Index _ | A | B | C | D | E | F | G | I | L | M | N | O | P | R | S | T | U | V _ __version__ (in module sid) _add_additional_information_to_states() (in module sid.simulate) _add_color_to_gantt_groups() (in module sid.plotting) _add_default_duration_to_models() (in module sid.simulate) _add_positions() (in module sid.plotting) _adjust_channel_infected_by_contact_to_new_known_cases() (in module sid.plotting) _are_states_prepared() (in module sid.simulate) _calculate_demand_probabilities() (in module sid.testing_demand) _calculate_infections_by_random_contacts() (in module sid.contacts) _calculate_infections_by_recurrent_contacts() (in module sid.contacts) _combine_column_lists() (in module sid.simulate) _complete_dates() (in module sid.plotting) _compute_who_receives_rapid_tests() (in module sid.rapid_tests) _consolidate_reason_of_infection() (in module sid.contacts) _create_folders() (in module sid.visualize_simulation_results) _create_group_codes_and_info() (in module sid.simulate) _create_group_codes_names() (in module sid.simulate) _create_output_directory() (in module sid.simulate) _create_rate_plots() (in module sid.visualize_simulation_results) _create_rates_for_all_data() (in module sid.visualize_simulation_results) _create_sensitivity() (in module sid.rapid_tests) _create_statistics() (in module sid.visualize_simulation_results) _create_transition_matrix_from_own_prob() (in module sid.matching_probabilities) _create_y_ticks_and_labels() (in module sid.plotting) _draw_countdowns() (in module sid.pathogenesis) _dump_periodic_states() (in module sid.simulate) _einsum_kronecker_product() (in module sid.matching_probabilities) _export_plots_and_layout() (in module sid.visualize_simulation_results) _factorize_boolean_infections() (in module sid.virus_strains) _find_channel_of_infection_for_individuals() (in module sid.plotting) _find_date_where_policy_is_active() (in module sid.policies) _flatten_index() (in module sid.msm) _generate_einsum_signature() (in module sid.matching_probabilities) _generate_seeds() (in module sid.simulate) _get_index_refining_search() (in module sid.contacts) _get_mono_colors() (in module sid.colors) _get_transition_matrix_from_params() (in module sid.matching_probabilities) _get_waning_immunity_coefficients() (in module sid.update_states) _harmonize_input() (in module sid.msm) _integrate_immune_individuals() (in module sid.initial_conditions) _is_data_prepared_for_heatmap() (in module sid.plotting) _is_diagonal() (in module sid.msm) _is_dict_of_callables() (in module sid.msm) _join_transition_matrices() (in module sid.matching_probabilities) _kill_people_over_icu_limit() (in module sid.update_states) _load_data() (in module sid.visualize_simulation_results) _mono_list_to_triangle() (in module sid.colors) _msm() (in module sid.msm) _nice_str() (in module sid.visualize_simulation_results) _normalize_probabilities() (in module sid.testing_demand) _numpy_replace() (in module sid.contacts) _patch_channel_infected_by_contact() (in module sid.plotting) _plot_rates() (in module sid.visualize_simulation_results) _prepare_assortative_matching_cumulative_probabilities() (in module sid.simulate) _prepare_assortative_matching_indexers() (in module sid.simulate) _prepare_time_series() (in module sid.simulate) _prepend_column_level() (in module sid.visualize_simulation_results) _process_assort_bys() (in module sid.simulate) _process_initial_states() (in module sid.simulate) _process_saved_columns() (in module sid.simulate) _reduce_random_contacts_with_infection_probs() (in module sid.contacts) _sample_factorized_virus_strains_for_infections() (in module sid.initial_conditions) _sample_reason_for_demanding_a_test() (in module sid.testing_demand) _sample_test_outcome() (in module sid.rapid_tests) _sample_which_individuals_demand_a_test() (in module sid.testing_demand) _scale_up_initial_infections() (in module sid.initial_conditions) _scale_up_initial_infections_numba() (in module sid.initial_conditions) _simulate() (in module sid.simulate) _sort_contact_models() (in module sid.simulate) _spread_out_initial_infections() (in module sid.initial_conditions) _style() (in module sid.visualize_simulation_results) _sum_preserving_round() (in module sid.contacts) _update_countdowns() (in module sid.update_states) _update_immunity_level() (in module sid.update_states) _update_info_on_new_tests() (in module sid.update_states) _update_info_on_new_vaccinations() (in module sid.update_states) _update_info_on_newly_infected() (in module sid.update_states) _update_states_with_rapid_tests_outcomes() (in module sid.rapid_tests) _validate_model_function() (in module sid.validation) A allocate_tests() (in module sid.testing_allocation) apply_contact_policies() (in module sid.policies) apply_reactions_to_rapid_tests() (in module sid.rapid_tests) B boolean_choice() (in module sid.shared) boolean_choices() (in module sid.shared) BOOLEAN_STATE_COLUMNS (in module sid.config) C calculate_contacts() (in module sid.contacts) calculate_demand_for_tests() (in module sid.testing_demand) calculate_infections_by_contacts() (in module sid.contacts) calculate_infections_by_events() (in module sid.events) calculate_r_effective() (in module sid.statistics) calculate_r_zero() (in module sid.statistics) CAT_LIST (in module sid.colors) categorize_factorized_infections() (in module sid.virus_strains) choose_other_group() (in module sid.contacts) choose_other_individual() (in module sid.contacts) combine_first_factorized_infections() (in module sid.virus_strains) COMMON_ARGS (in module sid.validation) compute_pseudo_effect_sizes_of_policies() (in module sid.policies) compute_waning_immunity() (in module sid.update_states) COUNTDOWNS (in module sid.countdowns) COUNTDOWNS_WITH_DRAWS (in module sid.countdowns) COUNTDOWNS_WITHOUT_DRAWS (in module sid.countdowns) create_cumulative_group_transition_probabilities() (in module sid.matching_probabilities) create_group_indexer() (in module sid.contacts) D DEFAULT_FIGURE_KWARGS (in module sid.plotting) DEFAULT_IR_PER_CM_KWARGS (in module sid.plotting) DEFAULT_VIRUS_STRAINS (in module sid.config) draw_course_of_disease() (in module sid.pathogenesis) DTYPE_CONTACT_MODEL_CODES (in module sid.config) DTYPE_COUNTDOWNS (in module sid.config) DTYPE_DRAW_COURSE_OF_DISEASE (in module sid.config) DTYPE_GROUP_CODE (in module sid.config) DTYPE_GROUP_TRANSITION_PROBABILITIES (in module sid.config) DTYPE_IMMUNITY (in module sid.config) DTYPE_INDEX (in module sid.config) DTYPE_INFECTION_COUNTER (in module sid.config) DTYPE_N_CONTACTS (in module sid.config) DTYPE_SID_PERIOD (in module sid.config) DTYPE_VIRUS_STRAIN (in module sid.config) DTYPE_VIRUS_STRAIN_CODES (in module sid.config) E ERROR_MISSING_CHANNEL (in module sid.plotting) F factorize_assortative_variables() (in module sid.shared) factorize_boolean_or_categorical_infections() (in module sid.virus_strains) factorize_categorical_infections() (in module sid.virus_strains) factorize_initial_infections() (in module sid.virus_strains) fast_condition_evaluator() (in module sid.shared) G get_colors() (in module sid) (in module sid.colors) get_date() (in module sid) (in module sid.time) get_diag_weighting_matrix() (in module sid.msm) get_flat_moments() (in module sid.msm) get_msm_func() (in module sid) (in module sid.msm) get_simulate_func() (in module sid) (in module sid.simulate) I INDEX_NAMES (in module sid.config) INITIAL_CONDITIONS (in module sid.config) L load_epidemiological_parameters() (in module sid) (in module sid.shared) logger (in module sid.simulate) M module sid sid._version sid.colors sid.config sid.contacts sid.countdowns sid.events sid.initial_conditions sid.matching_probabilities sid.msm sid.parse_model sid.pathogenesis sid.plotting sid.policies sid.rapid_tests sid.seasonality sid.shared sid.simulate sid.statistics sid.susceptibility sid.testing sid.testing_allocation sid.testing_demand sid.testing_processing sid.time sid.update_states sid.vaccination sid.validation sid.virus_strains sid.visualize_simulation_results MONO_COLORS (in module sid.colors) N NECESSARY_CONTACT_MODEL_KEYS (in module sid.validation) NECESSARY_CONTACT_POLICY_KEYS (in module sid.validation) O ORDERED (in module sid.colors) P parse_duration() (in module sid.parse_model) parse_initial_conditions() (in module sid.parse_model) parse_virus_strains() (in module sid.parse_model) perform_rapid_tests() (in module sid.rapid_tests) perform_testing() (in module sid.testing) period_to_timestamp() (in module sid.time) plot_colors() (in module sid.colors) plot_infection_rates_by_contact_models() (in module sid.plotting) plot_policy_gantt_chart() (in module sid.plotting) post_process_contacts() (in module sid.contacts) prepare_data_for_infection_rates_by_contact_models() (in module sid.plotting) prepare_seasonality_factor() (in module sid.seasonality) prepare_susceptibility_factor() (in module sid.susceptibility) prepare_virus_strain_factors() (in module sid.virus_strains) process_tests() (in module sid.testing_processing) R random_choice() (in module sid.shared) RELATIVE_POPULATION_PARAMETER (in module sid.config) ROOT_DIR (in module sid.config) S sample_initial_distribution_of_infections_and_immunity() (in module sid.initial_conditions) sample_initial_immunity() (in module sid) (in module sid.initial_conditions) sample_initial_infections() (in module sid) (in module sid.initial_conditions) SAVED_COLUMNS (in module sid.config) separate_contact_model_names() (in module sid.shared) sid module sid._version module sid.colors module sid.config module sid.contacts module sid.countdowns module sid.events module sid.initial_conditions module sid.matching_probabilities module sid.msm module sid.parse_model module sid.pathogenesis module sid.plotting module sid.policies module sid.rapid_tests module sid.seasonality module sid.shared module sid.simulate module sid.statistics module sid.susceptibility module sid.testing module sid.testing_allocation module sid.testing_demand module sid.testing_processing module sid.time module sid.update_states module sid.vaccination module sid.validation module sid.virus_strains module sid.visualize_simulation_results module sid_period_to_timestamp (in module sid) (in module sid.time) SID_TIME_START (in module sid.config) T timestamp_to_period() (in module sid.time) timestamp_to_sid_period (in module sid) (in module sid.time) U update_derived_state_variables() (in module sid.update_states) update_pending_tests() (in module sid.testing_allocation) update_states() (in module sid.update_states) V vaccinate_individuals() (in module sid.vaccination) validate_contact_models() (in module sid.validation) validate_contact_policies() (in module sid.validation) validate_initial_states() (in module sid.validation) validate_params() (in module sid.validation) validate_prepared_initial_states() (in module sid.validation) validate_return_is_series_or_ndarray() (in module sid.validation) validate_testing_models() (in module sid.validation) validate_vaccination_models() (in module sid.validation) version (in module sid._version) version_tuple (in module sid._version) visualize_simulation_results() (in module sid.visualize_simulation_results)