Index

_

__init__() (dynode.config.bins.AgeBin method) (dynode.config.bins.Bin method) (dynode.config.bins.DiscretizedPositiveIntBin method) (dynode.config.bins.WaneBin method) (dynode.config.deterministic_parameter.DeterministicParameter method) (dynode.config.dimension.Dimension method) (dynode.config.dimension.FullStratifiedImmuneHistoryDimension method) (dynode.config.dimension.ImmuneHistoryDimension method) (dynode.config.dimension.LastStrainImmuneHistoryDimension method) (dynode.config.dimension.VaccinationDimension method) (dynode.config.dimension.WaneDimension method) (dynode.config.initializer.Initializer method) (dynode.config.params.Params method) (dynode.config.params.SolverParams method) (dynode.config.params.TransmissionParams method) (dynode.config.placeholder_sample.PlaceholderSample method) (dynode.config.simulation_config.Compartment method) (dynode.config.simulation_config.SimulationConfig method) (dynode.config.strains.Strain method) (dynode.infer.inference.InferenceProcess method) (dynode.infer.inference.MCMCProcess method) (dynode.infer.inference.SVIProcess method) (dynode.simulation.odes.AbstractODEParams method) (dynode.utils.custom_log_formatter.CustomLogFormatter method) _abc_impl (dynode.config.bins.AgeBin attribute) (dynode.config.bins.Bin attribute) (dynode.config.bins.DiscretizedPositiveIntBin attribute) (dynode.config.bins.WaneBin attribute) (dynode.config.dimension.Dimension attribute) (dynode.config.dimension.FullStratifiedImmuneHistoryDimension attribute) (dynode.config.dimension.ImmuneHistoryDimension attribute) (dynode.config.dimension.LastStrainImmuneHistoryDimension attribute) (dynode.config.dimension.VaccinationDimension attribute) (dynode.config.dimension.WaneDimension attribute) (dynode.config.initializer.Initializer attribute) (dynode.config.params.Params attribute) (dynode.config.params.SolverParams attribute) (dynode.config.params.TransmissionParams attribute) (dynode.config.simulation_config.Compartment attribute) (dynode.config.simulation_config.SimulationConfig attribute) (dynode.config.strains.Strain attribute) (dynode.infer.inference.InferenceProcess attribute) (dynode.infer.inference.MCMCProcess attribute) (dynode.infer.inference.SVIProcess attribute) (dynode.simulation.odes.AbstractODEParams attribute)

_bin_valid_side() (dynode.config.bins.DiscretizedPositiveIntBin method) _check_bin_names_unique() (dynode.config.dimension.Dimension class method) _check_bins_same_type() (dynode.config.dimension.Dimension class method) _create_introduction_ages_mask_encoding() (dynode.config.simulation_config.SimulationConfig method) _inference_complete (dynode.infer.inference.InferenceProcess attribute) _inference_state (dynode.infer.inference.InferenceProcess attribute) _inferer (dynode.infer.inference.InferenceProcess attribute) _inferer_kwargs (dynode.infer.inference.InferenceProcess attribute) _validate_dimensions_names() (dynode.config.simulation_config.Compartment method) _validate_discretized_int_bins_sorted() (dynode.config.dimension.Dimension class method) _validate_immune_histories() (dynode.config.simulation_config.SimulationConfig method) _validate_introduced_strains() (dynode.config.simulation_config.SimulationConfig method) _validate_no_gaps_discretized_int_bins() (dynode.config.dimension.Dimension class method) _validate_no_shared_compartment_names() (dynode.config.simulation_config.SimulationConfig method) _validate_shared_compartment_dimensions() (dynode.config.simulation_config.SimulationConfig method) _validate_strain_interactions() (dynode.config.params.TransmissionParams method) _validate_strains_field_matching() (dynode.config.params.TransmissionParams class method) _validate_strains_field_not_empty() (dynode.config.params.TransmissionParams class method) _validate_wane_bins_end_in_inf() (dynode.config.dimension.WaneDimension method)

A

AbstractODEParams (class in dynode.simulation.odes)

AgeBin (class in dynode.config.bins)

B

base_equation() (in module dynode.utils.splines) base_protection (dynode.config.bins.WaneBin attribute)

Bin (class in dynode.config.bins) bins (dynode.config.dimension.Dimension attribute) build_saveat() (in module dynode.simulation.odes)

C

checkpoint_compartment_sizes() (in module dynode.infer.checkpointing) Compartment (class in dynode.config.simulation_config) compartments (dynode.config.simulation_config.SimulationConfig attribute)

conditional_knots() (in module dynode.utils.splines) constant_step_size (dynode.config.params.SolverParams attribute) CustomLogFormatter (class in dynode.utils.custom_log_formatter)

D

date_to_epi_week() (in module dynode.utils.datetime_utils) date_to_sim_day() (in module dynode.utils.datetime_utils) description (dynode.config.initializer.Initializer attribute) DeterministicParameter (class in dynode.config.deterministic_parameter) Dimension (class in dynode.config.dimension) dimensions (dynode.config.simulation_config.Compartment attribute) discontinuity_points (dynode.config.params.SolverParams attribute) DiscretizedPositiveIntBin (class in dynode.config.bins) drop_keys_with_substring() (in module dynode.utils.utils) dynode module dynode.config module dynode.config.bins module dynode.config.deterministic_parameter module dynode.config.dimension module dynode.config.initializer module dynode.config.params module dynode.config.placeholder_sample module dynode.config.simulation_config module dynode.config.simulation_date module dynode.config.strains module

dynode.infer module dynode.infer.checkpointing module dynode.infer.inference module dynode.infer.sample module dynode.simulation module dynode.simulation.odes module dynode.typing module dynode.typing.typing module dynode.utils module dynode.utils.custom_log_formatter module dynode.utils.datetime_utils module dynode.utils.log module dynode.utils.log_decorator module dynode.utils.splines module dynode.utils.utils module dynode.utils.vis_utils module

E

evaluate_cubic_spline() (in module dynode.utils.splines)

exposed_to_infectious (dynode.config.strains.Strain attribute)

F

flatten_bins() (dynode.config.simulation_config.SimulationConfig method) flatten_dims() (dynode.config.simulation_config.SimulationConfig method) flatten_list_parameters() (in module dynode.utils.utils)

format() (dynode.utils.custom_log_formatter.CustomLogFormatter method) from_tuple() (dynode.simulation.odes.AbstractODEParams method) FullStratifiedImmuneHistoryDimension (class in dynode.config.dimension)

G

get_compartment() (dynode.config.simulation_config.SimulationConfig method) get_dynode_init_date_flag() (in module dynode.config.simulation_date) get_initial_state() (dynode.config.initializer.Initializer method) get_samples() (dynode.infer.inference.InferenceProcess method) (dynode.infer.inference.MCMCProcess method) (dynode.infer.inference.SVIProcess method)

guide_class (dynode.infer.inference.SVIProcess attribute) guide_init_strategy (dynode.infer.inference.SVIProcess attribute) guide_kwargs (dynode.infer.inference.SVIProcess attribute)

I

identify_distribution_indexes() (in module dynode.utils.utils) idx (dynode.config.dimension.Dimension property) (dynode.config.simulation_config.Compartment property) (dynode.config.simulation_config.SimulationConfig property) ImmuneHistoryDimension (class in dynode.config.dimension) infectious_period (dynode.config.strains.Strain attribute) infer() (dynode.infer.inference.InferenceProcess method) (dynode.infer.inference.MCMCProcess method) (dynode.infer.inference.SVIProcess method) inference_prngkey (dynode.infer.inference.InferenceProcess attribute)

InferenceProcess (class in dynode.infer.inference) initialize_date (dynode.config.initializer.Initializer attribute) Initializer (class in dynode.config.initializer) initializer (dynode.config.simulation_config.SimulationConfig attribute) introduction_ages (dynode.config.strains.Strain attribute) introduction_ages_mask_vector (dynode.config.strains.Strain attribute) introduction_percentage (dynode.config.strains.Strain attribute) introduction_scale (dynode.config.strains.Strain attribute) introduction_time (dynode.config.strains.Strain attribute) is_introduced (dynode.config.strains.Strain attribute) items() (dynode.simulation.odes.AbstractODEParams method)

K

keys() (dynode.simulation.odes.AbstractODEParams method)

L

LastStrainImmuneHistoryDimension (class in dynode.config.dimension)

M

max_shots (dynode.config.dimension.VaccinationDimension property) max_steps (dynode.config.params.SolverParams attribute) max_value (dynode.config.bins.DiscretizedPositiveIntBin attribute) mcmc_kwargs (dynode.infer.inference.MCMCProcess attribute) MCMCProcess (class in dynode.infer.inference) min_value (dynode.config.bins.DiscretizedPositiveIntBin attribute) model_config (dynode.config.bins.AgeBin attribute) (dynode.config.bins.Bin attribute) (dynode.config.bins.DiscretizedPositiveIntBin attribute) (dynode.config.bins.WaneBin attribute) (dynode.config.dimension.Dimension attribute) (dynode.config.dimension.FullStratifiedImmuneHistoryDimension attribute) (dynode.config.dimension.ImmuneHistoryDimension attribute) (dynode.config.dimension.LastStrainImmuneHistoryDimension attribute) (dynode.config.dimension.VaccinationDimension attribute) (dynode.config.dimension.WaneDimension attribute) (dynode.config.initializer.Initializer attribute) (dynode.config.params.Params attribute) (dynode.config.params.SolverParams attribute) (dynode.config.params.TransmissionParams attribute) (dynode.config.simulation_config.Compartment attribute) (dynode.config.simulation_config.SimulationConfig attribute) (dynode.config.strains.Strain attribute) (dynode.infer.inference.InferenceProcess attribute) (dynode.infer.inference.MCMCProcess attribute) (dynode.infer.inference.SVIProcess attribute) model_post_init() (dynode.infer.inference.InferenceProcess method) (dynode.infer.inference.MCMCProcess method) (dynode.infer.inference.SVIProcess method)

module dynode dynode.config dynode.config.bins dynode.config.deterministic_parameter dynode.config.dimension dynode.config.initializer dynode.config.params dynode.config.placeholder_sample dynode.config.simulation_config dynode.config.simulation_date dynode.config.strains dynode.infer dynode.infer.checkpointing dynode.infer.inference dynode.infer.sample dynode.simulation dynode.simulation.odes dynode.typing dynode.typing.typing dynode.utils dynode.utils.custom_log_formatter dynode.utils.datetime_utils dynode.utils.log dynode.utils.log_decorator dynode.utils.splines dynode.utils.utils dynode.utils.vis_utils

N

name (dynode.config.bins.Bin attribute) (dynode.config.dimension.Dimension attribute) (dynode.config.simulation_config.Compartment attribute) num_chains (dynode.infer.inference.MCMCProcess attribute) num_iterations (dynode.infer.inference.SVIProcess attribute) num_samples (dynode.infer.inference.MCMCProcess attribute) (dynode.infer.inference.SVIProcess attribute)

num_warmup (dynode.infer.inference.MCMCProcess attribute) numpyro_model (dynode.infer.inference.InferenceProcess attribute) nuts_init_strategy (dynode.infer.inference.MCMCProcess attribute) nuts_kwargs (dynode.infer.inference.MCMCProcess attribute) nuts_max_tree_depth (dynode.infer.inference.MCMCProcess attribute)

O

ode_solver_abs_tolerance (dynode.config.params.SolverParams attribute)

ode_solver_rel_tolerance (dynode.config.params.SolverParams attribute) optimizer (dynode.infer.inference.SVIProcess attribute)

P

parameters (dynode.config.simulation_config.SimulationConfig attribute) Params (class in dynode.config.params) PlaceholderSample (class in dynode.config.placeholder_sample) plot_checkpoint_inference_correlation_pairs() (in module dynode.utils.vis_utils) plot_mcmc_chains() (in module dynode.utils.vis_utils)

plot_model_overview_subplot_matplotlib() (in module dynode.utils.vis_utils) plot_prior_distributions() (in module dynode.utils.vis_utils) plot_violin_plots() (in module dynode.utils.vis_utils) population_size (dynode.config.initializer.Initializer attribute) progress_bar (dynode.infer.inference.MCMCProcess attribute) (dynode.infer.inference.SVIProcess attribute)

R

r0 (dynode.config.strains.Strain attribute) replace() (dynode.simulation.odes.AbstractODEParams method)

resolve() (dynode.config.deterministic_parameter.DeterministicParameter method) resolve_deterministic() (in module dynode.infer.sample)

S

sample() (dynode.config.placeholder_sample.PlaceholderSample method) sample_distributions() (in module dynode.infer.sample) sample_then_resolve() (in module dynode.infer.sample) SamplePlaceholderError seasonal_vaccination (dynode.config.dimension.VaccinationDimension attribute) set_dynode_init_date_flag() (in module dynode.config.simulation_date) shape (dynode.config.simulation_config.Compartment property) sim_day_to_date() (in module dynode.utils.datetime_utils) sim_day_to_epiweek() (in module dynode.utils.datetime_utils) simulate() (in module dynode.simulation.odes)

simulation_day() (in module dynode.config.simulation_date) SimulationConfig (class in dynode.config.simulation_config) solver_method (dynode.config.params.SolverParams attribute) solver_params (dynode.config.params.Params attribute) SolverParams (class in dynode.config.params) static_keynames (dynode.simulation.odes.AbstractODEParams attribute) Strain (class in dynode.config.strains) strain_interactions (dynode.config.params.TransmissionParams attribute) strain_name (dynode.config.strains.Strain attribute) strains (dynode.config.params.TransmissionParams attribute) SVIProcess (class in dynode.infer.inference)

T

to_arviz() (dynode.infer.inference.InferenceProcess method) (dynode.infer.inference.MCMCProcess method) (dynode.infer.inference.SVIProcess method)

to_tuple() (dynode.simulation.odes.AbstractODEParams method) transmission_params (dynode.config.params.Params attribute) TransmissionParams (class in dynode.config.params)

U

use_logging() (in module dynode.utils.log)

V

VaccinationDimension (class in dynode.config.dimension) vaccine_efficacy (dynode.config.strains.Strain attribute)

values() (dynode.simulation.odes.AbstractODEParams method) vectorize_objects() (in module dynode.utils.utils) VisualizationError

W

waiting_time (dynode.config.bins.WaneBin attribute)

WaneBin (class in dynode.config.bins) WaneDimension (class in dynode.config.dimension)