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
Modifier('trans_traced_1', 'rel_days', trans_traced_1_time, contact_traced_fraction,
trans_traced_0, trans_traced_1, enabled=False, model=bc_model))
# vaccination start
n_vacc_periods = 6
for i in range(n_vacc_periods):
j = i+1
vaccination_time = Parameter('vacc_time_'+str(j), 75+i, 0, 600,
'first day of vaccination period '+str(j),
parameter_type='int')
vaccination_number = Parameter('vacc_number_'+str(j), 10., 0., 5000000.,
'change in number vaccinated each day for period '+str(j))
bc_model.add_transition(
Injector('vaccination_'+str(j), 'rel_days', vaccination_time, daily_vaccinated_pop,
vaccination_number, enabled=False, model=bc_model))
# outbreaks
outbreak_pop = Population('outbreaks', 0,
'Infection outbreaks')
outbreak_1_time = Parameter('outbreak_1_time', 14, 0, 600,
'number of days since t0 when outbreak_1 established',
parameter_type='int', hidden=False)
outbreak_1_number = Parameter('outbreak_1_number', 10., 0., 50000.,
'number of infections in outbreak_1',
hidden=False)
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',
parameter_type='int', hidden=False)
outbreak_1_number = Parameter('outbreak_1_number', 10., 0., 50000.,
'number of infections in outbreak_1',
hidden=False)
bc_model.add_transition(
Injector('outbreak_1', 'rel_days', outbreak_1_time, outbreak_pop,
outbreak_1_number, enabled=False, model=bc_model))
outbreak_fraction = Parameter('outbreak_frac', 1., 0., 1.,
'fraction of infected in outbreak active ==1')
outbreak_delay_pars = {
'mean': Parameter('outbreak_delay_mean', 7., 0., 50.,
'mean delay time for outbreak', hidden=False),
'sigma': Parameter('outbreak_delay_sigma', 1., 0.01, 20.,
'standard deviation of outbreak times',
hidden=False)
}
outbreak_delay = Delay('outbreak_delay', 'norm', outbreak_delay_pars, bc_model)
bc_model.add_connector(
Propagator('outbreaks to infected', outbreak_pop, infected_pop,
outbreak_fraction, outbreak_delay))
'number of days since t0 when outbreak_1 established',
parameter_type='int',
hidden=False)
outbreak_1_number = Parameter('outbreak_1_number',
10.,
0.,
50000.,
'number of infections in outbreak_1',
hidden=False)
bc_model.add_transition(
Injector('outbreak_1',
'rel_days',
outbreak_1_time,
outbreak_pop,
outbreak_1_number,
enabled=False,
model=bc_model))
outbreak_fraction = Parameter('outbreak_frac', 1., 0., 1.,
'fraction of infected in outbreak active ==1')
outbreak_delay_pars = {
'mean':
Parameter('outbreak_delay_mean',
7.,
0.,
50.,
'mean delay time for outbreak',
hidden=False),
'sigma':