Adding non-predation mortality and semelparity to the Animal Module.

tests/conftest.py

@@ -191,41 +191,47 @@ def fixture_config():
         taxa = "bird"
         diet = "carnivore"
         metabolic_type = "endothermic"
+        reproductive_type = "iteroparous"
         birth_mass = 0.1
         adult_mass = 1.0
         [[animals.functional_groups]]
         name = "herbivorous_bird"
         taxa = "bird"
         diet = "herbivore"
         metabolic_type = "endothermic"
+        reproductive_type = "iteroparous"
         birth_mass = 0.05
         adult_mass = 0.5
         [[animals.functional_groups]]
         name = "carnivorous_mammal"
         taxa = "mammal"
         diet = "carnivore"
         metabolic_type = "endothermic"
+        reproductive_type = "iteroparous"
         birth_mass = 4.0
         adult_mass = 40.0
         [[animals.functional_groups]]
         name = "herbivorous_mammal"
         taxa = "mammal"
         diet = "herbivore"
         metabolic_type = "endothermic"
+        reproductive_type = "iteroparous"
         birth_mass = 1.0
         adult_mass = 10.0
         [[animals.functional_groups]]
         name = "carnivorous_insect"
         taxa = "insect"
         diet = "carnivore"
         metabolic_type = "ectothermic"
+        reproductive_type = "semelparous"
         birth_mass = 0.001
         adult_mass = 0.01
         [[animals.functional_groups]]
         name = "herbivorous_insect"
         taxa = "insect"
         diet = "herbivore"
         metabolic_type = "ectothermic"
+        reproductive_type = "iteroparous"
         birth_mass = 0.0005
         adult_mass = 0.005
         """

tests/core/data/all_config.toml

@@ -36,6 +36,7 @@ diet = "carnivore"
 metabolic_type = "endothermic"
 birth_mass = 0.1
 adult_mass = 1.0
+reproductive_type = "iteroparous"
 
 [[animals.functional_groups]]
 name = "herbivorous_bird"
@@ -44,6 +45,7 @@ diet = "herbivore"
 metabolic_type = "endothermic"
 birth_mass = 0.05
 adult_mass = 0.5
+reproductive_type = "iteroparous"
 
 [[animals.functional_groups]]
 name = "carnivorous_mammal"
@@ -52,6 +54,7 @@ diet = "carnivore"
 metabolic_type = "endothermic"
 birth_mass = 4.0
 adult_mass = 40.0
+reproductive_type = "iteroparous"
 
 [[animals.functional_groups]]
 name = "herbivorous_mammal"
@@ -60,6 +63,7 @@ diet = "herbivore"
 metabolic_type = "endothermic"
 birth_mass = 1.0
 adult_mass = 10.0
+reproductive_type = "iteroparous"
 
 [[animals.functional_groups]]
 name = "carnivorous_insect"
@@ -68,6 +72,7 @@ diet = "carnivore"
 metabolic_type = "ectothermic"
 birth_mass = 0.001
 adult_mass = 0.01
+reproductive_type = "iteroparous"
 
 [[animals.functional_groups]]
 name = "herbivorous_insect"
@@ -76,3 +81,4 @@ diet = "herbivore"
 metabolic_type = "ectothermic"
 birth_mass = 0.0005
 adult_mass = 0.005
+reproductive_type = "semelparous"

tests/models/animals/data/example_functional_group_import.csv

@@ -1,7 +1,9 @@
-name,taxa,diet,metabolic_type,birth_mass,adult_mass
-carnivorous_bird,bird,carnivore,endothermic,0.1,1.0
-herbivorous_bird,bird,herbivore,endothermic,0.05,0.5
-carnivorous_mammal,mammal,carnivore,endothermic,4.0,40.0
-herbivorous_mammal,mammal,herbivore,endothermic,1.0,10.0
-carnivorous_insect,insect,carnivore,ectothermic,0.001,0.01
-herbivorous_insect,insect,herbivore,ectothermic,0.0005,0.005
+name,taxa,diet,metabolic_type,reproductive_type,birth_mass,adult_mass
+carnivorous_bird,bird,carnivore,endothermic,iteroparous,0.1,1.0
+herbivorous_bird,bird,herbivore,endothermic,iteroparous,0.05,0.5
+carnivorous_mammal,mammal,carnivore,endothermic,iteroparous,4.0,40.0
+herbivorous_mammal,mammal,herbivore,endothermic,iteroparous,1.0,10.0
+carnivorous_insect_iteroparous,insect,carnivore,ectothermic,iteroparous,0.001,0.01
+herbivorous_insect_iteroparous,insect,herbivore,ectothermic,iteroparous,0.0005,0.005
+carnivorous_insect_semelparous,insect,carnivore,ectothermic,semelparous,0.001,0.01
+herbivorous_insect_semelparous,insect,herbivore,ectothermic,semelparous,0.0005,0.005

tests/models/animals/test_animal_cohorts.py

@@ -1015,3 +1015,131 @@ def test_migrate_juvenile_probability(
         assert (
             probability_of_dispersal == expected_probability
         ), "The probability calculated did not match the expected probability."
+
+    @pytest.mark.parametrize(
+        "is_mature, u_bg, lambda_se, t_to_maturity, t_since_maturity, lambda_max, J_st,"
+        "zeta_st, mass_current, mass_max, dt, expected_dead",
+        [
+            pytest.param(
+                True,
+                0.001,
+                0.003,
+                365,
+                30,
+                1.0,
+                0.6,
+                0.05,
+                600,
+                600,
+                30,
+                13,
+                id="mature_with_all_mortalities",
+            ),
+            pytest.param(
+                False,
+                0.001,
+                0.003,
+                365,
+                30,
+                1.0,
+                0.6,
+                0.05,
+                600,
+                600,
+                30,
+                4,
+                id="immature_without_senescence",
+            ),
+        ],
+    )
+    def test_inflict_non_predation_mortality(
+        self,
+        mocker,
+        is_mature,
+        u_bg,
+        lambda_se,
+        t_to_maturity,
+        t_since_maturity,
+        lambda_max,
+        J_st,
+        zeta_st,
+        mass_current,
+        mass_max,
+        dt,
+        expected_dead,
+        predator_cohort_instance,
+        carcass_pool_instance,
+    ):
+        """Test the calculation of total non-predation mortality in a cohort."""
+        from math import ceil, exp
+
+        import virtual_ecosystem.models.animals.scaling_functions as sf
+
+        # Use the predator cohort instance and set initial individuals to 100
+        cohort = predator_cohort_instance
+        cohort.individuals = 100  # Set initial individuals count
+        cohort.is_mature = is_mature
+        cohort.mass_current = mass_current
+        cohort.time_to_maturity = t_to_maturity
+        cohort.time_since_maturity = t_since_maturity
+        cohort.functional_group.adult_mass = mass_max
+
+        # Mocking the mortality functions to return predefined values
+        mocker.patch(
+            "virtual_ecosystem.models.animals.scaling_functions.background_mortality",
+            return_value=u_bg,
+        )
+        mocker.patch(
+            "virtual_ecosystem.models.animals.scaling_functions.senescence_mortality",
+            return_value=(
+                lambda_se * exp(t_since_maturity / t_to_maturity) if is_mature else 0.0
+            ),
+        )
+        mocker.patch(
+            "virtual_ecosystem.models.animals.scaling_functions.starvation_mortality",
+            return_value=(
+                lambda_max
+                / (1 + exp((mass_current - J_st * mass_max) / (zeta_st * mass_max)))
+            ),
+        )
+
+        # Diagnostics
+        print(f"Initial individuals: {cohort.individuals}")
+
+        # Run the method
+        cohort.inflict_non_predation_mortality(dt, carcass_pool_instance)
+
+        # Calculate expected number of deaths inside the test
+        u_bg_value = sf.background_mortality(u_bg)
+        u_se_value = (
+            sf.senescence_mortality(lambda_se, t_to_maturity, t_since_maturity)
+            if is_mature
+            else 0.0
+        )
+        u_st_value = sf.starvation_mortality(
+            lambda_max, J_st, zeta_st, mass_current, mass_max
+        )
+        u_t = u_bg_value + u_se_value + u_st_value
+
+        number_dead = ceil(100 * (1 - exp(-u_t * dt)))
+
+        # Diagnostics
+        print(
+            f"background: {u_bg_value},"
+            f"senescence: {u_se_value},"
+            f"starvation: {u_st_value}"
+        )
+        print(f"Calculated total mortality rate: {u_t}")
+        print(
+            f"Calculated number dead: {number_dead},"
+            f"Expected number dead: {expected_dead}"
+        )
+        print(
+            f"Remaining individuals: {cohort.individuals},"
+            f"Expected remaining: {100 - expected_dead}"
+        )
+
+        # Verify
+        assert (
+            cohort.individuals == 100 - expected_dead
+        ), "The calculated number of dead individuals doesn't match the expected value."