vivarium
stable
Installing Vivarium
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Concepts
API Reference
Glossary
vivarium
Index
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Index
Symbols
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A
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B
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C
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D
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E
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F
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G
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H
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I
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K
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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)
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