def test_migration(self):
"""
Test for migration
Returns
-------
"""
i1 = Island(ISLE_MAP2)
Herbivore.set_parameters({'mu': 1.0})
Carnivore.set_parameters({'mu': 1.0})
coordinate = (2, 3)
i1.add_animal_island(coordinate, INI_HERB[0]['pop'])
i1.add_animal_island(coordinate, INI_CARN[0]['pop'])
for herbivore in i1.cells[2, 3].herbivores:
herbivore.fitness = 1
for carnivore in i1.cells[2, 3].carnivores:
carnivore.fitness = 1
i1.migration()
# can only move left or down
len_left_herb = len(i1.cells[2, 2].herbivores)
len_down_herb = len(i1.cells[3, 3].herbivores)
len_left_carn = len(i1.cells[2, 2].carnivores)
len_down_carn = len(i1.cells[3, 3].carnivores)
assert (len_down_herb + len_left_herb,
len_left_carn + len_down_carn) == (20, 20)
def test_feed(self, herbivore_list):
carnivore = Carnivore(5, 100)
sorted_list = sorted(herbivore_list, key=lambda var: var.fitness)
length_a = len(sorted_list)
weight_a = carnivore.weight
new_list = carnivore.feed(sorted_list)
length_b = len(new_list)
weight_b = carnivore.weight
assert length_b < length_a
assert weight_a < weight_b
assert weight_b - weight_a <= carnivore.F * carnivore.beta
# Should add tests that changes DeltaPhiMax and checks
# that part of the code
carnivore.set_parameters(DeltaPhiMax=0.5)
carnivore = Carnivore(5, 100)
assert carnivore.fitness > 0.5
sorted_list = sorted(herbivore_list, key=lambda var: var.fitness)
for herbivore in sorted_list:
herbivore.weight = 200
herbivore._compute_fitness = False
herbivore._fitness = 0.0
times_to_eat = len(sorted_list)
herbivores_eaten = 0
while len(sorted_list) > 0:
carnivore.feed(sorted_list)
herbivores_eaten += 1
assert herbivores_eaten == times_to_eat
reset_parameters()
def set_default_animal(self):
"""
Method for resetting parameters for herbivores and carnivores.
Returns
-------
"""
Herbivore.set_parameters(DEFAULT_HERBIVORE_PARAMETERS)
Carnivore.set_parameters(DEFAULT_CARNIVORE_PARAMETERS)
def test_heatmap(self):
"""
Tests that heatmap makes array with correct number of herbivores.
:return:
"""
Carnivore.set_parameters({"gamma": 0, "omega": 0, "mu": 0})
Herbivore.set_parameters({"gamma": 0, "omega": 0, "mu": 0})
initial_herbivores = 80
initial_carnivores = 20
herbivores, carnivores = self.sim.heatmap(self.sim.island.one_year())
nt.assert_equal(initial_carnivores, np.sum(carnivores))
nt.assert_equal(initial_herbivores, np.sum(herbivores))
nt.assert_equal(initial_herbivores, herbivores[2][2])
nt.assert_equal(initial_carnivores, carnivores[4][2])
def set_animal_parameters(self, species, params):
"""
Sets parameter for animals
Parameters
----------
species: object
params: dict
Returns
-------
"""
if species == 'Herbivore':
Herbivore.set_parameters(params)
elif species == 'Carnviore':
Carnivore.set_parameters(params)
def test_animals_must_migrate(self):
"""
Tests that no animals are left in cell after migration
"""
Herbivore.set_parameters({"mu": 1})
Carnivore.set_parameters({"mu": 1})
island = Island(self.geogr_simple)
island.build_map()
island.island[1][1].herbivores = [Herbivore() for _ in range(20)]
island.island[1][1].carnivores = [Carnivore() for _ in range(20)]
for herb in island.island[1][1].herbivores:
herb.fitness = 1
for carn in island.island[1][1].carnivores:
carn.fitness = 1
island.migration()
nt.assert_equal(island.island[1][1].herbivores, [])
nt.assert_equal(island.island[1][1].carnivores, [])
def test_procreation(self):
"""
Test that the number of animals increase
:return:
"""
Herbivore.set_parameters({"gamma": 1})
Carnivore.set_parameters({"gamma": 1})
original = 60
new = 0
self.island.procreation()
for row in self.island.island:
for cell in row:
new += \
cell.number_of_individuals()["herbivores"] + \
cell.number_of_individuals()["carnivores"]
nt.assert_greater(new, original)
nt.assert_less_equal(new, original * 2)
def test_feeding_carnivore_fit(self):
"""
Test for carnivore feeding method, with fit carnivore.
Returns
-------
"""
c1 = Carnivore(1, 3000) # fitness ~= 1
c1.set_parameters({'DeltaPhiMax': 1.00001})
j1 = Jungle()
j1.add_herbivore(5,10)
j1.herbivores[0].fitness = 0
boolean = c1.feeding(j1.herbivores)
c1.set_parameters({'DeltaPhiMax': 10.0}) # default-value
assert c1.weight == 3007.5
assert boolean == [False]
def test_one_year(self):
"""
tests that attributes changes after a year
"""
island = Island(self.geogr_simple)
island.build_map()
Herbivore.set_parameters({"mu": 0})
Carnivore.set_parameters({"mu": 0})
island.island[1][1].herbivores = [Herbivore(40, 5)]
island.island[1][1].carnivores = [Carnivore(20, 5)]
for carnivore in island.island[1][1].carnivores:
carnivore.fitness = 1
for herbivore in island.island[1][1].herbivores:
herbivore.fitness = 1
island.one_year()
nt.assert_equal(island.island[1][1].herbivores[0].age, 6)
nt.assert_equal(island.island[1][1].carnivores[0].age, 6)
nt.assert_not_equal(island.island[1][1].herbivores[0].weight, 40)
nt.assert_not_equal(island.island[1][1].carnivores[0].weight, 20)
def test_feeding_carnivore_appetite(self):
"""
Test for a fit carnivore's feeding method, with low appetite.
Returns
-------
"""
c1 = Carnivore(1, 20)
c1.fitness = 1
c1.set_parameters({'DeltaPhiMax': 1.00001, 'F': 10.0})
j1 = Jungle()
j1.add_herbivore(5,20)
j1.herbivores[0].fitness = 0
boolean = c1.feeding(j1.herbivores)
c1.set_parameters({'DeltaPhiMax': 10.0, 'F': 50.0}) # default-value
assert c1.weight == 27.5
assert boolean == [False]
def test_standard_arguments():
"""
Tests that simulation works without any given arguments.
"""
initial_herbivores = 150
initial_carnivores = 40
sim_ = BioSim()
Carnivore.set_parameters({"gamma": 0, "omega": 0, "mu": 0})
Herbivore.set_parameters({"gamma": 0, "omega": 0, "mu": 1})
for row in sim_.island.island:
for cell in row:
for herb in cell.herbivores:
herb.fitness = 1
sim_.island.migration()
herbivores, carnivores = sim_.heatmap(sim_.island.one_year())
nt.assert_equal(initial_carnivores, np.sum(carnivores))
nt.assert_equal(initial_herbivores, np.sum(herbivores))
nt.assert_equal(initial_carnivores, carnivores[2][2])
def reset_parameters():
herbivore_parameters_right = {
'w_birth': 8.0,
'sigma_birth': 1.5,
'beta': 0.9,
'eta': 0.05,
'a_half': 40.0,
'phi_age': 0.2,
'w_half': 10.0,
'phi_weight': 0.1,
'mu': 0.25,
'lambda_': 1.0,
'gamma': 0.2,
'zeta': 3.5,
'xi': 1.2,
'omega': 0.4,
'F': 10.0
}
carnivore_parameters_right = {
'w_birth': 6.0,
'sigma_birth': 1.0,
'beta': 0.75,
'eta': 0.125,
'a_half': 60.0,
'phi_age': 0.4,
'w_half': 4.0,
'phi_weight': 0.4,
'mu': 0.4,
'lambda_': 1.0,
'gamma': 0.8,
'zeta': 3.5,
'xi': 1.1,
'omega': 0.9,
'F': 50.0,
'DeltaPhiMax': 10.0
}
Carnivore.set_parameters(**carnivore_parameters_right)
Herbivore.set_parameters(**herbivore_parameters_right)
def test_cell_move_herbivore_and_carnivore(self):
"""
Test for moving herbivore and carnivore
Returns
-------
"""
i1 = Island(ISLE_MAP2)
Herbivore.set_parameters({'mu': 1.0})
Carnivore.set_parameters({'mu': 1.0})
coordinate = (2, 3)
i1.add_animal_island(coordinate, INI_HERB[0]['pop'])
i1.add_animal_island(coordinate, INI_CARN[0]['pop'])
for herbivore in i1.cells[2, 3].herbivores:
herbivore.fitness = 1
for carnivore in i1.cells[2, 3].carnivores:
carnivore.fitness = 1
assert len(i1.cells[2, 3].herbivores) == 20
assert len(i1.cells[2, 3].carnivores) == 20
i1.cell_move_herbivores(coordinate)
i1.cell_move_carnivores(coordinate)
assert len(i1.cells[2, 3].herbivores) == 0
assert len(i1.cells[2, 3].carnivores) == 0
# can only move left or down
len_left_herb = len(i1.cells[2, 2].herbivores_new)
len_down_herb = len(i1.cells[3, 3].herbivores_new)
len_left_carn = len(i1.cells[2, 2].carnivores_new)
len_down_carn = len(i1.cells[3, 3].carnivores_new)
assert (len_down_herb + len_left_herb,
len_left_carn + len_down_carn) == (20, 20)
def test_death(self):
"""
Runs multiple times to minimise chance of failure due to all animals
surviving.
:return:
"""
original = 40 * 5
new = 0
test = Island(self.geogr_simple)
test.build_map()
Herbivore.set_parameters({"omega": 1})
Carnivore.set_parameters({"omega": 1})
test.island[1][1].herbivores = [Herbivore() for _ in range(10)]
test.island[1][2].herbivores = [Herbivore() for _ in range(10)]
test.island[1][1].carnivores = [Carnivore() for _ in range(10)]
test.island[1][2].carnivores = [Carnivore() for _ in range(10)]
test.death()
for _ in range(5):
for row in test.island:
for cell in row:
new += \
cell.number_of_individuals()["herbivores"] + \
cell.number_of_individuals()["carnivores"]
nt.assert_less(new, original)
def test_set_parameters(self, carnivore_parameters_right,
carnivore_parameters_wrong):
carnivore = Carnivore(30, 10)
with pytest.raises(TypeError):
carnivore.set_parameters(**carnivore_parameters_wrong)
carnivore.set_parameters(eta=1, phi_age=200)
assert carnivore.eta == 1
assert carnivore.phi_age == 200
carnivore.set_parameters(**carnivore_parameters_right)
assert carnivore.eta == 0.125
assert carnivore.phi_age == 0.4
reset_parameters()
} for _ in range(150)]
}]
ini_carns = [{
'loc': (10, 10),
'pop': [{
'species': 'Carnivore',
'age': 5,
'weight': 20
} for _ in range(40)]
}]
Herbivore.set_parameters({'zeta': 3.2, 'xi': 1.8})
Carnivore.set_parameters({
'a_half': 70,
'phi_age': 0.5,
'omega': 0.3,
'F': 65,
'DeltaPhiMax': 9.
})
landscape.Jungle.set_parameters({'f_max': 700})
sim = biosim.simulation.\
BioSim(island_map=geogr, ini_pop=ini_herbs, seed=123456,
img_dir=biosim.simulation.DEFAULT_GRAPHICS_DIR)
sim.simulate(num_steps=100, vis_steps=1, img_steps=1)
sim.add_population(population=ini_carns)
sim.simulate(num_steps=100, vis_steps=1, img_steps=1)
sim.make_movie()
