def SIS(cause: str) -> DiseaseModel:
healthy = SusceptibleState(cause)
infected = DiseaseState(cause)
healthy.allow_self_transitions()
healthy.add_transition(infected, source_data_type='rate')
infected.allow_self_transitions()
infected.add_transition(healthy, source_data_type='rate')
return DiseaseModel(cause, states=[healthy, infected])
def SIS_fixed_duration(cause: str, duration: str) -> DiseaseModel:
duration = pd.Timedelta(days=float(duration) // 1, hours=(float(duration) % 1) * 24.0)
healthy = SusceptibleState(cause)
infected = DiseaseState(cause, get_data_functions={'dwell_time': lambda _, __: duration})
healthy.allow_self_transitions()
healthy.add_transition(infected, source_data_type='rate')
infected.add_transition(healthy)
infected.allow_self_transitions()
return DiseaseModel(cause, states=[healthy, infected])
def NeonatalSIS(cause):
with_condition_data_functions = {'birth_prevalence':
lambda cause, builder: builder.data.load(f"cause.{cause}.birth_prevalence")}
healthy = SusceptibleState(cause)
with_condition = DiseaseState(cause, get_data_functions=with_condition_data_functions)
healthy.allow_self_transitions()
healthy.add_transition(with_condition, source_data_type='rate')
with_condition.allow_self_transitions()
with_condition.add_transition(healthy, source_data_type='rate')
return DiseaseModel(cause, states=[healthy, with_condition])
def test_dwell_time(assign_cause_mock, base_config, base_plugins, disease,
base_data):
time_step = 10
assign_cause_mock.side_effect = lambda population, *args: pd.DataFrame(
{'condition_state': 'healthy'}, index=population.index)
base_config.update(
{
'time': {
'step_size': time_step
},
'population': {
'population_size': 10
}
}, **metadata(__file__))
healthy_state = BaseDiseaseState('healthy')
data_function = base_data(0)
data_function['dwell_time'] = lambda _, __: pd.Timedelta(days=28)
data_function['disability_weight'] = lambda _, __: 0.0
event_state = DiseaseState('event', get_data_functions=data_function)
done_state = BaseDiseaseState('sick')
healthy_state.add_transition(event_state)
event_state.add_transition(done_state)
model = DiseaseModel(disease,
initial_state=healthy_state,
states=[healthy_state, event_state, done_state])
simulation = InteractiveContext(components=[TestPopulation(), model],
configuration=base_config,
plugin_configuration=base_plugins)
# Move everyone into the event state
simulation.step()
event_time = simulation._clock.time
assert np.all(simulation.get_population()[disease] == 'event')
simulation.step()
simulation.step()
# Not enough time has passed for people to move out of the event state, so they should all still be there
assert np.all(simulation.get_population()[disease] == 'event')
simulation.step()
# Now enough time has passed so people should transition away
assert np.all(simulation.get_population()[disease] == 'sick')
assert np.all(simulation.get_population().event_event_time ==
pd.to_datetime(event_time))
assert np.all(simulation.get_population().event_event_count == 1)
def Stroke(stroke_name):
stroke_types = [
'ischemic_stroke', 'subarachnoid_hemorrhage',
'intracerebral_hemorrhage'
]
if stroke_name not in stroke_types:
raise ValueError(
f'Stroke name must be one of {stroke_types}. You supplied {stroke_name}'
)
susceptible = SusceptibleState(stroke_name)
data_funcs = {'dwell_time': lambda *args: pd.Timedelta(days=28)}
acute = DiseaseState(f'acute_{stroke_name}',
cause_type='sequela',
get_data_functions=data_funcs)
#data_funcs = {'dwell_time': lambda *args: pd.Timedelta(days=365.25)}
post = RelapseState(f'post_{stroke_name}', cause_type='sequela')
susceptible.allow_self_transitions()
data_funcs = {
'incidence_rate':
lambda _, builder: builder.data.load(
f'cause.{stroke_name}.incidence_rate')
}
susceptible.add_transition(acute,
source_data_type='rate',
get_data_functions=data_funcs)
acute.allow_self_transitions()
acute.add_transition(post)
post.allow_self_transitions()
data_funcs = {
'relapse_rate':
lambda _, builder: builder.data.load(
f'cause.{stroke_name}.incidence_rate')
}
post.add_transition(acute,
source_data_type='rate',
get_data_functions=data_funcs)
#post.add_transition(susceptible, source_data_type='time')
return DiseaseModel(stroke_name, states=[susceptible, acute, post])
def IschemicHeartDisease():
susceptible = SusceptibleState('ischemic_heart_disease')
data_funcs = {'dwell_time': lambda *args: pd.Timedelta(days=28)}
acute_mi = DiseaseState('acute_myocardial_infarction',
cause_type='sequela',
get_data_functions=data_funcs)
#data_funcs = {'dwell_time': lambda *args: pd.Timedelta(days=365.25)}
post_mi = RelapseState(
'post_myocardial_infarction',
cause_type='sequela',
)
susceptible.allow_self_transitions()
data_funcs = {
'incidence_rate':
lambda _, builder: builder.data.load(
'cause.ischemic_heart_disease.incidence_rate')
}
susceptible.add_transition(acute_mi,
source_data_type='rate',
get_data_functions=data_funcs)
acute_mi.allow_self_transitions()
acute_mi.add_transition(post_mi)
post_mi.allow_self_transitions()
data_funcs = {
'relapse_rate':
lambda _, builder: builder.data.load(
'cause.ischemic_heart_disease.incidence_rate')
}
post_mi.add_transition(acute_mi,
source_data_type='rate',
get_data_functions=data_funcs)
#post_mi.add_transition(susceptible, source_data_type='time')
return DiseaseModel('ischemic_heart_disease',
states=[susceptible, acute_mi, post_mi])
def test_dwell_time_with_mortality(base_config, base_plugins, disease):
year_start = base_config.time.start.year
year_end = base_config.time.end.year
time_step = 10
pop_size = 100
base_config.update(
{
'time': {
'step_size': time_step
},
'population': {
'population_size': pop_size
}
}, **metadata(__file__))
healthy_state = BaseDiseaseState('healthy')
mort_get_data_funcs = {
'dwell_time':
lambda _, __: pd.Timedelta(days=14),
'excess_mortality_rate':
lambda _, __: build_table(0.7, year_start - 1, year_end),
'disability_weight':
lambda _, __: 0.0
}
mortality_state = DiseaseState('event',
get_data_functions=mort_get_data_funcs)
done_state = BaseDiseaseState('sick')
healthy_state.add_transition(mortality_state)
mortality_state.add_transition(done_state)
model = DiseaseModel(disease,
initial_state=healthy_state,
states=[healthy_state, mortality_state, done_state])
mortality = Mortality()
simulation = InteractiveContext(
components=[TestPopulation(), model, mortality],
configuration=base_config,
plugin_configuration=base_plugins)
# Move everyone into the event state
simulation.step()
assert np.all(simulation.get_population()[disease] == 'event')
simulation.step()
# Not enough time has passed for people to move out of the event state, so they should all still be there
assert np.all(simulation.get_population()[disease] == 'event')
simulation.step()
# Make sure some people have died and remained in event state
assert (simulation.get_population()['alive'] == 'alive').sum() < pop_size
assert ((simulation.get_population()['alive'] == 'dead').sum() == (
simulation.get_population()[disease] == 'event').sum())
# enough time has passed so living people should transition away to sick
assert ((simulation.get_population()['alive'] == 'alive').sum() == (
simulation.get_population()[disease] == 'sick').sum())