Complete Public API Map¶
Python-facing port of
public-api-map.Rmdfrom the frozen R gp3bayes 0.5.0 reference. The statistical and governance framing below follows the canonical vignette; executable Python workflows use the mapped APIs listed later.
This article is a discoverability index for the frozen development API. It groups every exported function by its primary interface role. Function names are linked by pkgdown to their full reference documentation. The map is not a recommendation to call every low-level adapter directly.
Frozen development API size: 324 exported functions.
Audits¶
audit_backend_parity()audit_design_support()audit_duration_boundaries()audit_duration_unit_invariance()audit_estimand_invariance()audit_fixed_effect_design()audit_missingness_structure()audit_model_readiness()audit_model_readiness_strict()audit_prediction_support()audit_random_effects_support()
Checks¶
check_binary_posterior_predictive()check_binary_ppc_details()check_binary_prior_predictive()check_cmdstan_backend()check_duration_posterior_predictive()check_duration_ppc_details()check_duration_prior_predictive()check_model_ppc()
Constructors and bundles¶
create_analysis_bundle()create_analysis_figure_set()create_analysis_manifest()create_binary_model_report()create_brms_sbc_plan()create_complete_evidence_inventory()create_contrast_coding_sensitivity_specification()create_custom_sbc_plan()create_diagnostic_dashboard()create_diagnostic_dashboard_figures()create_duration_model_report()create_duration_unit_sensitivity_specification()create_figure_set()create_group_deletion_sensitivity_plan()create_loo_influence_atlas()create_model_card()create_model_contract()create_model_evidence_report()create_model_specification()create_prediction_contrast_profile()create_prediction_grid()create_prediction_profile()create_prediction_surface()create_predictive_distribution_atlas()create_predictor_scaling_sensitivity_specification()create_prior_specification()create_publication_registry()create_publication_table_set()create_random_slope_sensitivity_plan()create_reporting_checklist()create_sensitivity_suite_plan()create_transformation_recipe()
Execution workflows¶
run_binary_recovery()run_duration_recovery()run_group_deletion_sensitivity()run_random_slope_sensitivity()run_sbc_plan()run_sensitivity_suite()
Explicit writers¶
write_analysis_bundle_report()write_diagnostic_dashboard_report()write_model_card()write_publication_registry()write_reproducibility_report()
Extraction¶
extract_expected_predictions()extract_linear_predictions()extract_log_likelihood()extract_posterior_draws()extract_posterior_predictions()extract_sampler_diagnostics()
Freezing and reproducibility¶
freeze_analysis_manifest()freeze_gp3bayes_schema()
Model fitting¶
fit_binary_model()fit_binary_model_backend()fit_binary_model_cmdstanr()fit_duration_model()fit_duration_model_backend()fit_duration_model_cmdstanr()
Other public workflows¶
apply_transformation_recipe()assess_binary_prior_sensitivity()assess_duration_prior_sensitivity()assess_powerscaled_sensitivity()backend_capabilities()bayesian_backend_capabilities()binary_calibration_error()binary_calibration_uncertainty()binary_group_calibration()binary_precision_recall_curve()binary_prediction_scores()binary_roc_curve()binary_threshold_metrics()build_model_formula()capture_gp3bayes_schema()collect_model_evidence()compare_analysis_manifests()compare_estimand_sensitivity()compare_gp3bayes_schemas()compare_psis_loo()compute_kfold_cv()compute_loo_model_weights()compute_psis_loo()compute_psis_loo_from_log_lik()detect_binary_separation()diagnose_binary_fit()diagnose_duration_fit()diagnose_model_fit()duration_prediction_scores()duration_quantile_calibration()duration_tail_check()estimate_model_estimands()estimate_standardized_duration_estimands()estimate_standardized_probability_contrast()evaluate_pathological_simulation()gp3bayes_specification_traceability()group_prediction_summary()grouped_prediction_check()identify_identifier_like_predictors()identify_loo_influential_observations()identify_mcmc_issues()interaction_prior_summary()invert_transformation_recipe()loo_flagged_data()loo_influence_summary()model_workflow_status()posterior_predictive_statistic()powerscale_sequence_for_fit()preflight_model_specification()prepare_hierarchical_binary_data()prepare_hierarchical_duration_data()prior_posterior_bridge()prior_posterior_draws_long()random_intercept_variance_partition()register_publication_figure()review_duration_extremes()save_figure_set()save_publication_registry_figures()specify_binary_model()specify_binary_model_with_interaction_prior()specify_duration_model()specify_duration_model_with_interaction_prior()theme_gp3bayes()translate_binary_model_to_brms()translate_binary_model_with_interaction_prior()translate_duration_model_to_brms()translate_duration_model_with_interaction_prior()
Plots and graphics¶
plot_autocorrelation()plot_backend_environment_gg()plot_backend_parity_gg()plot_binary_calibration()plot_binary_calibration_uncertainty()plot_binary_group_calibration()plot_binary_precision_recall()plot_binary_roc()plot_binary_threshold_metrics()plot_design_support_gg()plot_diagnostic_dashboard()plot_duration_pit()plot_duration_qq()plot_duration_quantile_calibration()plot_duration_tail()plot_estimand_intervals()plot_estimand_sensitivity_gg()plot_exceedance_probability()plot_group_deletion_sensitivity()plot_group_effect_distribution()plot_group_effect_rank_probability()plot_group_effects()plot_group_predictions()plot_grouped_prediction_check()plot_loo_group_elpd()plot_loo_group_influence()plot_loo_influence()plot_loo_influence_rank()plot_loo_pareto_vs_elpd()plot_loo_pointwise_elpd()plot_manifest_comparison_gg()plot_mcmc_quality()plot_missingness_gg()plot_model_comparison()plot_model_evidence_gg()plot_model_weights()plot_posterior_areas()plot_posterior_correlations()plot_posterior_density()plot_posterior_intervals()plot_posterior_pairs()plot_powerscale_sensitivity_gg()plot_ppc_statistic()plot_prediction_contrast_profile()plot_prediction_draws()plot_prediction_gradient()plot_prediction_interval_width()plot_prediction_intervals()plot_prediction_profile()plot_prediction_rank_probabilities()plot_prediction_score_uncertainty()plot_prediction_support()plot_prediction_surface()plot_prediction_surface_uncertainty()plot_predictive_atlas_statistics()plot_predictive_coverage()plot_predictive_quantile_envelope()plot_predictive_residuals()plot_prior_posterior_contraction()plot_prior_posterior_density()plot_prior_posterior_intervals()plot_prior_posterior_shift()plot_prior_sensitivity()plot_prior_sensitivity_scenarios()plot_random_intercept_variance_partition()plot_random_slope_sensitivity()plot_rank_diagnostics()plot_recovery_bias()plot_recovery_coverage()plot_recovery_estimates()plot_recovery_fit_status()plot_recovery_rmse()plot_reporting_checklist()plot_sampler_diagnostics()plot_sampling_diagnostics()plot_sbc_coverage_gg()plot_sbc_ecdf_gg()plot_sbc_rank_gg()plot_sbc_simulated_vs_estimated_gg()plot_schema_comparison_gg()plot_sensitivity_suite_gg()plot_uncertainty_decomposition()plot_variance_components()
Prediction¶
predict_binary_probability()predict_duration()predict_model()prediction_contrast()prediction_draws_long()prediction_exceedance_probability()prediction_interval_width()prediction_pairwise_contrasts()prediction_rank_probabilities()prediction_score_uncertainty()prediction_uncertainty_decomposition()predictive_quantile_envelope()predictive_residuals()
Readers¶
read_analysis_manifest()read_gp3bayes_schema()
Simulation¶
simulate_binary_pathology()simulate_declared_prior_draws()simulate_duration_pathology()simulate_hierarchical_binary_data()simulate_hierarchical_duration_data()
Summaries¶
summarise_binary_group_variation()summarise_binary_posterior()summarise_condition_balance()summarise_duration_posterior()summarise_estimand_draws()summarise_mcmc_quality()summarise_model_posterior()summarise_sbc_result()summarise_sensitivity_suite()
Tables and adapters¶
analysis_bundle_table()analysis_manifest_table()backend_environment_table()backend_parity_table()binary_calibration_table()binary_calibration_uncertainty_table()binary_confusion_table()design_support_table()diagnostic_dashboard_table()duration_pit_table()duration_qq_table()estimand_sensitivity_table()evidence_inventory_table()group_deletion_sensitivity_table()group_effect_draws_table()group_effect_rank_probability_table()group_effect_table()loo_diagnostic_table()loo_group_influence_table()loo_influence_atlas_table()loo_pointwise_table()loo_summary_table()manifest_comparison_table()mcmc_diagnostic_table()missingness_audit_table()model_card_table()model_comparison_table()model_evidence_table()model_weights_table()posterior_correlation_table()posterior_interval_table()posterior_predictive_summary_table()posterior_probability_table()powerscale_sensitivity_table()ppc_statistic_table()prediction_contrast_profile_table()prediction_gradient_table()prediction_profile_table()prediction_score_uncertainty_table()prediction_support_table()prediction_surface_table()prediction_table()predictive_coverage_table()predictive_distribution_atlas_table()prior_posterior_distance_table()prior_posterior_summary_table()prior_sensitivity_scenario_table()prior_sensitivity_table()prior_specification_table()publication_registry_table()random_intercept_variance_partition_table()random_slope_sensitivity_table()recovery_estimate_table()recovery_fit_status_table()recovery_parameter_table()register_publication_table()sampler_diagnostic_table()sbc_overview_table()sbc_stats_table()schema_comparison_table()sensitivity_suite_table()variance_component_table()
Validation¶
validate_analysis_manifest()validate_backend_environment()validate_gp3bayes_object()validate_gp3bayes_schema()validate_prior_specification()validate_publication_registry()validate_transformation_replay()
Python API mapping¶
gp3bayespy.analysis_bundle_tablegp3bayespy.analysis_manifest_tablegp3bayespy.apply_transformation_recipegp3bayespy.assess_binary_prior_sensitivitygp3bayespy.assess_duration_prior_sensitivitygp3bayespy.assess_powerscaled_sensitivitygp3bayespy.audit_backend_paritygp3bayespy.audit_design_supportgp3bayespy.audit_duration_boundariesgp3bayespy.audit_duration_unit_invariancegp3bayespy.audit_estimand_invariancegp3bayespy.audit_fixed_effect_designgp3bayespy.audit_missingness_structuregp3bayespy.audit_model_readinessgp3bayespy.audit_model_readiness_strictgp3bayespy.audit_prediction_supportgp3bayespy.audit_random_effects_supportgp3bayespy.backend_capabilitiesgp3bayespy.backend_environment_tablegp3bayespy.backend_parity_tablegp3bayespy.bayesian_backend_capabilitiesgp3bayespy.binary_calibration_errorgp3bayespy.binary_calibration_tablegp3bayespy.binary_calibration_uncertaintygp3bayespy.binary_calibration_uncertainty_tablegp3bayespy.binary_confusion_tablegp3bayespy.binary_group_calibrationgp3bayespy.binary_precision_recall_curvegp3bayespy.binary_prediction_scoresgp3bayespy.binary_roc_curvegp3bayespy.binary_threshold_metricsgp3bayespy.build_model_formulagp3bayespy.capture_gp3bayes_schemagp3bayespy.check_binary_posterior_predictivegp3bayespy.check_binary_ppc_detailsgp3bayespy.check_binary_prior_predictivegp3bayespy.check_cmdstan_backendgp3bayespy.check_duration_posterior_predictivegp3bayespy.check_duration_ppc_detailsgp3bayespy.check_duration_prior_predictivegp3bayespy.check_model_ppcgp3bayespy.collect_model_evidencegp3bayespy.compare_analysis_manifestsgp3bayespy.compare_estimand_sensitivitygp3bayespy.compare_gp3bayes_schemasgp3bayespy.compare_psis_loogp3bayespy.compute_kfold_cvgp3bayespy.compute_loo_model_weightsgp3bayespy.compute_psis_loogp3bayespy.compute_psis_loo_from_log_likgp3bayespy.create_analysis_bundlegp3bayespy.create_analysis_figure_setgp3bayespy.create_analysis_manifestgp3bayespy.create_binary_model_reportgp3bayespy.create_brms_sbc_plangp3bayespy.create_complete_evidence_inventorygp3bayespy.create_contrast_coding_sensitivity_specificationgp3bayespy.create_custom_sbc_plangp3bayespy.create_diagnostic_dashboardgp3bayespy.create_diagnostic_dashboard_figuresgp3bayespy.create_duration_model_reportgp3bayespy.create_duration_unit_sensitivity_specificationgp3bayespy.create_figure_setgp3bayespy.create_group_deletion_sensitivity_plangp3bayespy.create_loo_influence_atlasgp3bayespy.create_model_cardgp3bayespy.create_model_contractgp3bayespy.create_model_evidence_reportgp3bayespy.create_model_specificationgp3bayespy.create_prediction_contrast_profilegp3bayespy.create_prediction_gridgp3bayespy.create_prediction_profilegp3bayespy.create_prediction_surfacegp3bayespy.create_predictive_distribution_atlasgp3bayespy.create_predictor_scaling_sensitivity_specificationgp3bayespy.create_prior_specificationgp3bayespy.create_publication_registrygp3bayespy.create_publication_table_setgp3bayespy.create_random_slope_sensitivity_plangp3bayespy.create_reporting_checklistgp3bayespy.create_sensitivity_suite_plangp3bayespy.create_transformation_recipegp3bayespy.design_support_tablegp3bayespy.detect_binary_separationgp3bayespy.diagnose_binary_fitgp3bayespy.diagnose_duration_fitgp3bayespy.diagnose_model_fitgp3bayespy.diagnostic_dashboard_tablegp3bayespy.duration_pit_tablegp3bayespy.duration_prediction_scoresgp3bayespy.duration_qq_tablegp3bayespy.duration_quantile_calibrationgp3bayespy.duration_tail_checkgp3bayespy.estimand_sensitivity_tablegp3bayespy.estimate_model_estimandsgp3bayespy.estimate_standardized_duration_estimandsgp3bayespy.estimate_standardized_probability_contrastgp3bayespy.evaluate_pathological_simulationgp3bayespy.evidence_inventory_tablegp3bayespy.extract_expected_predictionsgp3bayespy.extract_linear_predictionsgp3bayespy.extract_log_likelihoodgp3bayespy.extract_posterior_drawsgp3bayespy.extract_posterior_predictionsgp3bayespy.extract_sampler_diagnosticsgp3bayespy.fit_binary_modelgp3bayespy.fit_binary_model_backendgp3bayespy.fit_binary_model_cmdstanrgp3bayespy.fit_duration_modelgp3bayespy.fit_duration_model_backendgp3bayespy.fit_duration_model_cmdstanrgp3bayespy.freeze_analysis_manifestgp3bayespy.freeze_gp3bayes_schemagp3bayespy.gp3bayes_specification_traceabilitygp3bayespy.group_deletion_sensitivity_tablegp3bayespy.group_effect_draws_tablegp3bayespy.group_effect_rank_probability_tablegp3bayespy.group_effect_tablegp3bayespy.group_prediction_summarygp3bayespy.grouped_prediction_checkgp3bayespy.identify_identifier_like_predictorsgp3bayespy.identify_loo_influential_observationsgp3bayespy.identify_mcmc_issuesgp3bayespy.interaction_prior_summarygp3bayespy.invert_transformation_recipegp3bayespy.loo_diagnostic_tablegp3bayespy.loo_flagged_datagp3bayespy.loo_group_influence_tablegp3bayespy.loo_influence_atlas_tablegp3bayespy.loo_influence_summarygp3bayespy.loo_pointwise_tablegp3bayespy.loo_summary_tablegp3bayespy.manifest_comparison_tablegp3bayespy.mcmc_diagnostic_tablegp3bayespy.missingness_audit_tablegp3bayespy.model_card_tablegp3bayespy.model_comparison_tablegp3bayespy.model_evidence_tablegp3bayespy.model_weights_tablegp3bayespy.model_workflow_statusgp3bayespy.plot_autocorrelationgp3bayespy.plot_backend_environment_gggp3bayespy.plot_backend_parity_gggp3bayespy.plot_binary_calibrationgp3bayespy.plot_binary_calibration_uncertaintygp3bayespy.plot_binary_group_calibrationgp3bayespy.plot_binary_precision_recallgp3bayespy.plot_binary_rocgp3bayespy.plot_binary_threshold_metricsgp3bayespy.plot_design_support_gggp3bayespy.plot_diagnostic_dashboardgp3bayespy.plot_duration_pitgp3bayespy.plot_duration_qqgp3bayespy.plot_duration_quantile_calibrationgp3bayespy.plot_duration_tailgp3bayespy.plot_estimand_intervalsgp3bayespy.plot_estimand_sensitivity_gggp3bayespy.plot_exceedance_probabilitygp3bayespy.plot_group_deletion_sensitivitygp3bayespy.plot_group_effect_distributiongp3bayespy.plot_group_effect_rank_probabilitygp3bayespy.plot_group_effectsgp3bayespy.plot_group_predictionsgp3bayespy.plot_grouped_prediction_checkgp3bayespy.plot_loo_group_elpdgp3bayespy.plot_loo_group_influencegp3bayespy.plot_loo_influencegp3bayespy.plot_loo_influence_rankgp3bayespy.plot_loo_pareto_vs_elpdgp3bayespy.plot_loo_pointwise_elpdgp3bayespy.plot_manifest_comparison_gggp3bayespy.plot_mcmc_qualitygp3bayespy.plot_missingness_gggp3bayespy.plot_model_comparisongp3bayespy.plot_model_evidence_gggp3bayespy.plot_model_weightsgp3bayespy.plot_posterior_areasgp3bayespy.plot_posterior_correlationsgp3bayespy.plot_posterior_densitygp3bayespy.plot_posterior_intervalsgp3bayespy.plot_posterior_pairsgp3bayespy.plot_powerscale_sensitivity_gggp3bayespy.plot_ppc_statisticgp3bayespy.plot_prediction_contrast_profilegp3bayespy.plot_prediction_drawsgp3bayespy.plot_prediction_gradientgp3bayespy.plot_prediction_interval_widthgp3bayespy.plot_prediction_intervalsgp3bayespy.plot_prediction_profilegp3bayespy.plot_prediction_rank_probabilitiesgp3bayespy.plot_prediction_score_uncertaintygp3bayespy.plot_prediction_supportgp3bayespy.plot_prediction_surfacegp3bayespy.plot_prediction_surface_uncertaintygp3bayespy.plot_predictive_atlas_statisticsgp3bayespy.plot_predictive_coveragegp3bayespy.plot_predictive_quantile_envelopegp3bayespy.plot_predictive_residualsgp3bayespy.plot_prior_posterior_contractiongp3bayespy.plot_prior_posterior_densitygp3bayespy.plot_prior_posterior_intervalsgp3bayespy.plot_prior_posterior_shiftgp3bayespy.plot_prior_sensitivitygp3bayespy.plot_prior_sensitivity_scenariosgp3bayespy.plot_random_intercept_variance_partitiongp3bayespy.plot_random_slope_sensitivitygp3bayespy.plot_rank_diagnosticsgp3bayespy.plot_recovery_biasgp3bayespy.plot_recovery_coveragegp3bayespy.plot_recovery_estimatesgp3bayespy.plot_recovery_fit_statusgp3bayespy.plot_recovery_rmsegp3bayespy.plot_reporting_checklistgp3bayespy.plot_sampler_diagnosticsgp3bayespy.plot_sampling_diagnosticsgp3bayespy.plot_sbc_coverage_gggp3bayespy.plot_sbc_ecdf_gggp3bayespy.plot_sbc_rank_gggp3bayespy.plot_sbc_simulated_vs_estimated_gggp3bayespy.plot_schema_comparison_gggp3bayespy.plot_sensitivity_suite_gggp3bayespy.plot_uncertainty_decompositiongp3bayespy.plot_variance_componentsgp3bayespy.posterior_correlation_tablegp3bayespy.posterior_interval_tablegp3bayespy.posterior_predictive_statisticgp3bayespy.posterior_predictive_summary_tablegp3bayespy.posterior_probability_tablegp3bayespy.powerscale_sensitivity_tablegp3bayespy.powerscale_sequence_for_fitgp3bayespy.ppc_statistic_tablegp3bayespy.predict_binary_probabilitygp3bayespy.predict_durationgp3bayespy.predict_modelgp3bayespy.prediction_contrastgp3bayespy.prediction_contrast_profile_tablegp3bayespy.prediction_draws_longgp3bayespy.prediction_exceedance_probabilitygp3bayespy.prediction_gradient_tablegp3bayespy.prediction_interval_widthgp3bayespy.prediction_pairwise_contrastsgp3bayespy.prediction_profile_tablegp3bayespy.prediction_rank_probabilitiesgp3bayespy.prediction_score_uncertaintygp3bayespy.prediction_score_uncertainty_tablegp3bayespy.prediction_support_tablegp3bayespy.prediction_surface_tablegp3bayespy.prediction_tablegp3bayespy.prediction_uncertainty_decompositiongp3bayespy.predictive_coverage_tablegp3bayespy.predictive_distribution_atlas_tablegp3bayespy.predictive_quantile_envelopegp3bayespy.predictive_residualsgp3bayespy.preflight_model_specificationgp3bayespy.prepare_hierarchical_binary_datagp3bayespy.prepare_hierarchical_duration_datagp3bayespy.prior_posterior_bridgegp3bayespy.prior_posterior_distance_tablegp3bayespy.prior_posterior_draws_longgp3bayespy.prior_posterior_summary_tablegp3bayespy.prior_sensitivity_scenario_tablegp3bayespy.prior_sensitivity_tablegp3bayespy.prior_specification_tablegp3bayespy.publication_registry_tablegp3bayespy.random_intercept_variance_partitiongp3bayespy.random_intercept_variance_partition_tablegp3bayespy.random_slope_sensitivity_tablegp3bayespy.read_analysis_manifestgp3bayespy.read_gp3bayes_schemagp3bayespy.recovery_estimate_tablegp3bayespy.recovery_fit_status_tablegp3bayespy.recovery_parameter_tablegp3bayespy.register_publication_figuregp3bayespy.register_publication_tablegp3bayespy.review_duration_extremesgp3bayespy.run_binary_recoverygp3bayespy.run_duration_recoverygp3bayespy.run_group_deletion_sensitivitygp3bayespy.run_random_slope_sensitivitygp3bayespy.run_sbc_plangp3bayespy.run_sensitivity_suitegp3bayespy.sampler_diagnostic_tablegp3bayespy.save_figure_setgp3bayespy.save_publication_registry_figuresgp3bayespy.sbc_overview_tablegp3bayespy.sbc_stats_tablegp3bayespy.schema_comparison_tablegp3bayespy.sensitivity_suite_tablegp3bayespy.simulate_binary_pathologygp3bayespy.simulate_declared_prior_drawsgp3bayespy.simulate_duration_pathologygp3bayespy.simulate_hierarchical_binary_datagp3bayespy.simulate_hierarchical_duration_datagp3bayespy.specify_binary_modelgp3bayespy.specify_binary_model_with_interaction_priorgp3bayespy.specify_duration_modelgp3bayespy.specify_duration_model_with_interaction_priorgp3bayespy.summarise_binary_group_variationgp3bayespy.summarise_binary_posteriorgp3bayespy.summarise_condition_balancegp3bayespy.summarise_duration_posteriorgp3bayespy.summarise_estimand_drawsgp3bayespy.summarise_mcmc_qualitygp3bayespy.summarise_model_posteriorgp3bayespy.summarise_sbc_resultgp3bayespy.summarise_sensitivity_suitegp3bayespy.theme_gp3bayesgp3bayespy.translate_binary_model_to_brmsgp3bayespy.translate_binary_model_with_interaction_priorgp3bayespy.translate_duration_model_to_brmsgp3bayespy.translate_duration_model_with_interaction_priorgp3bayespy.validate_analysis_manifestgp3bayespy.validate_backend_environmentgp3bayespy.validate_gp3bayes_objectgp3bayespy.validate_gp3bayes_schemagp3bayespy.validate_prior_specificationgp3bayespy.validate_publication_registrygp3bayespy.validate_transformation_replaygp3bayespy.variance_component_tablegp3bayespy.write_analysis_bundle_reportgp3bayespy.write_diagnostic_dashboard_reportgp3bayespy.write_model_cardgp3bayespy.write_publication_registrygp3bayespy.write_reproducibility_report
Python usage¶
import gp3bayespy as gp
# All functions listed above are available from the package root.
# Use help(gp.<function>) or the API reference for the exact Python signature.