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Installing Vivarium
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API Reference
Glossary
vivarium
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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)
age_simulants() (vivarium.testing_utilities.NonCRNTestPopulation 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.LookupTableInterface method)
(vivarium.framework.lookup.LookupTableManager method)
Builder (class in vivarium.framework.engine)
C
categorical_parameters (vivarium.interpolation.Interpolation attribute)
check_data_complete() (in module vivarium.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)
clean_args() (in module vivarium.framework.components.parser)
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.InterpolatedTable attribute)
(vivarium.framework.randomness.stream.RandomnessStream attribute)
clock() (vivarium.framework.time.TimeInterface method)
collapse_nested_dict() (in module vivarium.framework.utilities)
columns (vivarium.framework.population.manager.PopulationManager property)
(vivarium.framework.population.population_view.PopulationView property)
combiner (vivarium.framework.values.Pipeline attribute)
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.framework.artifact.manager.ArtifactManager attribute)
(vivarium.framework.lookup.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.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.interpolation.Interpolation attribute)
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.InterpolatedTable attribute)
(vivarium.interpolation.Interpolation attribute)
(vivarium.interpolation.Order0Interp attribute)
DateTimeClock (class in vivarium.framework.time)
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)
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.InterpolatedTable 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
generate_test_population() (vivarium.testing_utilities.NonCRNTestPopulation method)
(vivarium.testing_utilities.TestPopulation method)
get() (vivarium.framework.population.population_view.PopulationView 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_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_components() (in module vivarium.framework.components.parser)
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)
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)
Interpolation (class in vivarium.interpolation)
interpolation_order (vivarium.framework.lookup.InterpolatedTable 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.InterpolatedTable 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)
LookupTableInterface (class in vivarium.framework.lookup)
LookupTableManager (class in vivarium.framework.lookup)
M
Machine (class in vivarium.framework.state_machine)
make_dummy_column() (in module vivarium.testing_utilities)
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)
Model Specification
MODEL_SPECIFICATION
simulate-profile command line option
simulate-run command line option
module
vivarium
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.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.interpolation
vivarium.testing_utilities
mutators (vivarium.framework.values.Pipeline attribute)
N
name (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.LookupTable property)
(vivarium.framework.lookup.LookupTableManager property)
(vivarium.framework.metrics.Metrics 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.Machine property)
(vivarium.framework.state_machine.State property)
(vivarium.framework.state_machine.Transition 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)
(vivarium.testing_utilities.NonCRNTestPopulation property)
(vivarium.testing_utilities.TestPopulation 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_initialize_simulants() (vivarium.framework.population.manager.PopulationManager method)
on_post_setup() (vivarium.framework.event.EventManager method)
(vivarium.framework.values.ValuesManager method)
order (vivarium.interpolation.Interpolation attribute)
Order0Interp (class in vivarium.interpolation)
OrderedComponentSet (class in vivarium.framework.components.manager)
P
parameter_columns (vivarium.framework.lookup.InterpolatedTable attribute)
(vivarium.interpolation.Order0Interp attribute)
parse_artifact_path_config() (in module vivarium.framework.artifact.manager)
parse_component_config() (vivarium.framework.components.parser.ComponentConfigurationParser method)
parse_component_config_to_list() (in module vivarium.framework.components.parser)
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 (vivarium.framework.lookup.InterpolatedTable attribute)
(vivarium.framework.state_machine.Machine attribute)
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)
prep_components() (in module vivarium.framework.components.parser)
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)
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_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
ScalarTable (class in vivarium.framework.lookup)
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.framework.artifact.manager.ArtifactManager method)
(vivarium.framework.components.manager.ComponentManager method)
(vivarium.framework.engine.SimulationContext method)
(vivarium.framework.event.EventManager method)
(vivarium.framework.lookup.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.Machine method)
(vivarium.framework.state_machine.State method)
(vivarium.framework.state_machine.Transition method)
(vivarium.framework.state_machine.TransitionSet method)
(vivarium.framework.time.DateTimeClock method)
(vivarium.framework.time.SimpleClock method)
(vivarium.framework.values.ValuesManager method)
(vivarium.interface.interactive.InteractiveContext method)
(vivarium.testing_utilities.NonCRNTestPopulation method)
(vivarium.testing_utilities.TestPopulation 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
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
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)
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)
stop_time (vivarium.framework.time.SimulationClock property)
sub_components (vivarium.framework.state_machine.Machine property)
(vivarium.framework.state_machine.State property)
(vivarium.framework.state_machine.TransitionSet property)
subview() (vivarium.framework.population.population_view.PopulationView method)
T
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)
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)
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_call_data() (in module vivarium.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)
(in module vivarium.interpolation)
value (vivarium.config_tree.DuplicatedConfigurationError attribute)
(vivarium.framework.engine.Builder attribute)
value_columns (vivarium.framework.lookup.InterpolatedTable attribute)
(vivarium.framework.lookup.ScalarTable attribute)
values (vivarium.framework.lookup.ScalarTable 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.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.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.interpolation
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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