Index

Symbols

--artifact_path simulate-run command line option --location simulate-run command line option --no-process simulate-profile command line option --pdb simulate-run command line option --process simulate-profile command line option --quiet simulate-run command line option --results_directory simulate-profile command line option simulate-run command line option

--verbose simulate-run command line option -i simulate-run command line option -l simulate-run command line option -o simulate-profile command line option simulate-run command line option -q simulate-run command line option -v simulate-run command line option

A

accessed (vivarium.config_tree.ConfigNode property) add() (vivarium.framework.components.manager.OrderedComponentSet method) (vivarium.framework.population.manager.InitializerComponentSet method) add_components() (vivarium.framework.components.manager.ComponentManager method) (vivarium.framework.engine.SimulationContext method) add_constraint() (vivarium.framework.lifecycle.LifeCycleInterface method) (vivarium.framework.lifecycle.LifeCycleManager method) add_handlers() (vivarium.framework.lifecycle.LifeCycleInterface method) (vivarium.framework.lifecycle.LifeCycleManager method) (vivarium.framework.lifecycle.LifeCycleState method) add_managers() (vivarium.framework.components.manager.ComponentManager method) add_next() (vivarium.framework.lifecycle.LifeCyclePhase method) (vivarium.framework.lifecycle.LifeCycleState method) add_phase() (vivarium.framework.lifecycle.LifeCycle method) (vivarium.framework.lifecycle.LifeCycleManager method)

add_resources() (vivarium.framework.resource.ResourceInterface method) (vivarium.framework.resource.ResourceManager method) add_states() (vivarium.framework.state_machine.Machine method) add_transition() (vivarium.framework.state_machine.State method) allow_self_transitions() (vivarium.framework.state_machine.State method) append() (vivarium.framework.artifact.artifact.Keys method) (vivarium.framework.state_machine.TransitionSet method) apply_configuration_defaults() (vivarium.framework.components.manager.ComponentManager method) Artifact (class in vivarium.framework.artifact.artifact) ArtifactException ArtifactInterface (class in vivarium.framework.artifact.manager) ArtifactManager (class in vivarium.framework.artifact.manager) Attribute

B

build_model_specification() (in module vivarium.framework.configuration) build_simulation_configuration() (in module vivarium.framework.configuration) build_table() (in module vivarium.testing_utilities) (vivarium.framework.lookup.manager.LookupTableInterface method) (vivarium.framework.lookup.manager.LookupTableManager method)

Builder (class in vivarium.framework.engine)

C

call() (vivarium.framework.lookup.table.CategoricalTable method) (vivarium.framework.lookup.table.InterpolatedTable method) (vivarium.framework.lookup.table.LookupTable method) (vivarium.framework.lookup.table.ScalarTable method) categorical_parameters (vivarium.framework.lookup.interpolation.Interpolation attribute) CategoricalTable (class in vivarium.framework.lookup.table) check_data_complete() (in module vivarium.framework.lookup.interpolation) check_valid_state() (vivarium.framework.lifecycle.ConstraintMaker method) choice() (vivarium.framework.randomness.stream.RandomnessStream method) choose_new_state() (vivarium.framework.state_machine.TransitionSet method) cleanup() (vivarium.framework.state_machine.Machine method) cleanup_effect() (vivarium.framework.state_machine.State method) clear_cache() (vivarium.framework.artifact.artifact.Artifact method) clock (vivarium.framework.lookup.table.LookupTable attribute) (vivarium.framework.randomness.stream.RandomnessStream attribute) clock() (vivarium.framework.time.TimeInterface method) collapse_nested_dict() (in module vivarium.framework.utilities) collect_metrics_priority (vivarium.component.Component property) columns (vivarium.framework.population.manager.PopulationManager property) (vivarium.framework.population.population_view.PopulationView property) columns_created (vivarium.component.Component property) (vivarium.framework.time.SimulationClock property) (vivarium.testing_utilities.NonCRNTestPopulation property) columns_required (vivarium.component.Component property) (vivarium.framework.state_machine.Machine property) (vivarium.framework.time.SimulationClock property) combiner (vivarium.framework.values.Pipeline attribute) Component (class in vivarium.component) ComponentConfigError ComponentConfigurationParser (class in vivarium.framework.components.parser) ComponentInterface (class in vivarium.framework.components.manager)

ComponentManager (class in vivarium.framework.components.manager) components (vivarium.framework.engine.Builder attribute) ConfigNode (class in vivarium.config_tree) ConfigTree (class in vivarium.config_tree) Configuration CONFIGURATION_DEFAULTS (vivarium.component.Component attribute) configuration_defaults (vivarium.component.Component property) CONFIGURATION_DEFAULTS (vivarium.framework.artifact.manager.ArtifactManager attribute) (vivarium.framework.lookup.manager.LookupTableManager attribute) (vivarium.framework.population.manager.PopulationManager attribute) (vivarium.framework.randomness.manager.RandomnessManager attribute) (vivarium.framework.time.DateTimeClock attribute) (vivarium.framework.time.SimpleClock attribute) (vivarium.manager.Manager attribute) configuration_defaults (vivarium.manager.Manager property) CONFIGURATION_DEFAULTS (vivarium.testing_utilities.NonCRNTestPopulation attribute) ConfigurationError ConfigurationKeyError configure_logging() (vivarium.framework.logging.manager.LoggingManager method) configure_logging_to_file() (in module vivarium.framework.logging.utilities) configure_logging_to_terminal() (in module vivarium.framework.logging.utilities) constrain_normal_method() (vivarium.framework.lifecycle.ConstraintMaker method) ConstraintError ConstraintMaker (class in vivarium.framework.lifecycle) continuous_parameters (vivarium.framework.lookup.interpolation.Interpolation attribute) (vivarium.framework.lookup.interpolation.Order0Interp attribute) create_component_from_string() (vivarium.framework.components.parser.ComponentConfigurationParser method) create_hdf_with_keyspace() (vivarium.framework.artifact.artifact.Artifact static method) creation_time (vivarium.framework.population.manager.SimulantData attribute) creation_window (vivarium.framework.population.manager.SimulantData attribute) current_state (vivarium.framework.lifecycle.LifeCycleManager property) current_state() (vivarium.framework.lifecycle.LifeCycleInterface method) current_time (vivarium.interface.interactive.InteractiveContext property)

D

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

DateTimeClock (class in vivarium.framework.time) DEFAULT_EVENT_PRIORITY (in module vivarium.component) dependencies (vivarium.framework.resource.ResourceGroup property) DuplicatedConfigurationError DynamicValueError

E

emit() (vivarium.framework.event.EventChannel method) enter() (vivarium.framework.lifecycle.LifeCycleState method) EntityKey (class in vivarium.framework.artifact.hdf) entrance_count (vivarium.framework.lifecycle.LifeCycleState property) Event (class in vivarium.framework.event) event (vivarium.framework.engine.Builder attribute)

event_time (vivarium.framework.time.SimulationClock property) EventChannel (class in vivarium.framework.event) EventInterface (class in vivarium.framework.event) EventManager (class in vivarium.framework.event) extend() (vivarium.framework.state_machine.TransitionSet method) extrapolate (vivarium.framework.lookup.table.LookupTable attribute)

F

filter_data() (in module vivarium.framework.artifact.manager) filter_for_probability() (vivarium.framework.randomness.stream.RandomnessStream method) filter_for_rate() (vivarium.framework.randomness.stream.RandomnessStream method) filter_terms (vivarium.framework.artifact.artifact.Artifact property)

finalize() (vivarium.framework.engine.SimulationContext method) freeze() (vivarium.config_tree.ConfigNode method) (vivarium.config_tree.ConfigTree method) from_yearly() (in module vivarium.framework.utilities)

G

get() (vivarium.framework.population.population_view.PopulationView method) get_active_simulants() (vivarium.framework.time.SimulationClock method) get_base_filter_terms() (in module vivarium.framework.artifact.manager) get_channel() (vivarium.framework.event.EventManager method) get_component() (vivarium.framework.components.manager.ComponentInterface method) (vivarium.framework.components.manager.ComponentManager method) (vivarium.interface.interactive.InteractiveContext method) get_components() (vivarium.framework.components.parser.ComponentConfigurationParser method) get_components_by_type() (vivarium.framework.components.manager.ComponentInterface method) (vivarium.framework.components.manager.ComponentManager method) get_core_controllers() (vivarium.framework.plugins.PluginManager method) get_core_interfaces() (vivarium.framework.plugins.PluginManager method) get_draw() (vivarium.framework.randomness.stream.RandomnessStream method) get_emitter() (vivarium.framework.event.EventInterface method) (vivarium.framework.event.EventManager method) (vivarium.interface.interactive.InteractiveContext method) get_from_layer() (vivarium.config_tree.ConfigTree method) get_hash() (in module vivarium.framework.randomness.stream) get_initialization_parameters() (vivarium.component.Component method) (vivarium.framework.state_machine.Machine method) get_keys() (in module vivarium.framework.artifact.hdf) get_listeners() (vivarium.framework.event.EventManager method) (vivarium.interface.interactive.InteractiveContext method) get_logger() (vivarium.framework.logging.manager.LoggingInterface method) (vivarium.framework.logging.manager.LoggingManager method) get_optional_controllers() (vivarium.framework.plugins.PluginManager method) get_optional_interfaces() (vivarium.framework.plugins.PluginManager method) get_output_model_name_string() (in module vivarium.interface.utilities)

get_output_root() (in module vivarium.interface.utilities) get_performance_metrics() (vivarium.framework.engine.SimulationContext method) get_plugin() (vivarium.framework.plugins.PluginManager method) get_plugin_interface() (vivarium.framework.plugins.PluginManager method) get_population() (vivarium.framework.engine.SimulationContext method) (vivarium.framework.population.manager.PopulationManager method) (vivarium.interface.interactive.InteractiveContext method) get_randomness() (in module vivarium.testing_utilities) get_randomness_stream() (vivarium.framework.randomness.manager.RandomnessManager method) get_seed() (vivarium.framework.randomness.manager.RandomnessInterface method) (vivarium.framework.randomness.manager.RandomnessManager method) get_simulant_creator() (vivarium.framework.population.manager.PopulationInterface method) (vivarium.framework.population.manager.PopulationManager method) get_state() (vivarium.framework.lifecycle.LifeCycle method) (vivarium.framework.lifecycle.LifeCyclePhase method) get_state_names() (vivarium.framework.lifecycle.LifeCycle method) (vivarium.framework.lifecycle.LifeCycleManager method) get_stream() (vivarium.framework.randomness.manager.RandomnessInterface method) get_time_stamp() (in module vivarium.framework.time) get_value() (vivarium.config_tree.ConfigNode method) (vivarium.framework.values.ValuesInterface method) (vivarium.framework.values.ValuesManager method) (vivarium.interface.interactive.InteractiveContext method) get_view() (vivarium.framework.population.manager.PopulationInterface method) (vivarium.framework.population.manager.PopulationManager method) graph (vivarium.framework.resource.ResourceManager property) group (vivarium.framework.artifact.hdf.EntityKey property) group_name (vivarium.framework.artifact.hdf.EntityKey property) group_prefix (vivarium.framework.artifact.hdf.EntityKey property)

H

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

I

import_and_instantiate_component() (vivarium.framework.components.parser.ComponentConfigurationParser static method) import_by_path() (in module vivarium.framework.utilities) index (vivarium.framework.event.Event attribute) (vivarium.framework.population.manager.SimulantData attribute) IndexMap (class in vivarium.framework.randomness.index_map) initialization_requirements (vivarium.component.Component property) initialize_simulants() (vivarium.framework.engine.SimulationContext method) InitializerComponentSet (class in vivarium.framework.population.manager)

initializes_simulants() (vivarium.framework.population.manager.PopulationInterface method) InteractiveContext (class in vivarium.interface.interactive) InteractiveError InterpolatedTable (class in vivarium.framework.lookup.table) Interpolation (class in vivarium.framework.lookup.interpolation) interpolation_order (vivarium.framework.lookup.table.LookupTable attribute) InvalidTransitionError items() (vivarium.config_tree.ConfigTree method) (vivarium.framework.values.ValuesManager method)

K

key (vivarium.framework.randomness.stream.RandomnessStream attribute) key_columns (vivarium.framework.lookup.table.LookupTable attribute) Keys (class in vivarium.framework.artifact.artifact)

keys (vivarium.framework.artifact.artifact.Artifact property) keys() (vivarium.config_tree.ConfigTree method) (vivarium.framework.values.ValuesManager method) keyspace_node (vivarium.framework.artifact.artifact.Keys attribute)

L

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

list_loggers() (in module vivarium.framework.logging.utilities) list_values() (vivarium.interface.interactive.InteractiveContext method) load() (in module vivarium.framework.artifact.hdf) (vivarium.framework.artifact.artifact.Artifact method) (vivarium.framework.artifact.manager.ArtifactInterface method) (vivarium.framework.artifact.manager.ArtifactManager method) log_progress() (in module vivarium.interface.utilities) logging (vivarium.framework.engine.Builder attribute) LoggingInterface (class in vivarium.framework.logging.manager) LoggingManager (class in vivarium.framework.logging.manager) lookup (vivarium.framework.engine.Builder attribute) LookupTable (class in vivarium.framework.lookup.table) LookupTableInterface (class in vivarium.framework.lookup.manager) LookupTableManager (class in vivarium.framework.lookup.manager)

M

Machine (class in vivarium.framework.state_machine) make_dummy_column() (in module vivarium.testing_utilities) Manager (class in vivarium.manager) manager (vivarium.framework.values.Pipeline attribute) measure (vivarium.framework.artifact.hdf.EntityKey property) metadata (vivarium.config_tree.ConfigNode property) metadata() (in module vivarium.testing_utilities) (vivarium.config_tree.ConfigTree method) Metrics (class in vivarium.framework.metrics) minimum_step_size (vivarium.framework.time.SimulationClock property) model (vivarium.framework.state_machine.State property) Model Specification MODEL_SPECIFICATION simulate-profile command line option simulate-run command line option module vivarium vivarium.component vivarium.config_tree vivarium.exceptions vivarium.framework vivarium.framework.artifact vivarium.framework.artifact.artifact vivarium.framework.artifact.hdf vivarium.framework.artifact.manager vivarium.framework.components vivarium.framework.components.manager vivarium.framework.components.parser vivarium.framework.configuration vivarium.framework.engine vivarium.framework.event vivarium.framework.lifecycle vivarium.framework.logging vivarium.framework.logging.manager vivarium.framework.logging.utilities vivarium.framework.lookup vivarium.framework.lookup.interpolation vivarium.framework.lookup.manager vivarium.framework.lookup.table vivarium.framework.metrics vivarium.framework.plugins vivarium.framework.population vivarium.framework.population.exceptions vivarium.framework.population.manager vivarium.framework.population.population_view vivarium.framework.randomness vivarium.framework.randomness.exceptions vivarium.framework.randomness.index_map vivarium.framework.randomness.manager vivarium.framework.randomness.stream vivarium.framework.resource vivarium.framework.state_machine vivarium.framework.time vivarium.framework.utilities vivarium.framework.values vivarium.interface vivarium.interface.cli vivarium.interface.interactive vivarium.interface.utilities vivarium.manager vivarium.testing_utilities

move_simulants_to_end() (vivarium.framework.time.SimulationClock method) (vivarium.framework.time.TimeInterface method) mutators (vivarium.framework.values.Pipeline attribute)

N

name (vivarium.component.Component property) (vivarium.config_tree.ConfigNode property) (vivarium.framework.artifact.hdf.EntityKey property) (vivarium.framework.artifact.manager.ArtifactManager property) (vivarium.framework.components.manager.ComponentManager property) (vivarium.framework.engine.SimulationContext property) (vivarium.framework.event.EventManager property) (vivarium.framework.lifecycle.LifeCycleManager property) (vivarium.framework.lifecycle.LifeCyclePhase property) (vivarium.framework.lifecycle.LifeCycleState property) (vivarium.framework.logging.manager.LoggingManager property) (vivarium.framework.lookup.manager.LookupTableManager property) (vivarium.framework.lookup.table.LookupTable property) (vivarium.framework.population.manager.PopulationManager property) (vivarium.framework.population.population_view.PopulationView property) (vivarium.framework.randomness.manager.RandomnessManager property) (vivarium.framework.randomness.stream.RandomnessStream property) (vivarium.framework.resource.ResourceManager property) (vivarium.framework.state_machine.TransitionSet property) (vivarium.framework.time.DateTimeClock property) (vivarium.framework.time.SimpleClock property) (vivarium.framework.time.SimulationClock property) (vivarium.framework.values.Pipeline attribute) (vivarium.framework.values.ValuesManager property)

names (vivarium.framework.resource.ResourceGroup property) next_state() (vivarium.framework.state_machine.State method) NonCRNTestPopulation (class in vivarium.testing_utilities) NOT_TRIGGERED (vivarium.framework.state_machine.Trigger attribute)

O

on_collect_metrics() (vivarium.component.Component method) on_initialize_simulants() (vivarium.component.Component method) (vivarium.framework.population.manager.PopulationManager method) (vivarium.framework.time.SimulationClock method) (vivarium.testing_utilities.NonCRNTestPopulation method) (vivarium.testing_utilities.TestPopulation method) on_post_setup() (vivarium.component.Component method) (vivarium.framework.event.EventManager method) (vivarium.framework.time.SimulationClock method) (vivarium.framework.values.ValuesManager method)

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

P

parameter_columns (vivarium.framework.lookup.table.LookupTable attribute) parse_artifact_path_config() (in module vivarium.framework.artifact.manager) parse_component_config() (vivarium.framework.components.parser.ComponentConfigurationParser method) ParsingError path (vivarium.framework.artifact.artifact.Artifact property) (vivarium.framework.artifact.hdf.EntityKey property) Pipeline (class in vivarium.framework.values) Plugin PluginConfigurationError PluginManager (class in vivarium.framework.plugins) pop() (vivarium.framework.components.manager.OrderedComponentSet method) population (vivarium.framework.engine.Builder attribute) population_view_builder (vivarium.framework.lookup.table.LookupTable attribute)

population_view_query (vivarium.component.Component property) PopulationError PopulationInterface (class in vivarium.framework.population.manager) PopulationManager (class in vivarium.framework.population.manager) PopulationView (class in vivarium.framework.population.population_view) post_processor (vivarium.framework.values.Pipeline attribute) post_setup_priority (vivarium.component.Component property) prep_component() (vivarium.framework.components.parser.ComponentConfigurationParser method) print_initializer_order() (vivarium.interface.interactive.InteractiveContext method) print_lifecycle_order() (vivarium.interface.interactive.InteractiveContext method) probability() (vivarium.framework.state_machine.Transition method) probability_to_rate() (in module vivarium.framework.utilities) process_level() (vivarium.framework.components.parser.ComponentConfigurationParser method) producer (vivarium.framework.resource.ResourceGroup property)

Q

query (vivarium.framework.population.population_view.PopulationView property)

R

raise_if_not_setup() (in module vivarium.interface.utilities) RandomnessError RandomnessInterface (class in vivarium.framework.randomness.manager) RandomnessManager (class in vivarium.framework.randomness.manager) RandomnessStream (class in vivarium.framework.randomness.stream) rate_to_probability() (in module vivarium.framework.utilities) register_listener() (vivarium.framework.event.EventInterface method) (vivarium.framework.event.EventManager method) register_rate_producer() (vivarium.framework.values.ValuesInterface method) register_simulant_initializer() (vivarium.framework.population.manager.PopulationManager method) register_simulants() (vivarium.framework.randomness.manager.RandomnessInterface method) (vivarium.framework.randomness.manager.RandomnessManager method) register_step_size_modifier() (vivarium.framework.time.TimeInterface method) register_value_modifier() (vivarium.framework.values.ValuesInterface method) (vivarium.framework.values.ValuesManager method) register_value_producer() (vivarium.framework.values.ValuesInterface method) (vivarium.framework.values.ValuesManager method) remove() (in module vivarium.framework.artifact.hdf) (vivarium.framework.artifact.artifact.Artifact method) (vivarium.framework.artifact.artifact.Keys method)

replace() (vivarium.framework.artifact.artifact.Artifact method) replace_combiner() (in module vivarium.framework.values) report() (vivarium.framework.engine.SimulationContext method) rescale_post_processor() (in module vivarium.framework.values) reset_mocks() (in module vivarium.testing_utilities) RESIDUAL_CHOICE (in module vivarium.framework.randomness.stream) ResourceError ResourceGroup (class in vivarium.framework.resource) ResourceInterface (class in vivarium.framework.resource) ResourceManager (class in vivarium.framework.resource) resources (vivarium.framework.engine.Builder attribute) run() (vivarium.framework.engine.SimulationContext method) (vivarium.interface.interactive.InteractiveContext method) run_for() (vivarium.interface.interactive.InteractiveContext method) run_from_ipython() (in module vivarium.interface.utilities) run_simulation() (in module vivarium.framework.engine) run_until() (vivarium.interface.interactive.InteractiveContext method)

S

sample_from_distribution() (vivarium.framework.randomness.stream.RandomnessStream method) ScalarTable (class in vivarium.framework.lookup.table) seed (vivarium.framework.randomness.stream.RandomnessStream attribute) set_active() (vivarium.framework.state_machine.Transition method) set_inactive() (vivarium.framework.state_machine.Transition method) set_model() (vivarium.framework.state_machine.State method) set_state() (vivarium.framework.lifecycle.LifeCycleManager method) setup() (vivarium.component.Component method) (vivarium.framework.artifact.manager.ArtifactManager method) (vivarium.framework.components.manager.ComponentManager method) (vivarium.framework.engine.SimulationContext method) (vivarium.framework.event.EventManager method) (vivarium.framework.lookup.manager.LookupTableManager method) (vivarium.framework.metrics.Metrics method) (vivarium.framework.population.manager.PopulationManager method) (vivarium.framework.randomness.manager.RandomnessManager method) (vivarium.framework.resource.ResourceManager method) (vivarium.framework.state_machine.TransitionSet method) (vivarium.framework.time.DateTimeClock method) (vivarium.framework.time.SimpleClock method) (vivarium.framework.time.SimulationClock method) (vivarium.framework.values.ValuesManager method) (vivarium.interface.interactive.InteractiveContext method) (vivarium.manager.Manager method) (vivarium.testing_utilities.NonCRNTestPopulation method) (vivarium.testing_utilities.TestPopulation method) setup_component() (vivarium.component.Component method) setup_components() (vivarium.framework.components.manager.ComponentManager method) SIM_INDEX_COLUMN (vivarium.framework.randomness.index_map.IndexMap attribute) SimpleClock (class in vivarium.framework.time) Simulant simulant_next_event_times() (vivarium.framework.time.SimulationClock method) (vivarium.framework.time.TimeInterface method) simulant_step_sizes() (vivarium.framework.time.SimulationClock method) (vivarium.framework.time.TimeInterface method) SimulantData (class in vivarium.framework.population.manager) simulate-profile command line option --no-process --process --results_directory -o MODEL_SPECIFICATION

simulate-run command line option --artifact_path --location --pdb --quiet --results_directory --verbose -i -l -o -q -v MODEL_SPECIFICATION simulation_end_priority (vivarium.component.Component property) SimulationClock (class in vivarium.framework.time) SimulationContext (class in vivarium.framework.engine) sorted_nodes (vivarium.framework.resource.ResourceManager property) source (vivarium.config_tree.DuplicatedConfigurationError attribute) (vivarium.framework.values.Pipeline attribute) split() (vivarium.framework.event.Event method) standard_step_size (vivarium.framework.time.SimulationClock property) START_ACTIVE (vivarium.framework.state_machine.Trigger attribute) START_INACTIVE (vivarium.framework.state_machine.Trigger attribute) State (class in vivarium.framework.state_machine) State Table state_column (vivarium.framework.state_machine.Machine attribute) state_id (vivarium.framework.state_machine.State attribute) states (vivarium.framework.lifecycle.LifeCyclePhase property) (vivarium.framework.state_machine.Machine attribute) step() (vivarium.framework.engine.SimulationContext method) (vivarium.interface.interactive.InteractiveContext method) step_backward() (vivarium.framework.time.SimulationClock method) step_forward() (vivarium.framework.time.SimulationClock method) step_size (vivarium.framework.event.Event attribute) (vivarium.framework.time.SimulationClock property) step_size() (vivarium.framework.time.TimeInterface method) step_size_post_processor() (vivarium.framework.time.SimulationClock method) stop_time (vivarium.framework.time.SimulationClock property) sub_components (vivarium.component.Component property) (vivarium.framework.state_machine.Machine property) subview() (vivarium.framework.population.population_view.PopulationView method)

T

table_number (vivarium.framework.lookup.table.LookupTable attribute) take_steps() (vivarium.interface.interactive.InteractiveContext method) TEN_DIGIT_MODULUS (vivarium.framework.randomness.index_map.IndexMap attribute) TestPopulation (class in vivarium.testing_utilities) time (vivarium.framework.engine.Builder attribute) (vivarium.framework.event.Event attribute) (vivarium.framework.time.SimulationClock property) time_step_cleanup_priority (vivarium.component.Component property) time_step_prepare_priority (vivarium.component.Component property) time_step_priority (vivarium.component.Component property) TimeInterface (class in vivarium.framework.time) timings (vivarium.framework.lifecycle.LifeCycleManager property) to_dict() (vivarium.config_tree.ConfigTree method) to_guid() (vivarium.framework.lifecycle.ConstraintMaker static method)

to_list() (vivarium.framework.artifact.artifact.Keys method) to_yearly() (in module vivarium.framework.utilities) touch() (in module vivarium.framework.artifact.hdf) Transient (class in vivarium.framework.state_machine) TransientState (class in vivarium.framework.state_machine) Transition (class in vivarium.framework.state_machine) transition() (vivarium.framework.state_machine.Machine method) transition_effect() (vivarium.framework.state_machine.State method) transition_set (vivarium.framework.state_machine.State attribute) transition_side_effect() (vivarium.framework.state_machine.State method) TransitionSet (class in vivarium.framework.state_machine) Trigger (class in vivarium.framework.state_machine) type (vivarium.framework.artifact.hdf.EntityKey property) (vivarium.framework.resource.ResourceGroup property)

U

union_post_processor() (in module vivarium.framework.values) unused_keys() (vivarium.config_tree.ConfigTree method) update() (vivarium.config_tree.ConfigNode method) (vivarium.config_tree.ConfigTree method) (vivarium.framework.components.manager.OrderedComponentSet method) (vivarium.framework.population.population_view.PopulationView method) (vivarium.framework.randomness.index_map.IndexMap method)

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

V

valid_next_state() (vivarium.framework.lifecycle.LifeCycleState method) validate (vivarium.framework.lookup.table.LookupTable attribute) validate_build_table_parameters() (in module vivarium.framework.lookup.manager) validate_call_data() (in module vivarium.framework.lookup.interpolation) validate_filter_term() (in module vivarium.framework.artifact.manager) validate_model_specification_file() (in module vivarium.framework.configuration) validate_parameters() (in module vivarium.framework.lookup.interpolation) value (vivarium.config_tree.DuplicatedConfigurationError attribute) (vivarium.framework.engine.Builder attribute) value_columns (vivarium.framework.lookup.table.LookupTable attribute) values() (vivarium.config_tree.ConfigTree method) (vivarium.framework.values.ValuesManager method) ValuesInterface (class in vivarium.framework.values) ValuesManager (class in vivarium.framework.values) vivarium module vivarium.component module vivarium.config_tree module vivarium.exceptions module vivarium.framework module vivarium.framework.artifact module vivarium.framework.artifact.artifact module vivarium.framework.artifact.hdf module vivarium.framework.artifact.manager module vivarium.framework.components module vivarium.framework.components.manager module vivarium.framework.components.parser module vivarium.framework.configuration module vivarium.framework.engine module vivarium.framework.event module vivarium.framework.lifecycle module vivarium.framework.logging module vivarium.framework.logging.manager module vivarium.framework.logging.utilities module

vivarium.framework.lookup module vivarium.framework.lookup.interpolation module vivarium.framework.lookup.manager module vivarium.framework.lookup.table module vivarium.framework.metrics module vivarium.framework.plugins module vivarium.framework.population module vivarium.framework.population.exceptions module vivarium.framework.population.manager module vivarium.framework.population.population_view module vivarium.framework.randomness module vivarium.framework.randomness.exceptions module vivarium.framework.randomness.index_map module vivarium.framework.randomness.manager module vivarium.framework.randomness.stream module vivarium.framework.resource module vivarium.framework.state_machine module vivarium.framework.time module vivarium.framework.utilities module vivarium.framework.values module vivarium.interface module vivarium.interface.cli module vivarium.interface.interactive module vivarium.interface.utilities module vivarium.manager module vivarium.testing_utilities module VivariumError

W

with_measure() (vivarium.framework.artifact.hdf.EntityKey method)

write() (in module vivarium.framework.artifact.hdf) (vivarium.framework.artifact.artifact.Artifact method)