_rand - cull_reason_lower_limit) + self.days_born
-            )
+        Returns
+        -------
+        bool
+            ``True`` if the cow is selected for an acute sale, ``False`` otherwise.
+        """
+        average_daily_removal_rate = AnimalConfig.parity_acute_sale_probability[self._parity_index()] / 365
+        percent_other = 1 - percent_fresh
+
+        daily_removal_risk_other = average_daily_removal_rate / (2.55 * percent_fresh + percent_other)
+        daily_removal_risk_fresh = 2.55 * daily_removal_risk_other
 
-        return future_cull_date, cull_reason
+        daily_removal_risk = daily_removal_risk_fresh if self.days_in_milk < 50 else daily_removal_risk_other
+        return random() <= daily_removal_risk
 
     def update_pen_history(self, current_pen: int, current_day: int, animal_types_in_pen: set[AnimalType]) -> None:
         """

RUFAS/biophysical/animal/animal_config.py

@@ -146,37 +146,10 @@ class AnimalConfig:
     third_pregnancy_check_loss_rate : float
         Pregnancy loss probability during the third pregnancy check, (unitless).
     parity_death_probability : list[float]
-        List of probabilities of death based on parity number, (unitless).
-    death_day_probability : list[float]
-        Cumulative probability of cow death as a function of days in production, (unitless).
-    parity_cull_probability : list[float]
-        List of culling probabilities based on parity number, (unitless).
-    cull_day_count : list[int]
-        List of day intervals for culling analysis, (simulation day).
-    feet_leg_cull_probability : float
-        Probability of feet and leg-related culling, (unitless).
-    feet_leg_cull_day_probability : list[float]
-        Feet and leg-related culling probability over time, (unitless).
-    injury_cull_probability : float
-        Probability of culling due to injuries, (unitless).
-    injury_cull_day_probability : list[float]
-        Cumulative distribution for injury-related culling over time, (unitless).
-    mastitis_cull_probability : float
-        Probability of culling due to mastitis, (unitless).
-    mastitis_cull_day_probability : list[float]
-        Cumulative distribution for mastitis-related culling over time, (unitless).
-    disease_cull_probability : float
-        Probability of culling due to diseases, (unitless).
-    disease_cull_day_probability : list[float]
-        Cumulative distribution for disease-related culling over time, (unitless).
-    udder_cull_probability : float
-        Probability of culling due to udder-related issues, (unitless).
-    udder_cull_day_probability : list[float]
-        Cumulative distribution for udder-related culling over time, (unitless).
-    unknown_cull_probability : float
-        Probability of culling for unknown reasons, (unitless).
-    unknown_cull_day_probability : list[float]
-        Cumulative distribution for unknown reasons of culling over time, (unitless).
+        Annual, parity-indexed probability that a cow dies during a given year, (unitless).
+    parity_acute_sale_probability : list[float]
+        Annual, parity-indexed probability that a cow is sold for an acute / involuntary
+        reason during a given year, (unitless).
     methane_mitigation_method : str
         The mitigation method applied for methane reduction, e.g., "None", (unitless).
     methane_mitigation_additive_amount : float
@@ -268,112 +241,7 @@ class AnimalConfig:
     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, 0.60, 0.65, 0.70, 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,
-        0.90,
-        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,
-        0.90,
-        0.95,
-        1,
-    ]
-    mastitis_cull_probability: float = 0.2439
-    mastitis_cull_day_probability: list[float] = [
-        0,
-        0.06,
-        0.12,
-        0.19,
-        0.30,
-        0.43,
-        0.56,
-        0.68,
-        0.78,
-        0.85,
-        0.90,
-        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,
-        0.50,
-        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,
-        0.70,
-        0.77,
-        0.84,
-        0.92,
-        1,
-    ]
+    parity_acute_sale_probability: list[float] = [0.169, 0.233, 0.301, 0.408]
 
     methane_model: dict[str, Any] = {
         "calves": "Pattanaik",
@@ -515,32 +383,7 @@ def initialize_animal_config(cls) -> None:
         cls.third_pregnancy_check_loss_rate = animal_config_data["from_literature"]["repro"]["preg_loss_rate_3"]
 
         cls.parity_death_probability = animal_config_data["from_literature"]["culling"]["parity_death_prob"]
-        cls.death_day_probability = animal_config_data["from_literature"]["culling"]["death_day_prob"]
-
-        cls.parity_cull_probability = animal_config_data["from_literature"]["culling"]["parity_cull_prob"]
-        cls.cull_day_count = animal_config_data["from_literature"]["culling"]["cull_day_count"]
-        cls.feet_leg_cull_probability = animal_config_data["from_literature"]["culling"]["feet_leg_cull"]["probability"]
-        cls.feet_leg_cull_day_probability = animal_config_data["from_literature"]["culling"]["feet_leg_cull"][
-            "cull_day_prob"
-        ]
-        cls.injury_cull_probability = animal_config_data["from_literature"]["culling"]["injury_cull"]["probability"]
-        cls.injury_cull_day_probability = animal_config_data["from_literature"]["culling"]["injury_cull"][
-            "cull_day_prob"
-        ]
-        cls.mastitis_cull_probability = animal_config_data["from_literature"]["culling"]["mastitis_cull"]["probability"]
-        cls.mastitis_cull_day_probability = animal_config_data["from_literature"]["culling"]["mastitis_cull"][
-            "cull_day_prob"
-        ]
-        cls.disease_cull_probability = animal_config_data["from_literature"]["culling"]["disease_cull"]["probability"]
-        cls.disease_cull_day_probability = animal_config_data["from_literature"]["culling"]["disease_cull"][
-            "cull_day_prob"
-        ]
-        cls.udder_cull_probability = animal_config_data["from_literature"]["culling"]["udder_cull"]["probability"]
-        cls.udder_cull_day_probability = animal_config_data["from_literature"]["culling"]["udder_cull"]["cull_day_prob"]
-        cls.unknown_cull_probability = animal_config_data["from_literature"]["culling"]["unknown_cull"]["probability"]
-        cls.unknown_cull_day_probability = animal_config_data["from_literature"]["culling"]["unknown_cull"][
-            "cull_day_prob"
-        ]
+        cls.parity_acute_sale_probability = animal_config_data["from_literature"]["culling"]["parity_acute_sale_prob"]
 
         cls.methane_model = animal_data["methane_model"]
         methane_mitigation_data = animal_data["methane_mitigation"]

RUFAS/biophysical/animal/animal_constants.py

@@ -96,12 +96,7 @@
 HEIFER_REPRO_CULL = "culled for heifer reproductive problem"
 OVERSUPPLY_CULL = "culled for herd resize"
 DEATH_CULL = "culled for death"
-LAMENESS_CULL = "culled for lameness"
-INJURY_CULL = "culled for injury"
-MASTITIS_CULL = "culled for mastitis"
-DISEASE_CULL = "culled for disease"
-UDDER_CULL = "culled for udder"
-UNKNOWN_CULL = "culled for unknown"
+ACUTE_SALE_CULL = "culled for acute sale"
 
 # youngstock mortality (a loss from death, not a cull)
 CALF_MORTALITY_LOSS = "died from pre-wean mortality"

RUFAS/biophysical/animal/animal_module_reporter.py

@@ -842,12 +842,7 @@ def report_herd_statistics_data(cls, herd_statistics: HerdStatistics, simulation
         cull_reason_stats_units = {
             animal_constants.DEATH_CULL: MeasurementUnits.UNITLESS,
             animal_constants.OVERSUPPLY_CULL: MeasurementUnits.UNITLESS,
-            animal_constants.LAMENESS_CULL: MeasurementUnits.UNITLESS,
-            animal_constants.INJURY_CULL: MeasurementUnits.UNITLESS,
-            animal_constants.MASTITIS_CULL: MeasurementUnits.UNITLESS,
-            animal_constants.DISEASE_CULL: MeasurementUnits.UNITLESS,
-            animal_constants.UDDER_CULL: MeasurementUnits.UNITLESS,
-            animal_constants.UNKNOWN_CULL: MeasurementUnits.UNITLESS,
+            animal_constants.ACUTE_SALE_CULL: MeasurementUnits.UNITLESS,
         }
         om.add_variable(
             "cull_reason_stats",