Index

Symbols

--artifact_path simulate-run command line option --pdb simulate-run command line option --quiet simulate-run command line option --results_directory simulate-run command line option --verbose simulate-run command line option

-i simulate-run command line option -o simulate-run command line option -q simulate-run command line option -v simulate-run command line option

A

add() (vivarium.engine.framework.components.manager.OrderedComponentSet method) add_components() (vivarium.engine.framework.components.manager.ComponentManager method) (vivarium.engine.framework.engine.SimulationContext method) add_constraint() (vivarium.engine.framework.lifecycle.interface.LifeCycleInterface method) (vivarium.engine.framework.lifecycle.manager.LifeCycleManager method) add_handlers() (vivarium.engine.framework.lifecycle.entities.LifeCycleState method) (vivarium.engine.framework.lifecycle.interface.LifeCycleInterface method) (vivarium.engine.framework.lifecycle.manager.LifeCycleManager method) add_managers() (vivarium.engine.framework.components.manager.ComponentManager method) add_next() (vivarium.engine.framework.lifecycle.entities.LifeCyclePhase method) (vivarium.engine.framework.lifecycle.entities.LifeCycleState method) add_phase() (vivarium.engine.framework.lifecycle.entities.LifeCycle method) (vivarium.engine.framework.lifecycle.manager.LifeCycleManager method) add_private_columns() (vivarium.engine.framework.resource.interface.ResourceInterface method) (vivarium.engine.framework.resource.manager.ResourceManager method) add_resource() (vivarium.engine.framework.resource.interface.ResourceInterface method) (vivarium.engine.framework.resource.manager.ResourceManager method) add_results() (vivarium.engine.framework.results.observation.AddingObservation static method) add_states() (vivarium.engine.framework.state_machine.Machine method)

add_stratification() (vivarium.engine.framework.results.context.ResultsContext method) add_transition() (vivarium.engine.framework.state_machine.State method) AddingObservation (class in vivarium.engine.framework.results.observation) addition_combiner() (in module vivarium.engine.framework.values.combiners) aggregator (vivarium.engine.framework.results.observation.AddingObservation attribute) (vivarium.engine.framework.results.observation.StratifiedObservation attribute) aggregator_sources (vivarium.engine.framework.results.observation.AddingObservation attribute) (vivarium.engine.framework.results.observation.StratifiedObservation attribute) allow_null_transition (vivarium.engine.framework.state_machine.TransitionSet attribute) append() (vivarium.engine.framework.state_machine.TransitionSet method) apply_configuration_defaults() (vivarium.engine.framework.components.manager.ComponentManager method) ArtifactInterface (class in vivarium.engine.framework.artifact.interface) ArtifactManager (class in vivarium.engine.framework.artifact.manager) Attribute Attribute Pipeline AttributePipeline (class in vivarium.engine.framework.values.pipeline) AttributePostProcessor (class in vivarium.engine.framework.values.post_processors) attributes (vivarium.engine.framework.values.pipeline.AttributesValueSource attribute) AttributesValueSource (class in vivarium.engine.framework.values.pipeline)

B

build_lookup_table() (vivarium.engine.component.Component method) build_model_specification() (in module vivarium.engine.framework.configuration) build_simulation_configuration() (in module vivarium.engine.framework.configuration) build_table() (in module vivarium.engine.testing_utilities) (vivarium.engine.framework.lookup.interface.LookupTableInterface method) (vivarium.engine.framework.lookup.manager.LookupTableManager method)

Builder (class in vivarium.engine.framework.engine) builder_interface (vivarium.engine.framework.plugins.PluginGroup attribute)

C

categorical_parameters (vivarium.engine.framework.lookup.interpolation.Interpolation attribute) categories (vivarium.engine.framework.results.stratification.Stratification attribute) check_data_complete() (in module vivarium.engine.framework.lookup.interpolation) check_valid_state() (vivarium.engine.framework.lifecycle.constraint_maker.ConstraintMaker method) choice() (vivarium.engine.framework.randomness.stream.RandomnessStream method) choose_new_state() (vivarium.engine.framework.state_machine.TransitionSet method) cleanup() (vivarium.engine.framework.state_machine.Machine method) cleanup_effect() (vivarium.engine.framework.state_machine.State method) clock (vivarium.engine.framework.randomness.stream.RandomnessStream attribute) clock() (vivarium.engine.framework.time.interface.TimeInterface method) collapse_nested_dict() (in module vivarium.engine.framework.utilities) COLLECT_METRICS (in module vivarium.engine.framework.lifecycle.lifecycle_states) collect_metrics_priority (vivarium.engine.component.Component property) Column (class in vivarium.engine.framework.resource.resource) column_name (vivarium.engine.framework.values.pipeline.PrivateColumnValueSource attribute) combine_queries() (in module vivarium.engine.framework.population.utilities) combiner (vivarium.engine.framework.values.pipeline.Pipeline property) Component (class in vivarium.engine.component) component (vivarium.engine.framework.resource.resource.Resource property) ComponentConfigError ComponentConfigurationParser (class in vivarium.engine.framework.components.parser) ComponentInterface (class in vivarium.engine.framework.components.interface) ComponentManager (class in vivarium.engine.framework.components.manager) components (vivarium.engine.framework.engine.Builder attribute) concatenate_results() (vivarium.engine.framework.results.observation.ConcatenatingObservation static method) ConcatenatingObservation (class in vivarium.engine.framework.results.observation) Configuration configuration (vivarium.engine.framework.components.manager.ComponentManager property) (vivarium.engine.framework.engine.Builder attribute)

CONFIGURATION_DEFAULTS (vivarium.engine.component.Component attribute) configuration_defaults (vivarium.engine.component.Component property) CONFIGURATION_DEFAULTS (vivarium.engine.framework.artifact.manager.ArtifactManager attribute) (vivarium.engine.framework.lookup.manager.LookupTableManager attribute) (vivarium.engine.framework.population.manager.PopulationManager attribute) (vivarium.engine.framework.randomness.manager.RandomnessManager attribute) (vivarium.engine.framework.results.manager.ResultsManager attribute) configuration_defaults (vivarium.engine.framework.results.observer.Observer property) (vivarium.engine.framework.state_machine.State property) CONFIGURATION_DEFAULTS (vivarium.engine.framework.time.manager.DateTimeClock attribute) (vivarium.engine.framework.time.manager.SimpleClock attribute) (vivarium.engine.manager.Manager attribute) configuration_defaults (vivarium.engine.manager.Manager property) CONFIGURATION_DEFAULTS (vivarium.engine.testing_utilities.NonCRNTestPopulation attribute) configure_logging() (vivarium.engine.framework.logging.manager.LoggingManager method) configure_logging_to_file() (in module vivarium.engine.framework.logging.utilities) configure_logging_to_terminal() (in module vivarium.engine.framework.logging.utilities) constrain_normal_method() (vivarium.engine.framework.lifecycle.constraint_maker.ConstraintMaker method) ConstraintError ConstraintMaker (class in vivarium.engine.framework.lifecycle.constraint_maker) continuous_parameters (vivarium.engine.framework.lookup.interpolation.Interpolation attribute) controller (vivarium.engine.framework.plugins.PluginGroup attribute) create_component_from_string() (vivarium.engine.framework.components.parser.ComponentConfigurationParser method) create_empty_df() (vivarium.engine.framework.results.observation.UnstratifiedObservation static method) create_expanded_df() (vivarium.engine.framework.results.observation.StratifiedObservation method) creation_time (vivarium.engine.framework.population.manager.SimulantData attribute) creation_window (vivarium.engine.framework.population.manager.SimulantData attribute) current_state (vivarium.engine.framework.lifecycle.manager.LifeCycleManager property) current_state() (vivarium.engine.framework.lifecycle.interface.LifeCycleInterface method) current_time (vivarium.engine.framework.engine.SimulationContext property) (vivarium.engine.interface.interactive.InteractiveContext property)

D

data (vivarium.engine.framework.engine.Builder attribute) (vivarium.engine.framework.lookup.interpolation.Interpolation attribute) (vivarium.engine.framework.lookup.interpolation.Order0Interp attribute) (vivarium.engine.framework.lookup.table.LookupTable attribute)

DateTimeClock (class in vivarium.engine.framework.time.manager) DEFAULT_EVENT_PRIORITY (in module vivarium.engine.component) default_probability_function() (in module vivarium.engine.framework.state_machine) default_stratifications (vivarium.engine.framework.results.context.ResultsContext attribute) DynamicValueError

E

emit() (vivarium.engine.framework.event.manager.EventChannel method) enter() (vivarium.engine.framework.lifecycle.entities.LifeCycleState method) entrance_count (vivarium.engine.framework.lifecycle.entities.LifeCycleState property) Event (class in vivarium.engine.framework.event.manager) event (vivarium.engine.framework.engine.Builder attribute) event_time (vivarium.engine.framework.time.manager.SimulationClock property) EventChannel (class in vivarium.engine.framework.event.manager)

EventInterface (class in vivarium.engine.framework.event.interface) EventManager (class in vivarium.engine.framework.event.manager) excluded_categories (vivarium.engine.framework.results.context.ResultsContext attribute) (vivarium.engine.framework.results.stratification.Stratification attribute) extend() (vivarium.engine.framework.state_machine.TransitionSet method) extract_columns_from_query() (in module vivarium.engine.framework.population.utilities) extrapolate (vivarium.engine.framework.lookup.interpolation.Order0Interp attribute)

F

filter_data() (in module vivarium.engine.framework.artifact.manager) filter_for_probability() (vivarium.engine.framework.randomness.stream.RandomnessStream method)

filter_for_rate() (vivarium.engine.framework.randomness.stream.RandomnessStream method) finalize() (vivarium.engine.framework.engine.SimulationContext method) from_yearly() (in module vivarium.engine.framework.utilities)

G

gather_results() (vivarium.engine.framework.results.context.ResultsContext method) (vivarium.engine.framework.results.manager.ResultsManager method) get() (vivarium.engine.framework.population.population_view.PopulationView method) get_active_simulants() (vivarium.engine.framework.time.manager.SimulationClock method) get_all_attribute_names() (vivarium.engine.framework.population.manager.PopulationManager method) get_attribute() (vivarium.engine.framework.values.manager.ValuesManager method) get_attribute_names() (vivarium.engine.interface.interactive.InteractiveContext method) get_attribute_pipelines() (vivarium.engine.framework.values.interface.ValuesInterface method) (vivarium.engine.framework.values.manager.ValuesManager method) get_base_filter_terms() (in module vivarium.engine.framework.artifact.manager) get_callable_name() (vivarium.engine.framework.resource.resource.Resource static method) get_channel() (vivarium.engine.framework.event.manager.EventManager method) get_complete_stratified_results() (vivarium.engine.framework.results.observation.StratifiedObservation method) get_component() (vivarium.engine.framework.components.interface.ComponentInterface method) (vivarium.engine.framework.components.manager.ComponentManager method) (vivarium.engine.interface.interactive.InteractiveContext method) get_component_config_parser() (vivarium.engine.framework.plugins.PluginManager method) get_components() (vivarium.engine.framework.components.parser.ComponentConfigurationParser method) get_components_by_type() (vivarium.engine.framework.components.interface.ComponentInterface method) (vivarium.engine.framework.components.manager.ComponentManager method) get_configuration() (vivarium.engine.component.Component method) (vivarium.engine.framework.results.observer.Observer method) get_configuration_name() (vivarium.engine.framework.results.observer.Observer method) get_current_component() (vivarium.engine.framework.components.interface.ComponentInterface method) (vivarium.engine.framework.components.manager.ComponentManager method) get_current_component_or_manager() (vivarium.engine.framework.components.interface.ComponentInterface method) (vivarium.engine.framework.components.manager.ComponentManager method) get_data() (vivarium.engine.component.Component method) get_draw() (vivarium.engine.framework.randomness.stream.RandomnessStream method) get_emitter() (vivarium.engine.framework.event.interface.EventInterface method) (vivarium.engine.framework.event.manager.EventManager method) (vivarium.engine.interface.interactive.InteractiveContext method) get_filtered_index() (vivarium.engine.framework.population.population_view.PopulationView method) get_frame() (vivarium.engine.framework.population.population_view.PopulationView method) get_graph() (vivarium.engine.framework.resource.manager.ResourceManager method) get_hash() (in module vivarium.engine.framework.randomness.stream) get_initialization_parameters() (vivarium.engine.component.Component method) (vivarium.engine.framework.state_machine.Machine method) get_interface_from_name() (vivarium.engine.framework.plugins.PluginManager method) get_interface_name() (vivarium.engine.framework.plugins.PluginManager method) get_interface_type_from_name() (vivarium.engine.framework.plugins.PluginManager method) get_listeners() (vivarium.engine.framework.event.manager.EventManager method) (vivarium.engine.interface.interactive.InteractiveContext method) get_logger() (vivarium.engine.framework.logging.interface.LoggingInterface method) (vivarium.engine.framework.logging.manager.LoggingManager method) get_manager_name() (vivarium.engine.framework.plugins.PluginManager method) get_manager_type_from_name() (vivarium.engine.framework.plugins.PluginManager method) get_mapped_col_name() (in module vivarium.engine.framework.results.stratification)

get_name() (vivarium.engine.framework.lookup.table.LookupTable static method) get_number_of_steps_remaining() (vivarium.engine.framework.engine.SimulationContext method) get_observations() (vivarium.engine.framework.results.context.ResultsContext method) get_optional_controllers() (vivarium.engine.framework.plugins.PluginManager method) get_optional_interfaces() (vivarium.engine.framework.plugins.PluginManager method) get_original_col_name() (in module vivarium.engine.framework.results.stratification) get_output_model_name_string() (in module vivarium.engine.interface.utilities) get_output_root() (in module vivarium.engine.interface.utilities) get_performance_metrics() (vivarium.engine.framework.engine.SimulationContext method) get_plugin() (vivarium.engine.framework.plugins.PluginManager method) get_plugin_from_name() (vivarium.engine.framework.plugins.PluginManager method) get_plugin_interface() (vivarium.engine.framework.plugins.PluginManager method) get_population() (vivarium.engine.framework.population.manager.PopulationManager method) (vivarium.engine.interface.interactive.InteractiveContext method) get_population_index() (vivarium.engine.framework.population.interface.PopulationInterface method) (vivarium.engine.framework.population.manager.PopulationManager method) get_population_initializers() (vivarium.engine.framework.resource.interface.ResourceInterface method) (vivarium.engine.framework.resource.manager.ResourceManager method) get_private_column_names() (vivarium.engine.framework.population.manager.PopulationManager method) get_private_columns() (vivarium.engine.framework.population.manager.PopulationManager method) get_randomness() (in module vivarium.engine.testing_utilities) get_randomness_stream() (vivarium.engine.framework.randomness.manager.RandomnessManager method) get_required_attributes() (vivarium.engine.framework.results.context.ResultsContext method) get_resource_id() (vivarium.engine.framework.resource.resource.Resource class method) get_results() (vivarium.engine.framework.engine.SimulationContext method) (vivarium.engine.framework.results.manager.ResultsManager method) get_results_of_interest() (vivarium.engine.framework.results.observation.ConcatenatingObservation method) get_seed() (vivarium.engine.framework.randomness.interface.RandomnessInterface method) (vivarium.engine.framework.randomness.manager.RandomnessManager method) get_simulant_creator() (vivarium.engine.framework.population.interface.PopulationInterface method) (vivarium.engine.framework.population.manager.PopulationManager method) get_state() (vivarium.engine.framework.lifecycle.entities.LifeCycle method) (vivarium.engine.framework.lifecycle.entities.LifeCyclePhase method) get_state_names() (vivarium.engine.framework.lifecycle.entities.LifeCycle method) (vivarium.engine.framework.lifecycle.manager.LifeCycleManager method) get_stratifications() (vivarium.engine.framework.results.context.ResultsContext method) get_stream() (vivarium.engine.framework.randomness.interface.RandomnessInterface method) get_time_stamp() (in module vivarium.engine.framework.time.manager) get_tracked_query() (vivarium.engine.framework.population.interface.PopulationInterface method) (vivarium.engine.framework.population.manager.PopulationManager method) get_value() (vivarium.engine.framework.values.interface.ValuesInterface method) (vivarium.engine.framework.values.manager.ValuesManager method) (vivarium.engine.interface.interactive.InteractiveContext method) get_value_modifier() (vivarium.engine.framework.values.pipeline.Pipeline method) get_value_pipelines() (vivarium.engine.framework.values.manager.ValuesManager method) get_view() (vivarium.engine.framework.population.interface.PopulationInterface method) (vivarium.engine.framework.population.manager.PopulationManager method) grouped_observations (vivarium.engine.framework.results.context.ResultsContext attribute)

H

handle_exceptions() (in module vivarium.engine.framework.utilities)

has_initialization_weights() (vivarium.engine.framework.state_machine.State method)

I

import_and_instantiate_component() (vivarium.engine.framework.components.parser.ComponentConfigurationParser static method) import_by_path() (in module vivarium.engine.framework.utilities) include_untracked (vivarium.engine.framework.results.interface.PopulationFilter attribute) index (vivarium.engine.framework.event.manager.Event attribute) (vivarium.engine.framework.population.manager.SimulantData attribute) index_map (vivarium.engine.framework.randomness.stream.RandomnessStream attribute) IndexMap (class in vivarium.engine.framework.randomness.index_map) INITIALIZATION (in module vivarium.engine.framework.lifecycle.lifecycle_states) initialize() (vivarium.engine.framework.population.population_view.PopulationView method) initialize_individual_clock() (vivarium.engine.framework.time.manager.SimulationClock method) initialize_population() (vivarium.engine.testing_utilities.NonCRNTestPopulation method) (vivarium.engine.testing_utilities.TestPopulation method) initialize_simulants() (vivarium.engine.framework.engine.SimulationContext method) initialize_state() (vivarium.engine.framework.state_machine.Machine method)

Initializer (class in vivarium.engine.framework.resource.resource) initializer (vivarium.engine.framework.resource.resource.Initializer attribute) initializes_crn_attributes (vivarium.engine.framework.randomness.stream.RandomnessStream attribute) InteractiveContext (class in vivarium.engine.interface.interactive) InteractiveError Interface (class in vivarium.engine.manager) Interpolation (class in vivarium.engine.framework.lookup.interpolation) interpolation (vivarium.engine.framework.lookup.table.LookupTable attribute) InvalidTransitionError is_simple (vivarium.engine.framework.values.pipeline.AttributePipeline property) is_stratified() (vivarium.engine.framework.results.observation.Observation class method) (vivarium.engine.framework.results.observation.StratifiedObservation class method) (vivarium.engine.framework.results.observation.UnstratifiedObservation class method) is_vectorized (vivarium.engine.framework.results.stratification.Stratification attribute)

K

key (vivarium.engine.framework.randomness.stream.RandomnessStream attribute)

key_columns (vivarium.engine.framework.lookup.table.LookupTable attribute)

L

LifeCycle (class in vivarium.engine.framework.lifecycle.entities) lifecycle (vivarium.engine.framework.engine.Builder attribute) LifeCycleError LifeCycleInterface (class in vivarium.engine.framework.lifecycle.interface) LifeCycleManager (class in vivarium.engine.framework.lifecycle.manager) LifeCyclePhase (class in vivarium.engine.framework.lifecycle.entities) LifeCycleState (class in vivarium.engine.framework.lifecycle.entities) list_combiner() (in module vivarium.engine.framework.values.combiners) list_components() (vivarium.engine.framework.components.interface.ComponentInterface method) (vivarium.engine.framework.components.manager.ComponentManager method) (vivarium.engine.interface.interactive.InteractiveContext method) list_events() (vivarium.engine.framework.event.manager.EventManager method) (vivarium.engine.interface.interactive.InteractiveContext method) list_loggers() (in module vivarium.engine.framework.logging.utilities)

list_values() (vivarium.engine.interface.interactive.InteractiveContext method) load() (vivarium.engine.framework.artifact.interface.ArtifactInterface method) (vivarium.engine.framework.artifact.manager.ArtifactManager method) load_from_backup() (vivarium.engine.framework.engine.SimulationContext class method) log_progress() (in module vivarium.engine.interface.utilities) logger (vivarium.engine.component.Component property) (vivarium.engine.framework.results.context.ResultsContext attribute) logging (vivarium.engine.framework.engine.Builder attribute) LoggingInterface (class in vivarium.engine.framework.logging.interface) LoggingManager (class in vivarium.engine.framework.logging.manager) lookup (vivarium.engine.framework.engine.Builder attribute) lookup_table_value_columns (vivarium.engine.component.Component property) LookupTable (class in vivarium.engine.framework.lookup.table) LookupTableInterface (class in vivarium.engine.framework.lookup.interface) LookupTableManager (class in vivarium.engine.framework.lookup.manager)

M

Machine (class in vivarium.engine.framework.state_machine) Manager (class in vivarium.engine.manager) manager (vivarium.engine.framework.values.pipeline.Pipeline property) mapper (vivarium.engine.framework.results.stratification.Stratification attribute) metadata() (in module vivarium.engine.testing_utilities) Metrics minimum_step_size (vivarium.engine.framework.time.manager.SimulationClock property) MissingValueSource (class in vivarium.engine.framework.values.pipeline) model (vivarium.engine.framework.state_machine.State property) Model Specification MODEL_SPECIFICATION simulate-run command line option module vivarium.engine vivarium.engine.component vivarium.engine.exceptions vivarium.engine.framework vivarium.engine.framework.artifact vivarium.engine.framework.artifact.interface vivarium.engine.framework.artifact.manager vivarium.engine.framework.components vivarium.engine.framework.components.interface vivarium.engine.framework.components.manager vivarium.engine.framework.components.parser vivarium.engine.framework.configuration vivarium.engine.framework.engine vivarium.engine.framework.event vivarium.engine.framework.event.interface vivarium.engine.framework.event.manager vivarium.engine.framework.lifecycle vivarium.engine.framework.lifecycle.constraint_maker vivarium.engine.framework.lifecycle.entities vivarium.engine.framework.lifecycle.exceptions vivarium.engine.framework.lifecycle.interface vivarium.engine.framework.lifecycle.lifecycle_states vivarium.engine.framework.lifecycle.manager vivarium.engine.framework.logging vivarium.engine.framework.logging.interface vivarium.engine.framework.logging.manager vivarium.engine.framework.logging.utilities vivarium.engine.framework.lookup vivarium.engine.framework.lookup.interface vivarium.engine.framework.lookup.interpolation vivarium.engine.framework.lookup.manager vivarium.engine.framework.lookup.table vivarium.engine.framework.plugins vivarium.engine.framework.population vivarium.engine.framework.population.exceptions vivarium.engine.framework.population.interface vivarium.engine.framework.population.manager vivarium.engine.framework.population.population_view vivarium.engine.framework.population.utilities vivarium.engine.framework.randomness vivarium.engine.framework.randomness.exceptions vivarium.engine.framework.randomness.index_map vivarium.engine.framework.randomness.interface vivarium.engine.framework.randomness.manager vivarium.engine.framework.randomness.stream vivarium.engine.framework.resource vivarium.engine.framework.resource.exceptions vivarium.engine.framework.resource.interface vivarium.engine.framework.resource.manager vivarium.engine.framework.resource.resource vivarium.engine.framework.results vivarium.engine.framework.results.context vivarium.engine.framework.results.interface vivarium.engine.framework.results.manager vivarium.engine.framework.results.observation vivarium.engine.framework.results.observer vivarium.engine.framework.results.stratification vivarium.engine.framework.state_machine vivarium.engine.framework.time vivarium.engine.framework.time.interface vivarium.engine.framework.time.manager vivarium.engine.framework.utilities vivarium.engine.framework.values vivarium.engine.framework.values.combiners vivarium.engine.framework.values.exceptions vivarium.engine.framework.values.interface vivarium.engine.framework.values.manager vivarium.engine.framework.values.pipeline vivarium.engine.framework.values.post_processors vivarium.engine.interface vivarium.engine.interface.cli vivarium.engine.interface.interactive vivarium.engine.interface.utilities vivarium.engine.manager vivarium.engine.testing_utilities

move_simulants_to_end() (vivarium.engine.framework.time.interface.TimeInterface method) (vivarium.engine.framework.time.manager.SimulationClock method) multiplication_combiner() (in module vivarium.engine.framework.values.combiners) mutators (vivarium.engine.framework.values.pipeline.Pipeline attribute)

N

name (vivarium.engine.component.Component property) (vivarium.engine.framework.artifact.manager.ArtifactManager property) (vivarium.engine.framework.components.manager.ComponentManager property) (vivarium.engine.framework.engine.SimulationContext property) (vivarium.engine.framework.event.manager.Event attribute) (vivarium.engine.framework.event.manager.EventManager property) (vivarium.engine.framework.lifecycle.entities.LifeCyclePhase property) (vivarium.engine.framework.lifecycle.entities.LifeCycleState property) (vivarium.engine.framework.lifecycle.manager.LifeCycleManager property) (vivarium.engine.framework.logging.manager.LoggingManager property) (vivarium.engine.framework.lookup.manager.LookupTableManager property) (vivarium.engine.framework.plugins.PluginManager property) (vivarium.engine.framework.population.manager.PopulationManager property) (vivarium.engine.framework.population.population_view.PopulationView property) (vivarium.engine.framework.randomness.manager.RandomnessManager property) (vivarium.engine.framework.resource.manager.ResourceManager property) (vivarium.engine.framework.resource.resource.Resource attribute) (vivarium.engine.framework.resource.resource.ResourceId attribute) (vivarium.engine.framework.results.context.ResultsContext property) (vivarium.engine.framework.results.interface.ResultsInterface property) (vivarium.engine.framework.results.manager.ResultsManager property) (vivarium.engine.framework.results.observation.AddingObservation attribute) (vivarium.engine.framework.results.observation.ConcatenatingObservation attribute) (vivarium.engine.framework.results.observation.Observation attribute) (vivarium.engine.framework.results.observation.StratifiedObservation attribute) (vivarium.engine.framework.results.observation.UnstratifiedObservation attribute) (vivarium.engine.framework.results.stratification.Stratification attribute) (vivarium.engine.framework.state_machine.TransitionSet property) (vivarium.engine.framework.time.manager.DateTimeClock property) (vivarium.engine.framework.time.manager.SimpleClock property) (vivarium.engine.framework.time.manager.SimulationClock property) (vivarium.engine.framework.values.manager.ValuesManager property) (vivarium.engine.manager.Manager property)

next_state() (vivarium.engine.framework.state_machine.State method) NonCRNTestPopulation (class in vivarium.engine.testing_utilities) NOT_TRIGGERED (vivarium.engine.framework.state_machine.Trigger attribute) notify_dependencies_changed() (vivarium.engine.framework.resource.resource.Resource method)

O

Observation (class in vivarium.engine.framework.results.observation) observations (vivarium.engine.framework.results.context.ResultsContext attribute) observe() (vivarium.engine.framework.results.observation.Observation method) (vivarium.engine.framework.results.observation.StratifiedObservation method) Observer (class in vivarium.engine.framework.results.observer) on_collect_metrics() (vivarium.engine.component.Component method) (vivarium.engine.framework.results.manager.ResultsManager method) on_dependencies_changed (vivarium.engine.framework.resource.resource.Resource attribute) on_post_setup() (vivarium.engine.component.Component method) (vivarium.engine.framework.event.manager.EventManager method) (vivarium.engine.framework.lookup.manager.LookupTableManager method) (vivarium.engine.framework.population.manager.PopulationManager method) (vivarium.engine.framework.results.manager.ResultsManager method) (vivarium.engine.framework.state_machine.Machine method) (vivarium.engine.framework.time.manager.SimulationClock method) (vivarium.engine.framework.values.manager.ValuesManager method)

on_simulation_end() (vivarium.engine.component.Component method) on_time_step() (vivarium.engine.component.Component method) (vivarium.engine.framework.results.manager.ResultsManager method) (vivarium.engine.framework.state_machine.Machine method) (vivarium.engine.testing_utilities.NonCRNTestPopulation method) on_time_step_cleanup() (vivarium.engine.component.Component method) (vivarium.engine.framework.results.manager.ResultsManager method) (vivarium.engine.framework.state_machine.Machine method) on_time_step_prepare() (vivarium.engine.component.Component method) (vivarium.engine.framework.results.manager.ResultsManager method) order (vivarium.engine.framework.lookup.interpolation.Interpolation attribute) Order0Interp (class in vivarium.engine.framework.lookup.interpolation) OrderedComponentSet (class in vivarium.engine.framework.components.manager)

P

parameter_bins (vivarium.engine.framework.lookup.interpolation.Order0Interp attribute) parameter_columns (vivarium.engine.framework.lookup.table.LookupTable attribute) parse_artifact_path_config() (in module vivarium.engine.framework.artifact.manager) parse_component_config() (vivarium.engine.framework.components.parser.ComponentConfigurationParser method) ParsingError Pipeline (class in vivarium.engine.framework.values.pipeline) Plugin PluginConfigurationError PluginGroup (class in vivarium.engine.framework.plugins) PluginManager (class in vivarium.engine.framework.plugins) pop() (vivarium.engine.framework.components.manager.OrderedComponentSet method) population (vivarium.engine.framework.engine.Builder attribute) Population State Table POPULATION_CREATION (in module vivarium.engine.framework.lifecycle.lifecycle_states) population_filter (vivarium.engine.framework.results.observation.AddingObservation attribute) (vivarium.engine.framework.results.observation.ConcatenatingObservation attribute) (vivarium.engine.framework.results.observation.Observation attribute) (vivarium.engine.framework.results.observation.StratifiedObservation attribute) (vivarium.engine.framework.results.observation.UnstratifiedObservation attribute) population_view (vivarium.engine.component.Component property) (vivarium.engine.framework.lookup.table.LookupTable attribute)

PopulationError PopulationFilter (class in vivarium.engine.framework.results.interface) PopulationInterface (class in vivarium.engine.framework.population.interface) PopulationManager (class in vivarium.engine.framework.population.manager) PopulationView (class in vivarium.engine.framework.population.population_view) post_processor (vivarium.engine.framework.values.pipeline.AttributePipeline attribute) (vivarium.engine.framework.values.pipeline.Pipeline attribute) POST_SETUP (in module vivarium.engine.framework.lifecycle.lifecycle_states) post_setup_priority (vivarium.engine.component.Component property) PostProcessor (class in vivarium.engine.framework.values.post_processors) PPFCallable (class in vivarium.engine.framework.randomness.stream) prep_component() (vivarium.engine.framework.components.parser.ComponentConfigurationParser method) print_initializer_order() (vivarium.engine.interface.interactive.InteractiveContext method) print_lifecycle_order() (vivarium.engine.interface.interactive.InteractiveContext method) Private Column private_columns (vivarium.engine.component.Component property) (vivarium.engine.framework.population.manager.PopulationManager property) (vivarium.engine.framework.population.population_view.PopulationView property) PrivateColumnValueSource (class in vivarium.engine.framework.values.pipeline) probability() (vivarium.engine.framework.state_machine.Transition method) probability_to_rate() (in module vivarium.engine.framework.utilities) process_level() (vivarium.engine.framework.components.parser.ComponentConfigurationParser method) Public Column

Q

query (vivarium.engine.framework.results.interface.PopulationFilter attribute)

R

raise_if_not_setup() (in module vivarium.engine.interface.utilities) random (vivarium.engine.framework.state_machine.TransitionSet attribute) randomness (vivarium.engine.framework.engine.Builder attribute) RandomnessError RandomnessInterface (class in vivarium.engine.framework.randomness.interface) RandomnessManager (class in vivarium.engine.framework.randomness.manager) RandomnessStream (class in vivarium.engine.framework.randomness.stream) rate_conversion_type (vivarium.engine.framework.randomness.stream.RandomnessStream attribute) rate_to_probability() (in module vivarium.engine.framework.utilities) raw_union_post_processor() (in module vivarium.engine.framework.values.post_processors) register_adding_observation() (vivarium.engine.framework.results.interface.ResultsInterface method) register_attribute_modifier() (vivarium.engine.framework.values.interface.ValuesInterface method) (vivarium.engine.framework.values.manager.ValuesManager method) register_attribute_producer() (vivarium.engine.framework.values.interface.ValuesInterface method) (vivarium.engine.framework.values.manager.ValuesManager method) register_binned_stratification() (vivarium.engine.framework.results.interface.ResultsInterface method) (vivarium.engine.framework.results.manager.ResultsManager method) register_concatenating_observation() (vivarium.engine.framework.results.interface.ResultsInterface method) register_initializer() (vivarium.engine.framework.population.interface.PopulationInterface method) (vivarium.engine.framework.population.manager.PopulationManager method) register_listener() (vivarium.engine.framework.event.interface.EventInterface method) (vivarium.engine.framework.event.manager.EventManager method) register_observation() (vivarium.engine.framework.results.context.ResultsContext method) (vivarium.engine.framework.results.manager.ResultsManager method) register_observations() (vivarium.engine.framework.results.observer.Observer method) register_rate_producer() (vivarium.engine.framework.values.interface.ValuesInterface method) register_simulants() (vivarium.engine.framework.randomness.interface.RandomnessInterface method) (vivarium.engine.framework.randomness.manager.RandomnessManager method) register_step_size_modifier() (vivarium.engine.framework.time.interface.TimeInterface method) register_stratification() (vivarium.engine.framework.results.interface.ResultsInterface method) (vivarium.engine.framework.results.manager.ResultsManager method) register_stratified_observation() (vivarium.engine.framework.results.interface.ResultsInterface method) register_tracked_query() (vivarium.engine.framework.population.interface.PopulationInterface method) (vivarium.engine.framework.population.manager.PopulationManager method) register_unstratified_observation() (vivarium.engine.framework.results.interface.ResultsInterface method) register_value_modifier() (vivarium.engine.framework.values.interface.ValuesInterface method) (vivarium.engine.framework.values.manager.ValuesManager method) register_value_producer() (vivarium.engine.framework.values.interface.ValuesInterface method) (vivarium.engine.framework.values.manager.ValuesManager method) replace_combiner() (in module vivarium.engine.framework.values.combiners) REPORT (in module vivarium.engine.framework.lifecycle.lifecycle_states) report() (vivarium.engine.framework.engine.SimulationContext method) required_resources (vivarium.engine.framework.resource.resource.Resource property) requires_attributes (vivarium.engine.framework.results.observation.AddingObservation attribute) (vivarium.engine.framework.results.observation.ConcatenatingObservation attribute) (vivarium.engine.framework.results.observation.Observation attribute) (vivarium.engine.framework.results.observation.StratifiedObservation attribute) (vivarium.engine.framework.results.observation.UnstratifiedObservation attribute) (vivarium.engine.framework.results.stratification.Stratification attribute)

rescale_post_processor() (in module vivarium.engine.framework.values.post_processors) RESIDUAL_CHOICE (in module vivarium.engine.framework.randomness.stream) Resource (class in vivarium.engine.framework.resource.resource) resource_id (vivarium.engine.framework.resource.resource.Resource property) RESOURCE_TYPE (vivarium.engine.framework.lookup.table.LookupTable attribute) (vivarium.engine.framework.randomness.stream.RandomnessStream attribute) (vivarium.engine.framework.resource.resource.Column attribute) (vivarium.engine.framework.resource.resource.Initializer attribute) (vivarium.engine.framework.resource.resource.Resource attribute) resource_type (vivarium.engine.framework.resource.resource.ResourceId attribute) RESOURCE_TYPE (vivarium.engine.framework.values.pipeline.AttributePipeline attribute) (vivarium.engine.framework.values.pipeline.Pipeline attribute) (vivarium.engine.framework.values.pipeline.ValueModifier attribute) ResourceError ResourceId (class in vivarium.engine.framework.resource.resource) ResourceInterface (class in vivarium.engine.framework.resource.interface) ResourceManager (class in vivarium.engine.framework.resource.manager) resources (vivarium.engine.framework.engine.Builder attribute) results (vivarium.engine.framework.engine.Builder attribute) results_formatter (vivarium.engine.framework.results.observation.AddingObservation attribute) (vivarium.engine.framework.results.observation.ConcatenatingObservation attribute) (vivarium.engine.framework.results.observation.Observation attribute) (vivarium.engine.framework.results.observation.StratifiedObservation attribute) (vivarium.engine.framework.results.observation.UnstratifiedObservation attribute) results_gatherer (vivarium.engine.framework.results.observation.Observation attribute) (vivarium.engine.framework.results.observation.UnstratifiedObservation attribute) results_initializer (vivarium.engine.framework.results.observation.Observation attribute) results_updater (vivarium.engine.framework.results.observation.Observation attribute) (vivarium.engine.framework.results.observation.StratifiedObservation attribute) (vivarium.engine.framework.results.observation.UnstratifiedObservation attribute) ResultsContext (class in vivarium.engine.framework.results.context) ResultsFormatter (in module vivarium.engine.framework.results.interface) ResultsGatherer (in module vivarium.engine.framework.results.interface) ResultsInterface (class in vivarium.engine.framework.results.interface) ResultsManager (class in vivarium.engine.framework.results.manager) ResultsUpdater (in module vivarium.engine.framework.results.interface) return_type (vivarium.engine.framework.lookup.table.LookupTable attribute) run() (vivarium.engine.framework.engine.SimulationContext method) (vivarium.engine.interface.interactive.InteractiveContext method) run_for() (vivarium.engine.interface.interactive.InteractiveContext method) run_from_ipython() (in module vivarium.engine.interface.utilities) run_simulation() (vivarium.engine.framework.engine.SimulationContext method) run_until() (vivarium.engine.interface.interactive.InteractiveContext method)

S

sample_from_distribution() (vivarium.engine.framework.randomness.stream.RandomnessStream method) seed (vivarium.engine.framework.randomness.stream.RandomnessStream attribute) set_active() (vivarium.engine.framework.state_machine.Transition method) set_attributes() (vivarium.engine.framework.values.pipeline.Pipeline method) set_data() (vivarium.engine.framework.lookup.table.LookupTable method) set_default_stratifications() (vivarium.engine.framework.results.context.ResultsContext method) (vivarium.engine.framework.results.manager.ResultsManager method) set_inactive() (vivarium.engine.framework.state_machine.Transition method) set_model() (vivarium.engine.framework.state_machine.State method) set_results_dir() (vivarium.engine.framework.results.observer.Observer method) set_state() (vivarium.engine.framework.lifecycle.manager.LifeCycleManager method) set_stratifications() (vivarium.engine.framework.results.context.ResultsContext method) SETUP (in module vivarium.engine.framework.lifecycle.lifecycle_states) setup() (vivarium.engine.component.Component method) (vivarium.engine.framework.artifact.manager.ArtifactManager method) (vivarium.engine.framework.engine.SimulationContext method) (vivarium.engine.framework.event.manager.EventManager method) (vivarium.engine.framework.lookup.manager.LookupTableManager method) (vivarium.engine.framework.population.manager.PopulationManager method) (vivarium.engine.framework.randomness.manager.RandomnessManager method) (vivarium.engine.framework.resource.manager.ResourceManager method) (vivarium.engine.framework.results.context.ResultsContext method) (vivarium.engine.framework.results.manager.ResultsManager method) (vivarium.engine.framework.state_machine.Machine method) (vivarium.engine.framework.state_machine.State method) (vivarium.engine.framework.state_machine.TransitionSet method) (vivarium.engine.framework.time.manager.DateTimeClock method) (vivarium.engine.framework.time.manager.SimpleClock method) (vivarium.engine.framework.time.manager.SimulationClock method) (vivarium.engine.framework.values.manager.ValuesManager method) (vivarium.engine.interface.interactive.InteractiveContext method) (vivarium.engine.manager.Manager method) (vivarium.engine.testing_utilities.NonCRNTestPopulation method) (vivarium.engine.testing_utilities.TestPopulation method) setup_component() (vivarium.engine.component.Component method) (vivarium.engine.framework.results.observer.Observer method) setup_components() (vivarium.engine.framework.components.manager.ComponentManager method) setup_manager() (vivarium.engine.framework.components.manager.ComponentManager method) (vivarium.engine.manager.Manager method) SIM_INDEX_COLUMN (vivarium.engine.framework.randomness.index_map.IndexMap attribute) SimpleClock (class in vivarium.engine.framework.time.manager) Simulant simulant_next_event_times() (vivarium.engine.framework.time.interface.TimeInterface method) (vivarium.engine.framework.time.manager.SimulationClock method) simulant_step_sizes() (vivarium.engine.framework.time.interface.TimeInterface method) (vivarium.engine.framework.time.manager.SimulationClock method)

SimulantData (class in vivarium.engine.framework.population.manager) simulate-run command line option --artifact_path --pdb --quiet --results_directory --verbose -i -o -q -v MODEL_SPECIFICATION SIMULATION_END (in module vivarium.engine.framework.lifecycle.lifecycle_states) simulation_end_priority (vivarium.engine.component.Component property) SimulationClock (class in vivarium.engine.framework.time.manager) SimulationContext (class in vivarium.engine.framework.engine) sorted_nodes (vivarium.engine.framework.resource.manager.ResourceManager property) source (vivarium.engine.framework.values.pipeline.Pipeline attribute) split() (vivarium.engine.framework.event.manager.Event method) standard_step_size (vivarium.engine.framework.time.manager.SimulationClock property) START_ACTIVE (vivarium.engine.framework.state_machine.Trigger attribute) START_INACTIVE (vivarium.engine.framework.state_machine.Trigger attribute) State (class in vivarium.engine.framework.state_machine) state_column (vivarium.engine.framework.state_machine.Machine attribute) state_id (vivarium.engine.framework.state_machine.State attribute) (vivarium.engine.framework.state_machine.TransitionSet attribute) states (vivarium.engine.framework.lifecycle.entities.LifeCyclePhase property) (vivarium.engine.framework.state_machine.Machine attribute) step() (vivarium.engine.framework.engine.SimulationContext method) (vivarium.engine.interface.interactive.InteractiveContext method) step_backward() (vivarium.engine.framework.time.manager.SimulationClock method) step_forward() (vivarium.engine.framework.time.manager.SimulationClock method) step_size (vivarium.engine.framework.event.manager.Event attribute) (vivarium.engine.framework.time.manager.SimulationClock property) step_size() (vivarium.engine.framework.time.interface.TimeInterface method) step_size_post_processor() (vivarium.engine.framework.time.manager.SimulationClock method) stop_time (vivarium.engine.framework.time.manager.SimulationClock property) Stratification (class in vivarium.engine.framework.results.stratification) stratifications (vivarium.engine.framework.results.context.ResultsContext attribute) (vivarium.engine.framework.results.observation.AddingObservation attribute) (vivarium.engine.framework.results.observation.Observation attribute) StratifiedObservation (class in vivarium.engine.framework.results.observation) stratify() (vivarium.engine.framework.results.stratification.Stratification method) sub_components (vivarium.engine.component.Component property) (vivarium.engine.framework.state_machine.Machine property)

T

take_steps() (vivarium.engine.interface.interactive.InteractiveContext method) TEN_DIGIT_MODULUS (vivarium.engine.framework.randomness.index_map.IndexMap attribute) TestPopulation (class in vivarium.engine.testing_utilities) time (vivarium.engine.framework.engine.Builder attribute) (vivarium.engine.framework.event.manager.Event attribute) (vivarium.engine.framework.time.manager.SimulationClock property) TIME_STEP (in module vivarium.engine.framework.lifecycle.lifecycle_states) TIME_STEP_CLEANUP (in module vivarium.engine.framework.lifecycle.lifecycle_states) time_step_cleanup_priority (vivarium.engine.component.Component property) TIME_STEP_PREPARE (in module vivarium.engine.framework.lifecycle.lifecycle_states) time_step_prepare_priority (vivarium.engine.component.Component property) time_step_priority (vivarium.engine.component.Component property) time_steps_remaining (vivarium.engine.framework.time.manager.SimulationClock property) TimeInterface (class in vivarium.engine.framework.time.interface) timings (vivarium.engine.framework.lifecycle.manager.LifeCycleManager property) to_guid() (vivarium.engine.framework.lifecycle.constraint_maker.ConstraintMaker static method)

to_observe (vivarium.engine.framework.results.observation.AddingObservation attribute) (vivarium.engine.framework.results.observation.ConcatenatingObservation attribute) (vivarium.engine.framework.results.observation.Observation attribute) (vivarium.engine.framework.results.observation.StratifiedObservation attribute) (vivarium.engine.framework.results.observation.UnstratifiedObservation attribute) to_yearly() (in module vivarium.engine.framework.utilities) tracking_setup() (vivarium.engine.framework.components.manager.ComponentManager method) Transient (class in vivarium.engine.framework.state_machine) TransientState (class in vivarium.engine.framework.state_machine) Transition (class in vivarium.engine.framework.state_machine) transition() (vivarium.engine.framework.state_machine.Machine method) transition_effect() (vivarium.engine.framework.state_machine.State method) transition_set (vivarium.engine.framework.state_machine.State attribute) transition_side_effect() (vivarium.engine.framework.state_machine.State method) transitions (vivarium.engine.framework.state_machine.TransitionSet attribute) TransitionSet (class in vivarium.engine.framework.state_machine) Trigger (class in vivarium.engine.framework.state_machine)

U

union_post_processor() (in module vivarium.engine.framework.values.post_processors) UnstratifiedObservation (class in vivarium.engine.framework.results.observation) update() (vivarium.engine.framework.components.manager.OrderedComponentSet method) (vivarium.engine.framework.population.manager.PopulationManager method) (vivarium.engine.framework.population.population_view.PopulationView method) (vivarium.engine.framework.randomness.index_map.IndexMap method)

user_data (vivarium.engine.framework.event.manager.Event attribute) (vivarium.engine.framework.population.manager.SimulantData attribute)

V

valid_next_state() (vivarium.engine.framework.lifecycle.entities.LifeCycleState method) validate_call_data() (in module vivarium.engine.framework.lookup.interpolation) validate_filter_term() (in module vivarium.engine.framework.artifact.manager) validate_model_specification_file() (in module vivarium.engine.framework.configuration) validate_parameters() (in module vivarium.engine.framework.lookup.interpolation) Value value (vivarium.engine.framework.engine.Builder attribute) value_columns (vivarium.engine.framework.lookup.interpolation.Order0Interp attribute) (vivarium.engine.framework.lookup.table.LookupTable property) ValueCombiner (class in vivarium.engine.framework.values.combiners) ValueModifier (class in vivarium.engine.framework.values.pipeline) ValuesInterface (class in vivarium.engine.framework.values.interface) ValuesManager (class in vivarium.engine.framework.values.manager) ValueSource (class in vivarium.engine.framework.values.pipeline) vivarium.engine module vivarium.engine.component module vivarium.engine.exceptions module vivarium.engine.framework module vivarium.engine.framework.artifact module vivarium.engine.framework.artifact.interface module vivarium.engine.framework.artifact.manager module vivarium.engine.framework.components module vivarium.engine.framework.components.interface module vivarium.engine.framework.components.manager module vivarium.engine.framework.components.parser module vivarium.engine.framework.configuration module vivarium.engine.framework.engine module vivarium.engine.framework.event module vivarium.engine.framework.event.interface module vivarium.engine.framework.event.manager module vivarium.engine.framework.lifecycle module vivarium.engine.framework.lifecycle.constraint_maker module vivarium.engine.framework.lifecycle.entities module vivarium.engine.framework.lifecycle.exceptions module vivarium.engine.framework.lifecycle.interface module vivarium.engine.framework.lifecycle.lifecycle_states module vivarium.engine.framework.lifecycle.manager module vivarium.engine.framework.logging module vivarium.engine.framework.logging.interface module vivarium.engine.framework.logging.manager module vivarium.engine.framework.logging.utilities module vivarium.engine.framework.lookup module vivarium.engine.framework.lookup.interface module vivarium.engine.framework.lookup.interpolation module vivarium.engine.framework.lookup.manager module vivarium.engine.framework.lookup.table module vivarium.engine.framework.plugins module vivarium.engine.framework.population module

vivarium.engine.framework.population.exceptions module vivarium.engine.framework.population.interface module vivarium.engine.framework.population.manager module vivarium.engine.framework.population.population_view module vivarium.engine.framework.population.utilities module vivarium.engine.framework.randomness module vivarium.engine.framework.randomness.exceptions module vivarium.engine.framework.randomness.index_map module vivarium.engine.framework.randomness.interface module vivarium.engine.framework.randomness.manager module vivarium.engine.framework.randomness.stream module vivarium.engine.framework.resource module vivarium.engine.framework.resource.exceptions module vivarium.engine.framework.resource.interface module vivarium.engine.framework.resource.manager module vivarium.engine.framework.resource.resource module vivarium.engine.framework.results module vivarium.engine.framework.results.context module vivarium.engine.framework.results.interface module vivarium.engine.framework.results.manager module vivarium.engine.framework.results.observation module vivarium.engine.framework.results.observer module vivarium.engine.framework.results.stratification module vivarium.engine.framework.state_machine module vivarium.engine.framework.time module vivarium.engine.framework.time.interface module vivarium.engine.framework.time.manager module vivarium.engine.framework.utilities module vivarium.engine.framework.values module vivarium.engine.framework.values.combiners module vivarium.engine.framework.values.exceptions module vivarium.engine.framework.values.interface module vivarium.engine.framework.values.manager module vivarium.engine.framework.values.pipeline module vivarium.engine.framework.values.post_processors module vivarium.engine.interface module vivarium.engine.interface.cli module vivarium.engine.interface.interactive module vivarium.engine.interface.utilities module vivarium.engine.manager module vivarium.engine.testing_utilities module VivariumError

W

when (vivarium.engine.framework.results.observation.AddingObservation attribute) (vivarium.engine.framework.results.observation.ConcatenatingObservation attribute) (vivarium.engine.framework.results.observation.Observation attribute) (vivarium.engine.framework.results.observation.StratifiedObservation attribute) (vivarium.engine.framework.results.observation.UnstratifiedObservation attribute)

write_backup() (vivarium.engine.framework.engine.SimulationContext method)