def NeonatalSWC_without_incidence(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()
with_condition.allow_self_transitions()
return DiseaseModel(cause, states=[healthy, with_condition])
def IschemicStroke():
susceptible = SusceptibleState('ischemic_stroke')
data_funcs = {'dwell_time': lambda *args: pd.Timedelta(days=28)}
acute_stroke = DiseaseState('acute_ischemic_stroke',
cause_type='sequela',
get_data_functions=data_funcs)
post_stroke = DiseaseState(
'post_ischemic_stroke',
cause_type='sequela',
)
susceptible.allow_self_transitions()
data_funcs = {
'incidence_rate':
lambda _, builder: builder.data.load(
'cause.ischemic_stroke.incidence_rate')
}
susceptible.add_transition(acute_stroke,
source_data_type='rate',
get_data_functions=data_funcs)
acute_stroke.allow_self_transitions()
acute_stroke.add_transition(post_stroke)
post_stroke.allow_self_transitions()
data_funcs = {
'transition_rate':
lambda builder, *_: builder.data.load(
'cause.ischemic_stroke.incidence_rate')
}
post_stroke.add_transition(acute_stroke,
source_data_type='rate',
get_data_functions=data_funcs)
return DiseaseModel('ischemic_stroke',
states=[susceptible, acute_stroke, post_stroke])
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)
post_mi = DiseaseState(
'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 = {
'transition_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)
return DiseaseModel('ischemic_heart_disease',
states=[susceptible, acute_mi, post_mi])
def SI(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()
return DiseaseModel(cause, states=[healthy, infected])
def setup(self, builder):
healthy = SusceptibleState(self.cause)
infected = DementiaExcessMortalityState()
healthy.allow_self_transitions()
healthy.add_transition(infected, source_data_type='rate')
infected.allow_self_transitions()
builder.components.add_components([DiseaseModel(self.cause, states=[healthy, infected])])
def DiabetesMellitus():
susceptible = SusceptibleState(project_globals.DIABETES_MELLITUS.name)
transient = TransientDiseaseState(project_globals.DIABETES_MELLITUS.name)
moderate = DiseaseState(
f'moderate_{project_globals.DIABETES_MELLITUS.name}',
cause_type='sequela',
)
severe = DiseaseState(
f'severe_{project_globals.DIABETES_MELLITUS.name}',
cause_type='sequela',
)
# Self transitions
susceptible.allow_self_transitions()
moderate.allow_self_transitions()
severe.allow_self_transitions()
# Transitions from Susceptible
susceptible.add_transition(transient, source_data_type='rate')
# Transitions from Transient
data_funcs = {
'proportion':
lambda _, builder: builder.data.load(project_globals.DIABETES_MELLITUS.
MODERATE_DIABETES_PROPORTION)
}
transient.add_transition(moderate,
source_data_type='proportion',
get_data_functions=data_funcs)
data_funcs = {
'proportion':
lambda _, builder: builder.data.load(project_globals.DIABETES_MELLITUS.
SEVERE_DIABETES_PROPORTION)
}
transient.add_transition(severe,
source_data_type='proportion',
get_data_functions=data_funcs)
# Remission transitions
data_funcs = {
'transition_rate':
lambda builder, *_: builder.data.load(project_globals.DIABETES_MELLITUS
.REMISSION_RATE)
}
moderate.add_transition(susceptible,
source_data_type='rate',
get_data_functions=data_funcs)
severe.add_transition(susceptible,
source_data_type='rate',
get_data_functions=data_funcs)
return DiabetesDiseaseModel(
project_globals.DIABETES_MELLITUS.name,
states=[susceptible, transient, moderate, severe])
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 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])