Disease States

This module contains tools to manage standard disease states.

class vivarium_public_health.disease.state.BaseDiseaseState(state_id, allow_self_transition=False, side_effect_function=None, cause_type='cause')[source]

Parameters:

state_id (str) –
allow_self_transition (bool) –
side_effect_function (Callable | None) –
cause_type (str) –

property columns_created

Provides names of columns created by the component.

Returns:: Names of the columns created by this component, or an empty list if none.
Return type:: List[str]

property columns_required: List[str] | None

Provides names of columns required by the component.

Returns:: Names of required columns not created by this component. An empty list means all available columns are needed. None means no additional columns are necessary.
Return type:: Optional[List[str]]

property initialization_requirements: Dict[str, List[str]]

Provides the names of all values required by this component during simulant initialization.

Returns:: A dictionary containing the additional requirements of this component during simulant initialization. An omitted key or an empty list for a key implies no requirements for that key during initialization.
Return type:: Dict[str, List[str]]

on_initialize_simulants(pop_data)[source]

Adds this state’s columns to the simulation state table.

Parameters:: pop_data (SimulantData) –
Return type:: None

get_initialization_parameters()[source]

Exclude side effect function and cause type from name and __repr__.

Return type:: Dict[str, Any]

get_initial_event_times(pop_data)[source]

Parameters:: pop_data (SimulantData) –
Return type:: DataFrame

transition_side_effect(index, event_time)[source]

Updates the simulation state and triggers any side effects associated with this state.

Parameters:

index (Index) – An iterable of integer labels for the simulants.
event_time (pandas.Timestamp) – The time at which this transition occurs.

Return type:

None

get_transition_names()[source]

Return type:: List[str]

add_rate_transition(output, get_data_functions=None, triggered=Trigger.NOT_TRIGGERED)[source]

Builds a RateTransition from this state to the given state.

Parameters:

output (BaseDiseaseState) – The end state after the transition.
get_data_functions (Dict[str, Callable]) – map from transition type to the function to pull that transition’s data
triggered –

Returns:

The created transition object.

Return type:

RateTransition

add_proportion_transition(output, get_data_functions=None, triggered=Trigger.NOT_TRIGGERED)[source]

Builds a ProportionTransition from this state to the given state.

Parameters:

output (BaseDiseaseState) – The end state after the transition.
get_data_functions (Dict[str, Callable]) – map from transition type to the function to pull that transition’s data

Returns:

The created transition object.

Return type:

RateTransition

add_dwell_time_transition(output, triggered=Trigger.NOT_TRIGGERED)[source]

Parameters:: output (BaseDiseaseState) –
Return type:: Transition

class vivarium_public_health.disease.state.NonDiseasedState(state_id, allow_self_transition=False, side_effect_function=None, cause_type='cause', name_prefix='')[source]

Parameters:

state_id (str) –
allow_self_transition (bool) –
side_effect_function (Callable | None) –
cause_type (str) –
name_prefix (str) –

add_rate_transition(output, get_data_functions=None, **kwargs)[source]

Builds a RateTransition from this state to the given state.

Parameters:

output (BaseDiseaseState) – The end state after the transition.
get_data_functions (Dict[str, Callable]) – map from transition type to the function to pull that transition’s data
triggered –

Returns:

The created transition object.

Return type:

RateTransition

class vivarium_public_health.disease.state.SusceptibleState(state_id, allow_self_transition=False, side_effect_function=None, cause_type='cause')[source]

Parameters:

state_id (str) –
allow_self_transition (bool) –
side_effect_function (Callable | None) –
cause_type (str) –

class vivarium_public_health.disease.state.RecoveredState(state_id, allow_self_transition=False, side_effect_function=None, cause_type='cause')[source]

Parameters:

state_id (str) –
allow_self_transition (bool) –
side_effect_function (Callable | None) –
cause_type (str) –

class vivarium_public_health.disease.state.DiseaseState(state_id, allow_self_transition=False, side_effect_function=None, cause_type='cause', get_data_functions=None, cleanup_function=None)[source]

State representing a disease in a state machine model.

Parameters:

state_id (str) –
allow_self_transition (bool) –
side_effect_function (Callable | None) –
cause_type (str) –
get_data_functions (Dict[str, Callable]) –
cleanup_function (Callable) –

setup(builder)[source]

Performs this component’s simulation setup.

Parameters:: builder (engine.Builder) – Interface to several simulation tools.
Return type:: None

load_prevalence_data(builder)[source]

Parameters:: builder (Builder) –
Return type:: Number | timedelta | datetime | DataFrame | List[Number | timedelta | datetime] | Tuple[Number | timedelta | datetime]

get_prevalence(builder, prevalence_data)[source]

Builds a LookupTable for the prevalence of this state.

Parameters:

builder (Builder) – Interface to access simulation managers.
prevalence_data (Number | timedelta | datetime | DataFrame | List[Number | timedelta | datetime] | Tuple[Number | timedelta | datetime]) – The data to use to build the LookupTable.

Returns:

The LookupTable for the prevalence of this state.

Return type:

LookupTable

load_birth_prevalence_data(builder)[source]

Parameters:: builder (Builder) –
Return type:: Number | timedelta | datetime | DataFrame | List[Number | timedelta | datetime] | Tuple[Number | timedelta | datetime]

get_birth_prevalence(builder, birth_prevalence_data)[source]

Builds a LookupTable for the birth prevalence of this state.

Parameters:

builder (Builder) – Interface to access simulation managers.
birth_prevalence_data (Number | timedelta | datetime | DataFrame | List[Number | timedelta | datetime] | Tuple[Number | timedelta | datetime]) – The data to use to build the LookupTable.

Returns:

The LookupTable for the birth prevalence of this state.

Return type:

LookupTable

load_dwell_time_data(builder)[source]

Parameters:: builder (Builder) –
Return type:: Number | timedelta | datetime | DataFrame | List[Number | timedelta | datetime] | Tuple[Number | timedelta | datetime]

get_dwell_time_pipeline(builder, dwell_time_data)[source]

Parameters:

builder (Builder) –
dwell_time_data (Number | timedelta | datetime | DataFrame | List[Number | timedelta | datetime] | Tuple[Number | timedelta | datetime]) –

Return type:

Pipeline

load_disability_weight_data(builder)[source]

Parameters:: builder (Builder) –
Return type:: Number | timedelta | datetime | DataFrame | List[Number | timedelta | datetime] | Tuple[Number | timedelta | datetime]

get_base_disability_weight(builder, disability_weight_data)[source]

Builds a LookupTable for the base disability weight of this state.

Parameters:

builder (Builder) – Interface to access simulation managers.
disability_weight_data (Number | timedelta | datetime | DataFrame | List[Number | timedelta | datetime] | Tuple[Number | timedelta | datetime]) – The data to use to build the LookupTable.

Returns:

The LookupTable for the disability weight of this state.

Return type:

LookupTable

get_disability_weight_pipeline(builder)[source]

Parameters:: builder (Builder) –
Return type:: Pipeline

load_excess_mortality_rate_data(builder)[source]

Parameters:: builder (Builder) –
Return type:: Number | timedelta | datetime | DataFrame | List[Number | timedelta | datetime] | Tuple[Number | timedelta | datetime]

get_base_excess_mortality_rate(builder, excess_mortality_data)[source]

Builds a LookupTable for the base excess mortality rate of this state.

Parameters:

builder (Builder) – Interface to access simulation managers.
excess_mortality_data (Number | timedelta | datetime | DataFrame | List[Number | timedelta | datetime] | Tuple[Number | timedelta | datetime]) – The data to use to build the LookupTable.

Returns:

The LookupTable for the base excess mortality rate of this state.

Return type:

LookupTable

get_excess_mortality_rate_pipeline(builder)[source]

Parameters:: builder (Builder) –
Return type:: Pipeline

get_joint_paf(builder)[source]

Parameters:: builder (Builder) –
Return type:: Pipeline

get_randomness_prevalence(builder)[source]

Parameters:: builder (Builder) –
Return type:: RandomnessStream

add_rate_transition(output, get_data_functions=None, **kwargs)[source]

Builds a RateTransition from this state to the given state.

Parameters:

output (BaseDiseaseState) – The end state after the transition.
get_data_functions (Dict[str, Callable]) – map from transition type to the function to pull that transition’s data
triggered –

Returns:

The created transition object.

Return type:

RateTransition

add_dwell_time_transition(output, **kwargs)[source]

Parameters:: output (BaseDiseaseState) –
Return type:: Transition

next_state(index, event_time, population_view)[source]

Moves a population among different disease states.

Parameters:

index (Index) – An iterable of integer labels for the simulants.
event_time (Timestamp) – The time at which this transition occurs.
population_view (PopulationView) – A view of the internal state of the simulation.

Return type:

None

compute_disability_weight(index)[source]

Gets the disability weight associated with this state.

Parameters:: index (Index) – An iterable of integer labels for the simulants.
Returns:: An iterable of disability weights indexed by the provided index.
Return type:: pandas.Series

compute_excess_mortality_rate(index)[source]

Parameters:: index (Index) –
Return type:: Series

adjust_mortality_rate(index, rates_df)[source]

Modifies the baseline mortality rate for a simulant if they are in this state.

Parameters:

index (Index) – An iterable of integer labels for the simulants.
rates_df (pandas.DataFrame) –

Return type:

DataFrame

get_initial_event_times(pop_data)[source]

Parameters:: pop_data (SimulantData) –
Return type:: DataFrame

with_condition(index)[source]

Parameters:: index (Index) –
Return type:: Index

class vivarium_public_health.disease.state.TransientDiseaseState(state_id, allow_self_transition=False, side_effect_function=None, cause_type='cause')[source]

Parameters:

state_id (str) –
allow_self_transition (bool) –
side_effect_function (Callable | None) –
cause_type (str) –