def test__init__(self):
region_name = 'London'
age_groups = ['0-10', '10-25']
contact_data_matrix = np.array([[10, 5.2], [0, 3]])
region_data_matrix = np.array([[0.5, 1.2], [0.29, 6]])
pop_size = [18, 2]
dI = 4
contacts = em.ContactMatrix(age_groups, contact_data_matrix)
regional = em.RegionMatrix(region_name, age_groups, region_data_matrix)
next_gen = em.UniNextGenMatrix(pop_size, contacts, regional, dI)
self.assertEqual(next_gen.region, 'London')
npt.assert_array_equal(next_gen.ages, np.array(['0-10', '10-25']))
npt.assert_array_equal(next_gen.susceptibles, np.array([18, 2]))
npt.assert_array_equal(next_gen.contacts, contact_data_matrix)
npt.assert_array_equal(next_gen.regional_suscep, region_data_matrix)
self.assertEqual(next_gen.infection_period, 4)
pdt.assert_frame_equal(
next_gen.get_next_gen_matrix(),
pd.DataFrame(data=np.array([[360, 449.28], [0, 144]]),
index=['0-10', '10-25'],
columns=['0-10', '10-25']))
with self.assertRaises(TypeError):
em.UniNextGenMatrix(pop_size, 0, regional, dI)
with self.assertRaises(TypeError):
em.UniNextGenMatrix(pop_size, contacts, 0, dI)
with self.assertRaises(ValueError):
new_age_groups = ['0-15', '15-25']
regional1 = em.RegionMatrix(region_name, new_age_groups,
region_data_matrix)
em.UniNextGenMatrix(pop_size, contacts, regional1, dI)
with self.assertRaises(TypeError):
em.UniNextGenMatrix(pop_size, contacts, regional, '4')
with self.assertRaises(ValueError):
em.UniNextGenMatrix(pop_size, contacts, regional, 0)
with self.assertRaises(ValueError):
em.UniNextGenMatrix([[1], [2]], contacts, regional, dI)
with self.assertRaises(ValueError):
em.UniNextGenMatrix([0, 1, 1], contacts, regional, dI)
with self.assertRaises(ValueError):
em.UniNextGenMatrix([0, -1], contacts, regional, dI)
with self.assertRaises(TypeError):
em.UniNextGenMatrix([0, '1'], contacts, regional, dI)
def test__init__(self):
region_name = 'London'
age_groups = ['0-10', '10-25']
# Initial state of the system
contact_data_matrix_0 = np.array([[10, 0], [0, 3]])
region_data_matrix_0 = np.array([[0.5, 0], [0, 6]])
init_pop_size = [1, 2]
dI = 4
contacts_0 = em.ContactMatrix(age_groups, contact_data_matrix_0)
regional_0 = em.RegionMatrix(region_name, age_groups,
region_data_matrix_0)
next_gen_0 = em.UniNextGenMatrix(init_pop_size, contacts_0, regional_0,
dI)
initial_r = 0.5
infect = em.UniInfectivityMatrix(initial_r,
initial_nextgen_matrix=next_gen_0)
self.assertEqual(infect.r0, 0.5)
self.assertEqual(infect.r0_star, 144)
with self.assertRaises(TypeError):
em.UniInfectivityMatrix('0', initial_nextgen_matrix=next_gen_0)
with self.assertRaises(TypeError):
em.UniInfectivityMatrix(initial_r, initial_nextgen_matrix=0)
def test_compute_reproduction_number(self):
region_name = 'London'
age_groups = ['0-10', '10-25']
# Initial state of the system
contact_data_matrix_0 = np.array([[10, 0], [0, 3]])
region_data_matrix_0 = np.array([[0.5, 0], [0, 6]])
init_pop_size = [1, 2]
dI = 4
contacts_0 = em.ContactMatrix(age_groups, contact_data_matrix_0)
regional_0 = em.RegionMatrix(region_name, age_groups,
region_data_matrix_0)
next_gen_0 = em.UniNextGenMatrix(init_pop_size, contacts_0, regional_0,
dI)
# Later time state of the system
contact_data_matrix_1 = np.array([[10, 5.2], [0, 3]])
region_data_matrix_1 = np.array([[0.5, 1.2], [0.29, 6]])
current_pop_size = [18, 2]
contacts_1 = em.ContactMatrix(age_groups, contact_data_matrix_1)
regional_1 = em.RegionMatrix(region_name, age_groups,
region_data_matrix_1)
next_gen_1 = em.UniNextGenMatrix(current_pop_size, contacts_1,
regional_1, dI)
initial_r = 0.5
temp_variation = 1
infect = em.UniInfectivityMatrix(initial_r,
initial_nextgen_matrix=next_gen_0)
self.assertEqual(
infect.compute_reproduction_number(temp_variation, next_gen_1),
5 / 4)
with self.assertRaises(TypeError):
infect.compute_reproduction_number('1', next_gen_1)
with self.assertRaises(TypeError):
infect.compute_reproduction_number(temp_variation, 0)
def test_compute_dom_eigenvalue(self):
region_name = 'London'
age_groups = ['0-10', '10-25']
contact_data_matrix = np.array([[10, 0], [0, 3]])
region_data_matrix = np.array([[0.5, 0], [0, 6]])
pop_size = [1, 2]
dI = 4
contacts = em.ContactMatrix(age_groups, contact_data_matrix)
regional = em.RegionMatrix(region_name, age_groups, region_data_matrix)
next_gen = em.UniNextGenMatrix(pop_size, contacts, regional, dI)
self.assertEqual(next_gen.compute_dom_eigenvalue(), 144)