Index Symbols | _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | X | Y | Z Symbols --adm-mapping-file bucky-viz-plot command line option --cfg bucky command line option --columns bucky-viz-plot command line option --cpu bucky command line option --debug bucky command line option --input-dir bucky-viz-plot command line option --levels bucky-viz-plot command line option --nhist bucky-viz-plot command line option --no-color bucky command line option --num_proc bucky-viz-plot command line option --output-dir bucky-viz-plot command line option --plot_fit bucky-viz-plot command line option --plot_hist bucky-viz-plot command line option --run-dir bucky-run-postprocess command line option --runid bucky-run command line option bucky-run-model command line option --start-date bucky-run command line option bucky-run-model command line option --verbose bucky command line option --window bucky-viz-plot command line option -c bucky command line option bucky-run-postprocess command line option bucky-viz-plot command line option -d bucky command line option bucky-run command line option bucky-run-model command line option -g bucky-run-postprocess command line option -l bucky-viz-plot command line option -n bucky-run command line option bucky-run-model command line option -nh bucky-viz-plot command line option -np bucky-viz-plot command line option -s bucky-run command line option bucky-run-model command line option -v bucky command line option -w bucky-viz-plot command line option _ __delitem__() (bucky.util.nested_dict.NestedDict method) __get__() (bucky.util.cached_prop.cached_property method) __getattribute__() (bucky.model.state.buckyState method) __getitem__() (bucky.util.nested_dict.NestedDict method) __iter__() (bucky.util.nested_dict.NestedDict method) __len__() (bucky.data.adm_mapping.AdminLevel method) (bucky.util.nested_dict.NestedDict method) __post_init__() (bucky.data.CSSEData method) (bucky.data.timeseries.CSSEData method) (bucky.data.timeseries.SpatialStratifiedTimeseries method) __repr__() (bucky.data.adm_mapping.AdminLevel method) (bucky.data.adm_mapping.AdminLevelMapping method) (bucky.data.AdminLevelMapping method) (bucky.data.timeseries.SpatialStratifiedTimeseries method) (bucky.util.nested_dict.NestedDict method) __setattr__() (bucky.model.state.buckyState method) __setitem__() (bucky.util.nested_dict.NestedDict method) __version__ (in module bucky) _absorb_constraints() (in module bucky.util.spline_smooth) _banner() (in module bucky.util.util) _cached_polyfit() (in module bucky.util.extrapolate) _cast_floats() (bucky.config.BuckyConfig method) _compute_base_functions() (in module bucky.util.spline_smooth) _cr() (in module bucky.util.spline_smooth) _exec_shell_cmd() (in module bucky.util.data_sync) _find_knots_lower_bounds() (in module bucky.util.spline_smooth) _fixed_width_to_csv() (in module bucky.datasource_transforms.bin_bridged_race_census_csv) _gaussian_kernel() (in module bucky.util.loess) _generic_from_csv() (bucky.data.timeseries.SpatialStratifiedTimeseries static method) _get_free_crs_dmatrix() (in module bucky.util.spline_smooth) _get_natural_f() (in module bucky.util.spline_smooth) _git_clone() (in module bucky.util.data_sync) _git_pull() (in module bucky.util.data_sync) _hash_file_obj() (in module bucky.util.data_sync) _is_dict_type() (in module bucky.util.nested_dict) _is_list_type() (in module bucky.util.nested_dict) _load_one_cfg() (bucky.config.BuckyConfig method) _locate_included_data() (in module bucky.util.data_sync) _mask_date_range() (in module bucky.data.timeseries) _normalize() (bucky.model.adjmat.buckyAij method) _pool_plot() (in module bucky.viz.plot) _process_one_datasource() (in module bucky.util.data_sync) _set_default_variances() (bucky.config.BuckyConfig method) _thread_target() (in module bucky.util.async_thread) _to_arrays() (bucky.config.BuckyConfig method) _to_lists() (bucky.config.BuckyConfig method) _tricubic_kernel() (in module bucky.util.loess) _unzip_file_obj_to_dir() (in module bucky.util.data_sync) _write_filelike() (in module bucky.util.data_sync) A A (bucky.model.adjmat.buckyAij property) abbrs (bucky.data.adm_mapping.AdminLevel attribute) actual_adm1_ids() (bucky.data.adm_mapping.AdminLevelMapping method) (bucky.data.AdminLevelMapping method) add_derived_params() (in module bucky.model.derived_epi_params) add_npi() (bucky.model.mc_instance.buckyMCInstance method) add_simulation_data_to_axis() (in module bucky.viz.plot) add_vacc() (bucky.model.mc_instance.buckyMCInstance method) adm0 (bucky.cli.viz.AdmLevel attribute) (bucky.data.adm_mapping.AdminLevelMapping attribute) (bucky.data.AdminLevelMapping attribute) adm0_cum_case_hist() (bucky.model.data.buckyData method) adm0_cum_death_hist() (bucky.model.data.buckyData method) adm0_inc_case_hist() (bucky.model.data.buckyData method) adm0_inc_death_hist() (bucky.model.data.buckyData method) adm0_Ni() (bucky.model.data.buckyData method) adm1 (bucky.cli.viz.AdmLevel attribute) (bucky.data.adm_mapping.AdminLevelMapping attribute) (bucky.data.AdminLevelMapping attribute) adm1_cum_case_hist() (bucky.model.data.buckyData method) adm1_cum_death_hist() (bucky.model.data.buckyData method) adm1_inc_case_hist() (bucky.model.data.buckyData method) adm1_inc_death_hist() (bucky.model.data.buckyData method) adm1_Nij() (bucky.model.data.buckyData method) adm1_Nj() (bucky.model.data.buckyData method) adm2 (bucky.cli.viz.AdmLevel attribute) (bucky.data.adm_mapping.AdminLevelMapping attribute) (bucky.data.AdminLevelMapping attribute) adm_ids (bucky.data.timeseries.SpatialStratifiedTimeseries attribute) adm_level (bucky.data.timeseries.SpatialStratifiedTimeseries attribute) adm_mapping (bucky.data.timeseries.SpatialStratifiedTimeseries attribute) AdminLevel (class in bucky.data.adm_mapping) AdminLevelMapping (class in bucky.data) (class in bucky.data.adm_mapping) AdmLevel (class in bucky.cli.viz) age_bin_interp() (in module bucky.util.age_interp) Aij (bucky.model.mc_instance.buckyMCInstance property) ALLOW_FUNCTOOLS (in module bucky.util.cached_prop) app (in module bucky.cli.cfg) (in module bucky.cli.data) (in module bucky.cli.run) (in module bucky.cli.viz) apply() (bucky.util.nested_dict.NestedDict method) approx_betaincinv() (in module bucky.util.distributions) approx_mPERT() (in module bucky.util.distributions) ArrayLike (in module bucky._typing) AsyncQueueThread (class in bucky.util.async_thread) B base_cfg (in module bucky.config) BETA_eff() (bucky.model.mc_instance.buckyMCInstance method) bin_census_data() (in module bucky.datasource_transforms.bin_bridged_race_census_csv) BoxCox (class in bucky.util.power_transforms) boxcox() (in module bucky.util.power_transforms) bucky module bucky command line option --cfg --cpu --debug --no-color --verbose -c -d -v bucky-run command line option --runid --start-date -d -n -s bucky-run-model command line option --runid --start-date -d -n -s bucky-run-postprocess command line option --run-dir -c -g bucky-viz-plot command line option --adm-mapping-file --columns --input-dir --levels --nhist --num_proc --output-dir --plot_fit --plot_hist --window -c -l -nh -np -w bucky.__main__ module bucky._typing module bucky.cli module bucky.cli.__main__ module bucky.cli.cfg module bucky.cli.data module bucky.cli.main module bucky.cli.run module bucky.cli.typer_utils module bucky.cli.viz module bucky.config module bucky.data module bucky.data.adm_mapping module bucky.data.clean_historical_data module bucky.data.timeseries module bucky.datasource_transforms module bucky.datasource_transforms.bin_bridged_race_census_csv module bucky.datasource_transforms.csse_timeseries module bucky.datasource_transforms.extract_shapefile_data module bucky.datasource_transforms.hhs_hosp_cleanup module bucky.datasource_transforms.prem_2020_csv module bucky.exceptions module bucky.model module bucky.model.adjmat module bucky.model.data module bucky.model.derived_epi_params module bucky.model.estimation module bucky.model.exceptions module bucky.model.io module bucky.model.main module bucky.model.mc_instance module bucky.model.npi module bucky.model.rhs module bucky.model.state module bucky.model.vacc module bucky.numerical_libs module bucky.postprocess module bucky.util module bucky.util.age_interp module bucky.util.array_utils module bucky.util.async_thread module bucky.util.cached_prop module bucky.util.data_sync module bucky.util.detect_cupy module bucky.util.distributions module bucky.util.extrapolate module bucky.util.fractional_slice module bucky.util.import_by_name module bucky.util.loess module bucky.util.nested_dict module bucky.util.ode_constraints module bucky.util.power_transforms module bucky.util.scoring module bucky.util.spline_smooth module bucky.util.util module bucky.util.working_directory module bucky.viz module bucky.viz.plot module bucky.viz.readable_col_names module bucky.viz.utils module buckyAij (class in bucky.model.adjmat) BuckyConfig (class in bucky.config) buckyData (class in bucky.model.data) BuckyException BuckyFittedCaseData (class in bucky.data.timeseries) BuckyFittedData (class in bucky.data.timeseries) buckyMCInstance (class in bucky.model.mc_instance) buckyModelCovid (class in bucky.model.main) BuckyOutputWriter (class in bucky.model.io) buckyState (class in bucky.model.state) BuckySyncException buckyVaccAlloc (class in bucky.model.vacc) C cached_property (class in bucky.util.cached_prop) cached_scatter_add() (in module bucky.model.data) calc_beta() (in module bucky.model.derived_epi_params) calc_gamma() (in module bucky.model.derived_epi_params) calc_lagged_rate() (bucky.model.main.buckyModelCovid static method) calc_Reff() (in module bucky.model.derived_epi_params) calc_Te() (in module bucky.model.derived_epi_params) calc_Ti() (in module bucky.model.derived_epi_params) callback_to_click_command() (in module bucky.cli.typer_utils) cfg (in module bucky.config) Cij() (bucky.model.mc_instance.buckyMCInstance method) clean_historical_data() (in module bucky.data.clean_historical_data) close() (bucky.model.io.BuckyOutputWriter method) (bucky.util.async_thread.AsyncQueueThread method) common() (in module bucky.cli.main) constrain_y_range() (in module bucky.util.ode_constraints) CSSEData (class in bucky.data) (class in bucky.data.timeseries) cumulative_cases (bucky.data.CSSEData attribute) (bucky.data.timeseries.BuckyFittedCaseData attribute) (bucky.data.timeseries.BuckyFittedData attribute) (bucky.data.timeseries.CSSEData attribute) cumulative_deaths (bucky.data.CSSEData attribute) (bucky.data.timeseries.BuckyFittedCaseData attribute) (bucky.data.timeseries.BuckyFittedData attribute) (bucky.data.timeseries.CSSEData attribute) cupy_available() (in module bucky.util.detect_cupy) CUPY_FORCE_FP32 (in module bucky.numerical_libs) current_hospitalizations (bucky.data.HHSData attribute) (bucky.data.timeseries.HHSData attribute) D dates (bucky.data.timeseries.SpatialStratifiedTimeseries attribute) default_plot() (in module bucky.viz.plot) device_count (in module bucky.numerical_libs) diag (bucky.model.adjmat.buckyAij property) dtype (in module bucky.util.spline_smooth) E empty_like_pinned (in module bucky.numerical_libs) empty_pinned (in module bucky.numerical_libs) enable_cupy() (in module bucky.numerical_libs) end_date (bucky.data.timeseries.SpatialStratifiedTimeseries property) ensure_batched_qr() (in module bucky.numerical_libs) epi_params (bucky.model.mc_instance.buckyMCInstance property) EPS (in module bucky.util.power_transforms) estimate_cfr() (in module bucky.model.estimation) estimate_chr() (in module bucky.model.estimation) estimate_crr() (in module bucky.model.estimation) estimate_Rt() (in module bucky.model.estimation) ExperimentalWarning (in module bucky.numerical_libs) extract() (in module bucky.datasource_transforms.extract_shapefile_data) F file (in module bucky.config) find_command_info() (in module bucky.cli.typer_utils) find_typer_info() (in module bucky.cli.typer_utils) fit() (bucky.util.power_transforms.BoxCox method) (bucky.util.power_transforms.YeoJohnson method) (in module bucky.util.spline_smooth) fit_lam() (in module bucky.util.power_transforms) flatten() (bucky.util.nested_dict.NestedDict method) forward() (in module bucky.cli.typer_utils) frac_last_n_vals() (in module bucky.util.fractional_slice) from_csv() (bucky.data.adm_mapping.AdminLevelMapping static method) (bucky.data.AdminLevelMapping static method) (bucky.data.CSSEData static method) (bucky.data.HHSData static method) (bucky.data.timeseries.BuckyFittedCaseData static method) (bucky.data.timeseries.CSSEData static method) (bucky.data.timeseries.HHSData static method) from_dict() (bucky.util.nested_dict.NestedDict method) from_flat_dict() (bucky.util.nested_dict.NestedDict method) from_yaml() (bucky.config.YamlPath class method) G g() (bucky.util.spline_smooth.identity_link static method) (bucky.util.spline_smooth.log_link static method) g_prime() (bucky.util.spline_smooth.identity_link static method) (bucky.util.spline_smooth.log_link static method) generate_runid() (in module bucky.util.util) get_fitted_data() (in module bucky.viz.utils) get_historical_data() (in module bucky.viz.utils) get_npi_params() (in module bucky.model.npi) get_simulation_data() (in module bucky.viz.utils) H HHSData (class in bucky.data) (class in bucky.data.timeseries) I identity_link (class in bucky.util.spline_smooth) ids (bucky.data.adm_mapping.AdminLevel attribute) idx (bucky.data.adm_mapping.AdminLevel attribute) import_by_name() (in module bucky.util.import_by_name) incident_cases (bucky.data.CSSEData attribute) (bucky.data.timeseries.BuckyFittedCaseData attribute) (bucky.data.timeseries.BuckyFittedData attribute) (bucky.data.timeseries.CSSEData attribute) incident_deaths (bucky.data.CSSEData attribute) (bucky.data.timeseries.BuckyFittedCaseData attribute) (bucky.data.timeseries.BuckyFittedData attribute) (bucky.data.timeseries.CSSEData attribute) incident_hospitalizations (bucky.data.HHSData attribute) (bucky.data.timeseries.HHSData attribute) init_S() (bucky.model.state.buckyState method) init_write_thread() (in module bucky.model.io) integrator_args (bucky.model.mc_instance.buckyMCInstance property) interp_age_bins() (bucky.config.BuckyConfig method) interp_extrap() (in module bucky.util.extrapolate) inv() (bucky.util.power_transforms.BoxCox method) (bucky.util.power_transforms.YeoJohnson method) inv_boxcox() (in module bucky.util.power_transforms) inv_yeojohnson() (in module bucky.util.power_transforms) invoke() (in module bucky.cli.typer_utils) IS() (in module bucky.util.scoring) is_cupy (in module bucky.numerical_libs) K kumaraswamy_invcdf() (in module bucky.util.distributions) L level (bucky.data.adm_mapping.AdminLevel attribute) lin_reg() (in module bucky.util.spline_smooth) load_cfg() (bucky.config.BuckyConfig method) load_data() (bucky.model.main.buckyModelCovid method) locate_base_config() (in module bucky.config) locate_current_config() (in module bucky.config) loess() (in module bucky.util.loess) log_fmt (in module bucky.cli.main) log_link (class in bucky.util.spline_smooth) logistic() (in module bucky.util.scoring) logistic_fit() (in module bucky.util.spline_smooth) M main (in module bucky.cli.main) main() (in module bucky.model.main) (in module bucky.postprocess) (in module bucky.viz.plot) main_click_object (in module bucky.cli.main) make_DP() (in module bucky.util.spline_smooth) mapping() (bucky.data.adm_mapping.AdminLevelMapping method) (bucky.data.AdminLevelMapping method) mask_outliers() (in module bucky.data.clean_historical_data) merge_parquet_dataset() (in module bucky.model.io) MI_PRISON_UIDS (in module bucky.datasource_transforms.csse_timeseries) MockExperimentalWarning model() (in module bucky.cli.run) module bucky bucky.__main__ bucky._typing bucky.cli bucky.cli.__main__ bucky.cli.cfg bucky.cli.data bucky.cli.main bucky.cli.run bucky.cli.typer_utils bucky.cli.viz bucky.config bucky.data bucky.data.adm_mapping bucky.data.clean_historical_data bucky.data.timeseries bucky.datasource_transforms bucky.datasource_transforms.bin_bridged_race_census_csv bucky.datasource_transforms.csse_timeseries bucky.datasource_transforms.extract_shapefile_data bucky.datasource_transforms.hhs_hosp_cleanup bucky.datasource_transforms.prem_2020_csv bucky.exceptions bucky.model bucky.model.adjmat bucky.model.data bucky.model.derived_epi_params bucky.model.estimation bucky.model.exceptions bucky.model.io bucky.model.main bucky.model.mc_instance bucky.model.npi bucky.model.rhs bucky.model.state bucky.model.vacc bucky.numerical_libs bucky.postprocess bucky.util bucky.util.age_interp bucky.util.array_utils bucky.util.async_thread bucky.util.cached_prop bucky.util.data_sync bucky.util.detect_cupy bucky.util.distributions bucky.util.extrapolate bucky.util.fractional_slice bucky.util.import_by_name bucky.util.loess bucky.util.nested_dict bucky.util.ode_constraints bucky.util.power_transforms bucky.util.scoring bucky.util.spline_smooth bucky.util.util bucky.util.working_directory bucky.viz bucky.viz.plot bucky.viz.readable_col_names bucky.viz.utils mPERT() (in module bucky.util.distributions) mu() (bucky.util.spline_smooth.identity_link static method) (bucky.util.spline_smooth.log_link static method) N N() (bucky.model.data.buckyData method) n_adm1 (bucky.data.adm_mapping.AdminLevelMapping property) (bucky.data.AdminLevelMapping property) n_days (bucky.data.timeseries.SpatialStratifiedTimeseries property) n_loc (bucky.data.timeseries.SpatialStratifiedTimeseries property) names (bucky.data.adm_mapping.AdminLevel attribute) nan_fips_uid_map (in module bucky.datasource_transforms.csse_timeseries) NestedDict (class in bucky.util.nested_dict) Nj() (bucky.model.data.buckyData method) norm_cdf() (in module bucky.util.power_transforms) norm_Cij() (in module bucky.model.mc_instance) nunique() (in module bucky.util.spline_smooth) O opt_lam() (in module bucky.util.spline_smooth) optimize_kernels (in module bucky.numerical_libs) P PathLike (in module bucky._typing) perturb() (bucky.model.adjmat.buckyAij method) PIRLS() (in module bucky.util.spline_smooth) plot() (in module bucky.cli.viz) plot_historical_fits() (in module bucky.data.clean_historical_data) postprocess() (in module bucky.cli.run) postprocess_run() (bucky.model.main.buckyModelCovid method) print_() (in module bucky.cli.cfg) process_datasources() (in module bucky.util.data_sync) promote_sampled_values() (bucky.config.BuckyConfig method) put() (bucky.util.async_thread.AsyncQueueThread method) R read_npi_file() (in module bucky.model.npi) read_population_tensor() (in module bucky.model.data) readable_col_names (in module bucky.viz.readable_col_names) reimport_cache (in module bucky.numerical_libs) reimport_numerical_libs() (in module bucky.numerical_libs) replace() (bucky.data.timeseries.SpatialStratifiedTimeseries method) reroll_distribution() (bucky.model.vacc.buckyVaccAlloc method) reroll_doses() (bucky.model.vacc.buckyVaccAlloc method) reset() (bucky.model.main.buckyModelCovid method) RHS_func() (in module bucky.model.rhs) ridge() (in module bucky.util.spline_smooth) rolling_window() (in module bucky.util.array_utils) run_multiple() (bucky.model.main.buckyModelCovid method) run_no_subcmd() (in module bucky.cli.run) run_once() (bucky.model.main.buckyModelCovid method) S S_eff() (bucky.model.mc_instance.buckyMCInstance method) (bucky.model.vacc.buckyVaccAlloc method) sample_distributions() (bucky.config.BuckyConfig method) save_run() (bucky.model.main.buckyModelCovid method) scale_y_axis() (in module bucky.viz.plot) scatter_add (in module bucky.numerical_libs) set_seed() (bucky.model.main.buckyModelCovid static method) set_tmax() (bucky.model.mc_instance.buckyMCInstance method) signal (in module bucky.numerical_libs) SimulationException slice_to_cpu() (in module bucky.model.state) smooth_IS() (in module bucky.util.scoring) sparsity (bucky.model.adjmat.buckyAij property) SpatialStratifiedTimeseries (class in bucky.data.timeseries) special (in module bucky.numerical_libs) start_date (bucky.data.timeseries.SpatialStratifiedTimeseries property) state (bucky.model.mc_instance.buckyMCInstance property) state_shape (bucky.model.state.buckyState property) StateValidationException sum_adm1() (bucky.model.data.buckyData method) sum_adm_level() (bucky.data.timeseries.SpatialStratifiedTimeseries method) sync() (in module bucky.cli.data) sync_numerical_libs() (in module bucky.numerical_libs) T T (in module bucky.cli.typer_utils) test_dict (in module bucky.util.nested_dict) to_cpu (in module bucky.numerical_libs) to_cpu_noop() (in module bucky.numerical_libs) to_csv() (bucky.data.adm_mapping.AdminLevelMapping method) (bucky.data.AdminLevelMapping method) (bucky.data.timeseries.SpatialStratifiedTimeseries method) to_dataframe() (bucky.data.timeseries.SpatialStratifiedTimeseries method) to_dict() (bucky.data.timeseries.SpatialStratifiedTimeseries method) (bucky.util.nested_dict.NestedDict method) to_yaml() (bucky.config.BuckyConfig method) (bucky.config.YamlPath class method) (bucky.util.nested_dict.NestedDict method) todense() (bucky.model.adjmat.buckyAij method) tosparse() (bucky.model.adjmat.buckyAij method) transform() (in module bucky.datasource_transforms.csse_timeseries) (in module bucky.datasource_transforms.hhs_hosp_cleanup) (in module bucky.datasource_transforms.prem_2020_csv) truncnorm() (in module bucky.util.distributions) truncnorm_from_CI() (in module bucky.util.distributions) U unbroadcast() (in module bucky.util.array_utils) update() (bucky.util.nested_dict.NestedDict method) UT_LHD_UIDS (in module bucky.datasource_transforms.csse_timeseries) V V_eff() (bucky.model.vacc.buckyVaccAlloc method) V_tot() (bucky.model.vacc.buckyVaccAlloc method) validate_isfinite() (bucky.data.timeseries.SpatialStratifiedTimeseries method) validate_state() (bucky.model.state.buckyState method) W WIS() (in module bucky.util.scoring) working_directory() (in module bucky.util.working_directory) write_historical_data() (bucky.model.io.BuckyOutputWriter method) write_mc_data() (bucky.model.io.BuckyOutputWriter method) write_metadata() (bucky.model.io.BuckyOutputWriter method) write_par_files() (bucky.model.io.BuckyOutputWriter method) write_params() (bucky.model.io.BuckyOutputWriter method) write_parquet_dataset() (in module bucky.model.io) X xp (in module bucky.numerical_libs) xp_ivp (in module bucky.numerical_libs) xp_qr (in module bucky.numerical_libs) xp_sparse (in module bucky.numerical_libs) Y yaml (in module bucky.config) (in module bucky.util.nested_dict) yaml_tag (bucky.config.YamlPath attribute) YamlPath (class in bucky.config) YeoJohnson (class in bucky.util.power_transforms) yeojohnson() (in module bucky.util.power_transforms) Z zeros_like() (bucky.model.state.buckyState method) zeros_like_pinned (in module bucky.numerical_libs) zeros_pinned (in module bucky.numerical_libs)