def test_class_Injector():
"""tests to ensure the behaviour class Injector"""
test_model = Model('test_model')
number = 50.
inject = Parameter('inject', number, parameter_min=0., parameter_max=1000.)
time = 5
trans_time = Parameter('time', time, parameter_type='int', parameter_min=0, parameter_max=1000)
to_pop = Population('to_pop', 0)
test_injector = Injector('injector', 'rel_days', trans_time, to_pop, inject, model=test_model)
test_model.add_transition(test_injector)
for time_step in [1., 1. / 4.]:
test_model.set_time_step(time_step)
to_pop.reset()
test_injector.take_action()
assert to_pop.future[0] == number
assert np.abs(test_injector.trigger_step - time / time_step) < 0.1
def test_class_Modifier():
"""tests to ensure the behaviour class Modifier"""
test_model = Model('test_model')
mod_time = Parameter('time', 5, parameter_type='int', parameter_min=0, parameter_max=1000)
par_val = 0.3
par_0_val = 0.5
par_1_val = 0.7
parameter = Parameter('par', par_val)
parameter_0 = Parameter('par_0', par_0_val)
parameter_1 = Parameter('par_1', par_1_val)
test_modifier = Modifier('test_modifier', 'rel_days', mod_time, parameter, parameter_0, parameter_1,
model=test_model)
test_model.add_transition(test_modifier)
for time_step in [1., 1. / 4.]:
test_model.set_time_step(time_step)
parameter.reset()
assert parameter.get_value() == par_val
test_modifier.take_action()
assert parameter.get_value() == par_1_val
test_modifier.reset()
assert parameter.get_value() == par_0_val
assert np.abs(test_modifier.trigger_step - 5 / time_step) < 0.1
n_rt_visible = 4
times = []
alphas = [Parameter('alpha_0', 0.4, 0., 2.,
'initial transmission rate', hidden=False)]
for i in range(n_rate_transitions):
j = i+1
hidden = j > n_rt_visible
enabled = i==0
times.append(Parameter('trans_rate_'+str(j)+'_time', 20+i, 0, 600,
'day of trans rate change '+'str(j)',
parameter_type='int', hidden=hidden))
alphas.append(Parameter('alpha_'+str(j), 0.1, 0., 2.,
'alpha after transition '+str(j), hidden=hidden))
bc_model.add_transition(
Modifier('trans_rate_'+str(j), 'rel_days', times[i], trans_rate,
alphas[i], alphas[j], enabled=enabled, model=bc_model))
n_rate_transitions = 4
n_rt_visible = 0
times_v = []
alphas_v = [Parameter('alpha_0_v', 0.4, 0., 2.,
'initial variant transmission rate', hidden=False)]
for i in range(n_rate_transitions):
j = i+1
hidden = j > n_rt_visible
enabled = False
times_v.append(Parameter('trans_rate_'+str(j)+'_time_v', 20+i, 0, 600,
'day of variant trans rate change '+'str(j)',
parameter_type='int', hidden=hidden))
'transmission rate after 5th transition')
trans_rate_6 = Parameter('alpha_6', 0.1, 0., 2.,
'transmission rate after 6th transition')
trans_rate_7 = Parameter('alpha_7', 0.1, 0., 2.,
'transmission rate after 7th transition')
trans_rate_8 = Parameter('alpha_8', 0.1, 0., 2.,
'transmission rate after 8th transition')
bc_model.add_transition(
Modifier('trans_rate_1',
'rel_days',
trans_rate_1_time,
trans_rate,
trans_rate_0,
trans_rate_1,
enabled=True,
model=bc_model))
bc_model.add_transition(
Modifier('trans_rate_2',
'rel_days',
trans_rate_2_time,
trans_rate,
trans_rate_1,
trans_rate_2,
enabled=False,
model=bc_model))
parameter_type='int', hidden=False)
trans_rate_0 = Parameter('alpha_0', 0.385, 0., 2.,
'initial transmission rate', hidden=False)
trans_rate_1 = Parameter('alpha_1', 0.062, 0., 2.,
'transmission rate after 1st transition', hidden=False)
trans_rate_2 = Parameter('alpha_2', 0.062, 0., 2.,
'transmission rate after 2nd transition', hidden=False)
trans_rate_3 = Parameter('alpha_3', 0.062, 0., 2.,
'transmission rate after 3nd transition', hidden=False)
bc_model.add_transition(
Modifier('trans_rate_1', 'rel_days', trans_rate_1_time, trans_rate,
trans_rate_0, trans_rate_1, enabled=True, model=bc_model))
bc_model.add_transition(
Modifier('trans_rate_2', 'rel_days', trans_rate_2_time, trans_rate,
trans_rate_1, trans_rate_2, enabled=False, model=bc_model))
bc_model.add_transition(
Modifier('trans_rate_3', 'rel_days', trans_rate_3_time, trans_rate,
trans_rate_2, trans_rate_3, enabled=False, model=bc_model))
outbreak_pop = Population('outbreaks', 0,
'Infection outbreaks')
outbreak_1_time = Parameter('outbreak_1_time', 14, 0, 100,
'number of days since t0 when outbreak_1 established',
0.,
2.,
'transmission rate after 4th transition',
hidden=False)
trans_rate_5 = Parameter('alpha_5', 0.1, 0., 2.,
'transmission rate after 5th transition')
trans_rate_6 = Parameter('alpha_6', 0.1, 0., 2.,
'transmission rate after 6th transition')
bc_model.add_transition(
Modifier('trans_rate_1',
'rel_days',
trans_rate_1_time,
trans_rate,
trans_rate_0,
trans_rate_1,
enabled=True,
model=bc_model))
bc_model.add_transition(
Modifier('trans_rate_2',
'rel_days',
trans_rate_2_time,
trans_rate,
trans_rate_1,
trans_rate_2,
enabled=False,
model=bc_model))
2.,
'transmission rate after 2nd transition',
hidden=False)
trans_rate_3 = Parameter('alpha_3',
0.062,
0.,
2.,
'transmission rate after 3nd transition',
hidden=False)
bc_model.add_transition(
Modifier('trans_rate_1',
'rel_days',
trans_rate_1_time,
trans_rate,
trans_rate_0,
trans_rate_1,
enabled=True,
model=bc_model))
bc_model.add_transition(
Modifier('trans_rate_2',
'rel_days',
trans_rate_2_time,
trans_rate,
trans_rate_1,
trans_rate_2,
enabled=False,
model=bc_model))
