def test_total_infected():
params = Params(
total_population=5,
initial_num_E=1,
initial_num_I=0,
initial_num_M=0,
mu_ei=14, # takes a long time for E to goto I
alpha=1.0, # E is very infectivous
beta=0.0
)
params_vac = ParamsVac(
vac_time=1,
vac_count_per_day=2,
gamma=1.0,
s_proba=0.0,
v2_proba=0.0,
v1_proba=1.0, # all go to V1
time_to_take_effect=1,
ev1_to_r_time=100,
**params.kwargs
)
total_days = 5
sim = SimulatorWithVaccination(params_vac, total_days=total_days, verbose=VERBOSE)
sim.run()
assert np.isclose(sim.total_infected, 5) # EV1 should be counted as well
gamma=0.001)
# Issue 3 ends here
p0_time = T('29/11/2019') # set the start time of epidemic
# **Issue 1:**
# the `bed_info` below was for the Wuhan case
# bed_info = pkl.load(open('data/bed_info.pkl', 'rb'))
# to set a fixed value for bed info, use the following
bed_info = [(0, 3000)
] # say there are 3000 beds at the begining of the epidemic
total_days = 90
sim = SimulatorWithVaccination(params, p0_time, total_days, bed_info)
# **Issue 2:**
# the returned variables below store time-dependent statistics
# - total_array: total number of each state on each day
# - delta_array: the delta (change of value of day t w.r.t day t-1) value of each state on each day
# - delta_array: the delta plus (newly incoming population on day t w.r.t day t-1) value of each state on each day
# - trans_array: number of transitions of each transition type (S->E, E->I, etc) on each day
# - stats: some statistics
total_array, delta_array, delta_plus_array, trans_array, stats = sim.run()
# to access the value of some state (say V1) on some variable (say total_array), do the following
total_V1_over_time = total_array[:, sim.state_space.V1]
total_V2_over_time = total_array[:, sim.state_space.V2]
sim.set_state_ids_to_plot(exclude_ids=[sim.state_space.S])
def test_infection_from_E_and_EV1_slower_vaccination():
params = Params(
total_population=5,
initial_num_E=1,
initial_num_I=0,
initial_num_M=0,
mu_ei=14, # takes a long time for E to goto I
alpha=1.0, # E is very infectivous
beta=0.0
)
params_vac = ParamsVac(
vac_time=1,
vac_count_per_day=2,
gamma=1.0,
s_proba=0.0,
v2_proba=0.0,
v1_proba=1.0, # all go to V1
time_to_take_effect=1,
**params.kwargs
)
total_days = 5
sim = SimulatorWithVaccination(params_vac, total_days=total_days, verbose=VERBOSE)
sim.run()
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.S],
[4, 0, 0, 0, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.S],
[4, -4, 0, 0, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.S],
[4, 0, 0, 0, 0, 0]
)
# note that 2 S become E (not tested here)
# check V array
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.V],
[0, 2, 0, 0, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.V],
[0, 2, -2, 0, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.V],
[0, 2, 0, 0, 0, 0]
)
# check V1 array
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.V1],
[0, 0, 2, 0, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.V1],
[0, 0, 2, -2, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.V1],
[0, 0, 2, 0, 0, 0]
)
# check EV1 array
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.EV1],
[0, 0, 0, 2, 2, 2]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.EV1],
[0, 0, 0, 2, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.EV1],
[0, 0, 0, 2, 0, 0]
)
def test_EV1_to_O_slower_vaccination():
"""EV1 must move to O in the end
vaccination is slower (takes 2 batches)
"""
params = Params(
total_population=5,
initial_num_E=1,
initial_num_I=0,
initial_num_M=0,
mu_ei=14, # takes a long time for E to goto I
alpha=1.0, # E is very infectivous
beta=0.0
)
params_vac = ParamsVac(
vac_time=1,
vac_count_per_day=2,
gamma=1.0,
s_proba=0.0,
v2_proba=0.0,
v1_proba=1.0, # all go to V1
time_to_take_effect=1,
ev1_to_r_time=1,
**params.kwargs
)
total_days = 5
sim = SimulatorWithVaccination(params_vac, total_days=total_days, verbose=VERBOSE)
sim.run()
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.S],
[4, 0, 0, 0, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.S],
[4, -4, 0, 0, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.S],
[4, 0, 0, 0, 0, 0]
)
# check V array
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.V],
[0, 2, 0, 0, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.V],
[0, 2, -2, 0, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.V],
[0, 2, 0, 0, 0, 0]
)
# check V1 array
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.V1],
[0, 0, 2, 0, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.V1],
[0, 0, 2, -2, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.V1],
[0, 0, 2, 0, 0, 0]
)
# check EV1 array
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.EV1],
[0, 0, 0, 2, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.EV1],
[0, 0, 0, 2, -2, 0]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.EV1],
[0, 0, 0, 2, 0, 0]
)
# check O array
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.O],
[0, 0, 0, 0, 2, 2]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.O],
[0, 0, 0, 0, 2, 0]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.O],
[0, 0, 0, 0, 2, 0]
)
def test_infection_from_E_and_EV1():
params = Params(
total_population=6,
initial_num_E=1,
initial_num_I=0,
initial_num_M=0,
mu_ei=14, # takes a long time for E to goto I
alpha=10.0, # E is very infectivous
beta=0.0
)
params_vac = ParamsVac(
vac_time=1,
vac_count_per_day=5,
gamma=1.0,
s_proba=0.0,
v2_proba=0.0,
v1_proba=1.0, # all go to V1
time_to_take_effect=1,
**params.kwargs
)
total_days = 3
sim = SimulatorWithVaccination(params_vac, total_days=total_days, verbose=VERBOSE)
assert sim.inf_proba_EV1 == 0.0
sim.run()
sim.update_inf_probas(total_days + 1)
assert sim.inf_proba_EV1 > 0.0
assert sim.inf_proba == 1.0
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.S],
[5, 0, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.S],
[5, -5, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.S],
[5, 0, 0, 0]
)
# check V array
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.V],
[0, 5, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.V],
[0, 5, -5, 0]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.V],
[0, 5, 0, 0]
)
# check V1 array
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.V1],
[0, 0, 5, 0]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.V1],
[0, 0, 5, -5]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.V1],
[0, 0, 5, 0]
)
# check EV1 array
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.EV1],
[0, 0, 0, 5]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.EV1],
[0, 0, 0, 5]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.EV1],
[0, 0, 0, 5]
)
def test_imprefect_vaccination_2(infectiousless_params):
"""test case: no infection + imperfect vaccination (v2_proba < 1)
time for vaccination to take effect is short
note that s_proba > 0 and v1_proba = 0
"""
params_vac = ParamsVac(
vac_time=2,
vac_count_per_day=2,
gamma=0.0,
s_proba=0.5,
v2_proba=0.5,
v1_proba=0.0,
time_to_take_effect=1,
**infectiousless_params.kwargs
)
total_days = 8
sim = SimulatorWithVaccination(params_vac, total_days=total_days, verbose=VERBOSE)
sim.run()
# check S array
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.S],
[5, 5, 3, 2, 1, 1, 1/2, 1/2, 1/4]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.S],
[5, 0, -2, -1, -1, 0, -1/2, 0, -1/4]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.S],
[5, 0, 0, 1, 1, 1, 1/2, 1/2, 1/4]
)
# check V array
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.V],
[0, 0, 2, 2, 2, 1, 1, 1/2, 1/2]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.V],
[0, 0, 2, 0, 0, -1, 0, -1/2, 0]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.V],
[0, 0, 2, 2, 2, 1, 1, 1/2, 1/2]
)
# check V1 array
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.V1],
[0, 0, 0, 0, 0, 0, 0, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.V1],
[0, 0, 0, 0, 0, 0, 0, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.V1],
[0, 0, 0, 0, 0, 0, 0, 0, 0]
)
# check V2 array
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.V2],
[0, 0, 0, 1, 2, 3, 3+1/2, 4, 4+1/4]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.V2],
[0, 0, 0, 1, 1, 1, 1/2, 1/2, 1/4]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.V2],
[0, 0, 0, 1, 1, 1, 1/2, 1/2, 1/4]
)
def test_worst_possible_vaccination_2(infectiousless_params):
"""test case: no infection + worst possible vaccination (s_proba = 1.0)
time for vaccination to take effect is 2 days
"""
params_vac = ParamsVac(
vac_time=2,
vac_count_per_day=2,
gamma=0.0,
s_proba=1.0,
v2_proba=0.0,
v1_proba=0.0,
time_to_take_effect=2,
**infectiousless_params.kwargs
)
total_days = 6
sim = SimulatorWithVaccination(params_vac, total_days=total_days, verbose=VERBOSE)
sim.run()
# check S array
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.S],
[5, 5, 3, 1, 2, 2, 1]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.S],
[5, 0, -2, -2, 1, 0, -1]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.S],
[5, 0, 0, 0, 2, 2, 1]
)
# check V array
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.V],
[0, 0, 2, 4, 3, 3, 4]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.V],
[0, 0, 2, 2, -1, 0, 1]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.V],
[0, 0, 2, 2, 1, 2, 2]
)
# check V1 array
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.V1],
[0, 0, 0, 0, 0, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.V1],
[0, 0, 0, 0, 0, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.V1],
[0, 0, 0, 0, 0, 0, 0]
)
# check V2 array
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.V2],
[0, 0, 0, 0, 0, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.V2],
[0, 0, 0, 0, 0, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.V2],
[0, 0, 0, 0, 0, 0, 0]
)
def test_prefect_vaccination_1(infectiousless_params):
"""test case: no infection + perfect vaccination (v2_proba = 1)
and it takes long for the vaccination to take effect (people stay in V)
"""
params_vac = ParamsVac(
vac_time=2,
vac_count_per_day=2,
gamma=0.0,
s_proba=.0,
v2_proba=1.0,
v1_proba=0.0,
time_to_take_effect=100,
**infectiousless_params.kwargs
)
total_days = 5
sim = SimulatorWithVaccination(params_vac, total_days=total_days, verbose=VERBOSE)
sim.run()
# check S array
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.S],
[5, 5, 3, 1, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.S],
[5, 0, -2, -2, -1, 0]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.S],
[5, 0, 0, 0, 0, 0]
)
# check V array
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.V],
[0, 0, 2, 4, 5, 5]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.V],
[0, 0, 2, 2, 1, 0]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.V],
[0, 0, 2, 2, 1, 0]
)
# check V1 array
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.V1],
[0, 0, 0, 0, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.V1],
[0, 0, 0, 0, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.V1],
[0, 0, 0, 0, 0, 0]
)
# check V2 array
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.V2],
[0, 0, 0, 0, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.V2],
[0, 0, 0, 0, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.V2],
[0, 0, 0, 0, 0, 0]
)
def test_prefect_vaccination_2(infectiousless_params):
"""test case: no infection + perfect vaccination (v2_proba = 1)
time for vaccination to take effec is short
"""
params_vac = ParamsVac(
vac_time=2,
vac_count_per_day=2,
gamma=0.0,
s_proba=.0,
v2_proba=1.0,
v1_proba=0.0,
time_to_take_effect=1,
**infectiousless_params.kwargs
)
total_days = 5
sim = SimulatorWithVaccination(params_vac, total_days=total_days, verbose=VERBOSE)
sim.run()
# check S array
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.S],
[5, 5, 3, 1, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.S],
[5, 0, -2, -2, -1, 0]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.S],
[5, 0, 0, 0, 0, 0]
)
# check V array
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.V],
[0, 0, 2, 2, 1, 0]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.V],
[0, 0, 2, 0, -1, -1]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.V],
[0, 0, 2, 2, 1, 0]
)
# check V1 array
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.V1],
[0, 0, 0, 0, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.V1],
[0, 0, 0, 0, 0, 0]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.V1],
[0, 0, 0, 0, 0, 0]
)
# check V2 array
# basically, V2 is the same as V but shifted by `time_to_take_effect` days
np.testing.assert_almost_equal(
sim.total_array[:, sim.state_space.V2],
[0, 0, 0, 2, 4, 5]
)
np.testing.assert_almost_equal(
sim.delta_array[:, sim.state_space.V2],
[0, 0, 0, 2, 2, 1]
)
np.testing.assert_almost_equal(
sim.delta_plus_array[:, sim.state_space.V2],
[0, 0, 0, 2, 2, 1]
)