sensitivity analysis branch

README.md

@@ -1,9 +1,10 @@
-[![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-96%25-brightgreen)](https://github.com/RuminantFarmSystems/MASM/actions/workflows/combined_format_lint_test_mypy.yml)
+[![Flake8](https://img.shields.io/badge/Flake8-failed-red)](https://github.com/RuminantFarmSystems/MASM/actions/workflows/combined_format_lint_test_mypy.yml)
+[![Pytest](https://img.shields.io/badge/Pytest-failed-red)](https://github.com/RuminantFarmSystems/MASM/actions/workflows/combined_format_lint_test_mypy.yml)
+[![Coverage](https://img.shields.io/badge/Coverage-%25-red)](https://github.com/RuminantFarmSystems/MASM/actions/workflows/combined_format_lint_test_mypy.yml)
 [![Mypy](https://img.shields.io/badge/Mypy-3453%20errors-red)](https://github.com/RuminantFarmSystems/MASM/actions/workflows/combined_format_lint_test_mypy.yml)
 
 
+
 # Vision
 To support research and sustainable decision-making in ruminant animal production through a state-of-the-art, open-source modeling environment that is continuously adapting as technology and scientific knowledge advance.
 

RUFAS/routines/animal/animal_manager.py

@@ -549,7 +549,7 @@ def _calc_max_animal_spaces_per_pen(cls, num_stalls: int, max_stocking_density:
         if num_stalls < 0 or max_stocking_density < 0:
             raise ValueError("The number of stalls and maximum stocking density must be greater than or equal to 0.")
 
-        return int(num_stalls * max_stocking_density)
+        return max(int(num_stalls * max_stocking_density), 1)
 
     @classmethod
     def _calc_animal_space_shortage(cls, num_animals: int, pens: List[Pen]) -> int:

RUFAS/routines/animal/life_cycle/cow.py

@@ -390,7 +390,7 @@ def milking_update(self, sim_day: int, calving_interval: int | float) -> None:
         Journal of Dairy Science, Volume 105, Issue 9, 2022,
         Pages 7525-7538, ISSN 0022-0302.
         """
-        if self.days_in_preg == AnimalBase.config["days_in_preg_when_dry"]:
+        if self.days_in_preg >= AnimalBase.config["days_in_preg_when_dry"]:
             self.milking = False
             self.events.add_event(self.days_born, sim_day, const.DRY)
             self.days_in_milk = 0
@@ -716,9 +716,13 @@ def get_bw_change(self, CI: int | float) -> float:  # noqa
                 if self.days_in_preg == AnimalBase.config["days_in_preg_when_dry"] - 1:
                     self.tissue_changed = 40 * self.days_in_milk / 70 * math.exp(1 - self.days_in_milk / 70)
         else:  # dry period
-            bodyweight_tissue = self.tissue_changed / (
-                self.gestation_length - AnimalBase.config["days_in_preg_when_dry"]
-            )
+            # TODO
+            try:
+                bodyweight_tissue = self.tissue_changed / (
+                    self.gestation_length - AnimalBase.config["days_in_preg_when_dry"]
+                )
+            except Exception as e:
+                bodyweight_tissue = 0.0
 
         return target_adg_cow + conceptus_growth + bodyweight_tissue
 
@@ -748,7 +752,7 @@ def update(self, sim_day: int, calving_interval: int | float) -> bool:  # noqa
         new_born = False
         self.days_born += 1
 
-        if self.days_in_preg > 0 and self.days_in_preg == self.gestation_length:
+        if self.days_in_preg > 0 and self.days_in_preg >= self.gestation_length:
             self._repro_state_manager.reset()
             self.calves += 1
             self.milking = True

RUFAS/routines/animal/life_cycle/heiferIII.py

@@ -183,7 +183,7 @@ def update(self, sim_day: int) -> bool:
             self.body_weight = self.mature_body_weight
             self.events.add_event(self.days_born, sim_day, const.MATURE_BODY_WEIGHT_REGULAR)
 
-        if self.days_in_preg == self.gestation_length:
+        if self.days_in_preg >= self.gestation_length:
             self.days_born -= 1  # will be incremented again in next stage
             cow_stage = True
         return cow_stage

RUFAS/routines/animal/life_cycle/life_cycle.py

@@ -337,7 +337,7 @@ def daily_update(
         self._calculate_cull_reason_stats_percent()
         self._calculate_percent_cow_per_parity()
 
-        self.daily_milk_production = sum(cow.estimated_daily_milk_produced for cow in cows)
+        self.daily_milk_production = max(1.0, sum(cow.estimated_daily_milk_produced for cow in cows))
         self.dry_cows_daily_milk_production = sum(cow.estimated_daily_milk_produced for cow in cows if not cow.milking)
         self.herd_milk_fat_kg = sum(cow.milk_fat_kg for cow in cows if cow.milking)
         self.herd_milk_fat_percent = (self.herd_milk_fat_kg / self.daily_milk_production) * 100

RUFAS/util.py

@@ -72,6 +72,8 @@ def flatten_keys_to_nested_structure(input_dict: Dict[str, Any]) -> Dict[str, An
                         current.append([] if next_key_is_digit else {})
                     current = current[key]
                 else:
+                    if key.startswith("numberaskey"):
+                        key = key.replace("numberaskey", "")
                     if isinstance(current, list):
                         current = current[-1]
                     if key not in current:

helpful_scripts/get_runtime.py

@@ -0,0 +1,22 @@
+"""
+This script simply checks the runtimes for all simulations that have been run.
+Useful for benchmarking when running large batches of simulations, especially sensitivity analyses.
+"""
+
+import json
+import os
+
+import numpy as np
+
+logs_dir = "output/logs/"
+
+logs_files = [log_file for log_file in os.listdir(logs_dir) if "logs" in log_file and "benchmark" in log_file]
+
+run_times = []
+
+for log_file in logs_files:
+    with open(logs_dir + log_file) as log_fp:
+        log_dict = json.load(log_fp)
+        run_times.append(float(log_dict["SimulationEngine.simulate.total_simulation_time"]["values"][0].split(": ")[1]))
+
+print(np.mean(run_times))

input/data/animal/default_animal_100x.json

@@ -0,0 +1,202 @@
+{
+  "herd_information": {
+    "calf_num": 800,
+    "heiferI_num": 4400,
+    "heiferII_num": 3800,
+    "heiferIII_num_springers": 500,
+    "cow_num": 10000,
+    "replace_num": 50000,
+    "herd_num": 10000,
+    "breed": "HO",
+    "parity_fractions": {
+      "1": 0.386,
+      "2": 0.281,
+      "3": 0.333
+    },
+    "annual_milk_yield": null
+  },
+  "herd_initialization": {
+    "initial_animal_num": 10000,
+    "simulation_days": 5000
+  },
+  "animal_config": {
+    "management_decisions": {
+      "breeding_start_day_h": 380,
+      "heifer_repro_method": "ED",
+      "cow_repro_method": "ED-TAI",
+      "semen_type": "conventional",
+      "days_in_preg_when_dry": 218,
+      "heifer_repro_cull_time": 500,
+      "do_not_breed_time": 185,
+      "cull_milk_production": 30,
+      "cow_times_milked_per_day": 3,
+	    "milk_fat_percent": 4,
+	    "milk_protein_percent": 3.2
+    },
+    "farm_level": {
+      "calf": {
+        "male_calf_rate_sexed_semen": 0.1,
+        "male_calf_rate_conventional_semen": 0.53,
+        "keep_female_calf_rate": 1,
+        "wean_day": 60,
+        "wean_length": 7,
+        "milk_type": "whole"
+      },
+      "repro": {
+        "voluntary_waiting_period": 50,
+        "conception_rate_decrease": 0.026,
+        "decrease_conception_rate_in_rebreeding": false,
+        "decrease_conception_rate_by_parity": false,
+        "avg_gestation_len": 276,
+        "std_gestation_len": 6,
+        "prefresh_day": 21,
+        "calving_interval": 400,
+        "heifers": {
+            "estrus_detection_rate": 0.9,
+            "estrus_conception_rate": 0.6,
+            "repro_sub_protocol": "5dCG2P",
+            "repro_sub_properties": {
+                "conception_rate": 0.6,
+                "estrus_detection_rate": 0.9
+            }
+        },
+        "cows": {
+            "estrus_detection_rate": 0.6,
+            "ED_conception_rate": 0.5,
+            "presynch_program": "Double OvSynch",
+            "presynch_program_start_day": 50,
+            "ovsynch_program": "OvSynch 56",
+            "ovsynch_program_start_day": 64,
+            "ovsynch_program_conception_rate": 0.6,
+            "resynch_program": "TAIafterPD"
+        }
+			},
+			"bodyweight": {
+				"birth_weight_avg_ho": 43.9,
+				"birth_weight_std_ho": 1,
+				"birth_weight_avg_je": 27.2,
+				"birth_weight_std_je": 1,
+				"target_heifer_preg_day": 399,
+				"mature_body_weight_avg": 740.1,
+				"mature_body_weight_std": 73.5
+			}
+		},
+		"from_literature": {
+			"repro": {
+				"preg_check_day_1": 32,
+				"preg_loss_rate_1": 0.02,
+				"preg_check_day_2": 60,
+				"preg_loss_rate_2": 0.096,
+				"preg_check_day_3": 200,
+				"preg_loss_rate_3": 0.017,
+				"avg_estrus_cycle_return": 23,
+				"std_estrus_cycle_return": 6,
+				"avg_estrus_cycle_heifer": 21,
+				"std_estrus_cycle_heifer": 2.5,
+				"avg_estrus_cycle_cow": 21,
+				"std_estrus_cycle_cow": 4,
+				"avg_estrus_cycle_after_pgf": 5,
+				"std_estrus_cycle_after_pgf": 2
+			},
+			"culling": {
+				"cull_day_count": [0, 5, 15, 45, 90, 135, 180, 225, 270, 330, 380, 430, 480, 530],
+				"feet_leg_cull": {
+					"probability": 0.1633,
+					"cull_day_prob": [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": 0.2883,
+					"cull_day_prob": [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": 0.2439,
+					"cull_day_prob": [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": 0.1391,
+					"cull_day_prob": [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": 0.0645,
+					"cull_day_prob": [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": 0.1009,
+					"cull_day_prob": [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_death_prob": [0.039,0.056,0.085,0.117],
+				"parity_cull_prob": [0.169, 0.233, 0.301, 0.408],
+				"death_day_prob": [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]
+			},
+			"life_cycle": {
+				"still_birth_rate": 0.065
+			}
+		}
+	},
+	"methane_mitigation": {
+		"methane_mitigation_method": "None",
+		"methane_mitigation_additive_amount": 0,
+		"3-NOP_additive_amount": 70,
+		"monensin_additive_amount": 24,
+		"essential_oils_additive_amount": 0,
+		"seaweed_additive_amount": 0
+	},
+	"housing": "barn",
+	"pasture_concentrate": 0,
+	"methane_model": "IPCC",
+	"ration": {
+		"phosphorus_requirement_buffer": 0,
+		"user_input": false,
+		"formulation_interval": 30
+	},
+	"pen_information": [
+		{
+			"id": 0,
+			"pen_name": "",
+			"animal_combination": "CALF",
+			"vertical_dist_to_milking_parlor": 0.1,
+			"horizontal_dist_to_milking_parlor": 10,
+			"number_of_stalls": 3000,
+			"housing_type": "open air barn",
+			"pen_type": "freestall",
+			"max_stocking_density": 1.2,
+			"manure_management_scenario_id": 0
+		},
+		{
+			"id": 1,
+			"pen_name": "",
+			"animal_combination": "GROWING",
+			"vertical_dist_to_milking_parlor": 0.1,
+			"horizontal_dist_to_milking_parlor": 10,
+			"number_of_stalls": 12500,
+			"housing_type": "open air barn",
+			"pen_type": "freestall",
+			"max_stocking_density": 1.2,
+			"manure_management_scenario_id": 1
+		},
+		{
+			"id": 2,
+			"pen_name": "",
+			"animal_combination": "CLOSE_UP",
+			"vertical_dist_to_milking_parlor": 0.1,
+			"horizontal_dist_to_milking_parlor": 10,
+			"number_of_stalls": 6000,
+			"housing_type": "open air barn",
+			"pen_type": "freestall",
+			"max_stocking_density": 1.2,
+			"manure_management_scenario_id": 2
+		},
+		{
+			"id": 3,
+			"pen_name": "",
+			"animal_combination": "LAC_COW",
+			"vertical_dist_to_milking_parlor": 0.1,
+			"horizontal_dist_to_milking_parlor": 10,
+			"number_of_stalls": 15000,
+			"housing_type": "open air barn",
+			"pen_type": "freestall",
+			"max_stocking_density": 1.2,
+			"manure_management_scenario_id": 5
+		}
+	]
+}