QC / validation / reporting / governance

Signal-quality audits, missingness and dropout checks, exclusions, reproducibility, preregistration, audit trails, dashboards, and reports.

73 functions from the frozen 406-function contract are routed here by the documentation classifier.

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• Quality-control workflow
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Functions

add_gazepoint_decision

add_gazepoint_decision(log, stage, object_type, decision, object_id=None, reason=None, function_name=None, parameter=None, value=None, reviewer_note=None, timestamp=None)

audit_gazepoint_biometric_missingness

audit_gazepoint_biometric_missingness(data, columns=None)

audit_gazepoint_biometric_sampling

audit_gazepoint_biometric_sampling(data, group_columns=None, time_column=None, time_unit='seconds', expected_rate_hz=60, tolerance_hz=5)

audit_gazepoint_biometrics_file

audit_gazepoint_biometrics_file(path=None, data=None, expected_modalities=('time', 'eda', 'ppg', 'hr', 'ibi', 'pupil', 'gaze', 'events'), time_col=None, standardize=True, include_data=False, long_gap_s=None)

audit_gazepoint_condition_balance

audit_gazepoint_condition_balance(data, participant_col, condition_col, trial_col=None, expected_conditions=None)

audit_gazepoint_dataset_structure

audit_gazepoint_dataset_structure(root, expected_dirs=None, expected_files=None, expected_patterns=None, allowed_extensions=None, require_sidecars=False)

audit_gazepoint_distributional_drift

audit_gazepoint_distributional_drift(dat, signal_cols, session_col='session', participant_col=None, reference_session=None, bins=10, psi_warn=0.1, psi_fail=0.25)

audit_gazepoint_engagement_dial

audit_gazepoint_engagement_dial(data, value_column='DIAL', validity_column='DIALV', min_value=0, max_value=1, jump_threshold=None)

audit_gazepoint_experiment_design

audit_gazepoint_experiment_design(data, participant_col='participant', trial_col=None, condition_col=None, session_col=None, expected_conditions=None, min_trials_per_condition=1)

audit_gazepoint_export_schema

audit_gazepoint_export_schema(data, expected_roles=None, dictionary=None, strict=False)

audit_gazepoint_pipeline_steps

audit_gazepoint_pipeline_steps(pipeline, expected_steps=None, required_order=None, allow_extra=True)

audit_gazepoint_preregistration_consistency

audit_gazepoint_preregistration_consistency(checklist=None, evidence=None, require_required_fields=True)

audit_gazepoint_release_readiness

audit_gazepoint_release_readiness(path='.', required_files=('DESCRIPTION', 'NAMESPACE', 'R', 'man', 'tests/testthat', '_pkgdown.yml'), expected_exports=None, roadmap_terms=None, require_pkgdown=True)

audit_gazepoint_session_comparability

audit_gazepoint_session_comparability(data, metric_cols, group_cols=None, method='both', z_threshold=2, iqr_multiplier=1.5)

audit_gazepoint_signal_activity

audit_gazepoint_signal_activity(data, signal_cols=None, group_cols=None, zero_is_inactive=True, min_unique_nonzero=2, missing_as_inactive=True)

audit_gazepoint_smoke_privacy

audit_gazepoint_smoke_privacy(x, private_values=None)

audit_gazepoint_stabilization_period

audit_gazepoint_stabilization_period(dat, time_col='CNT', group_cols=None, stabilization_minutes=10, action='flag', output_col='in_stabilization_period', time_units='auto')

audit_gazepoint_time_resets

audit_gazepoint_time_resets(data, time_col=None, group_cols=None, allow_ties=True, split_on_negative_step=True, return_reindexed_time=False, min_segment_rows=1)

audit_gazepoint_timecourse_grid

audit_gazepoint_timecourse_grid(data, subject, condition, time, value=None, max_report_cells=1000)

check_gazepoint_biometric_columns

check_gazepoint_biometric_columns(data)

check_gazepoint_plot_contract

check_gazepoint_plot_contract(plot, require_plot_data=True, require_settings=True)

classify_gazepoint_signal_quality

classify_gazepoint_signal_quality(quality, rules=None)

compare_gazepoint_export_profiles

compare_gazepoint_export_profiles(*profiles, labels=None)

compute_gazepoint_quality_index

compute_gazepoint_quality_index(data, metric_cols, directions=None, weights=None, index_col='quality_index', component_prefix='quality_component_', overwrite=False)

compute_gazepoint_signal_quality

compute_gazepoint_signal_quality(data, signal_cols, group_cols=None, flatline_tolerance=0, long_missing_run_threshold=10, long_constant_run_threshold=10, spike_z=4, extreme_z=4)

create_gazepoint_analysis_decision_log

create_gazepoint_analysis_decision_log(study_id=None, analyst=None, description=None)

create_gazepoint_audit_index

create_gazepoint_audit_index(audits=None, audit_ids=None, include_summary_rows=False)

create_gazepoint_audit_report_section

create_gazepoint_audit_report_section(export_profile=None, design_audit=None, event_audit=None, condition_audit=None, decision_log=None, include_warnings=True)

create_gazepoint_biometrics_checklist

create_gazepoint_biometrics_checklist(data, require_active_signal=True)

create_gazepoint_biometrics_feature_inventory

create_gazepoint_biometrics_feature_inventory(include_internal=False)

create_gazepoint_biometrics_methods_text

create_gazepoint_biometrics_methods_text(checklist=None, data=None, include_cautions=True)

create_gazepoint_biometrics_report

create_gazepoint_biometrics_report(data=None, workflow=None, validation=None, quality=None, sampling=None, missingness=None, exclusions=None, report_tables=None, methods_text=None, checklist=None, title='Gazepoint Biometrics report', subtitle=None, output_file=None, format='markdown', include_timestamp=False, overwrite=False, max_table_rows=20)

create_gazepoint_biometrics_report_tables

create_gazepoint_biometrics_report_tables(workflow=None, validation=None, quality=None, sampling=None, diagnostics=None, exclusion_recommendations=None, ttl_events=None, max_ttl_events=20)

create_gazepoint_pipeline_map

create_gazepoint_pipeline_map(steps=None, edges=None, pipeline_id='gazepoint_pipeline', include_default=True)

create_gazepoint_preregistration_checklist

create_gazepoint_preregistration_checklist(study_id=None, include_optional=True, custom_items=None)

create_gazepoint_preregistration_template

create_gazepoint_preregistration_template(study_title='Gazepoint biometrics study', signal_standardization='within_participant_z', artifact_rules='kleckner_style', eda_min_us=0.01, eda_max_us=100, rapid_change_threshold=20, output_file=None)

create_gazepoint_quality_dashboard

create_gazepoint_quality_dashboard(data=None, audit=None, missingness=None, alignment=None, eventlocked=None, title='Gazepoint quality dashboard', output_dir=None)

create_gazepoint_release_checklist

create_gazepoint_release_checklist(audit=None, include_optional=True)

detect_gazepoint_nonwear

detect_gazepoint_nonwear(data, signal_cols, group_cols=None, time_col=None, min_run_length=10, zero_tolerance=0, constant_tolerance=0, low_variance_threshold=None, detect_missing=True, detect_zero=True, detect_constant=True, detect_low_variance=True)

export_gazepoint_audit_trail_markdown

export_gazepoint_audit_trail_markdown(audit_index, summary=None, title='Gazepoint audit trail', include_details=True, max_details=100, file=None)

export_gazepoint_biometrics_report_bundle

export_gazepoint_biometrics_report_bundle(bundle=None, output_dir=None, prefix='gpbiometrics_report', tables=None, text=None, plots=None, include_readme=True, include_session_info=True, overwrite=False)

export_gazepoint_pipeline_dot

export_gazepoint_pipeline_dot(pipeline, file=None, graph_name='gazepoint_pipeline', rankdir='LR', include_descriptions=False)

flag_gazepoint_artifacts_svm

flag_gazepoint_artifacts_svm(x, model=None, feature_cols=None, probability_threshold=0.5, **kwargs)

flag_gazepoint_biometric_dropouts

flag_gazepoint_biometric_dropouts(data, signal_cols=None, group_cols=None, time_col=None, min_missing_run=5, min_flatline_run=10, constant_tolerance=0, prefix='biometric_dropout')

flag_gazepoint_mad_artifacts

flag_gazepoint_mad_artifacts(dat, eda_col='GSR_US', time_col=None, group_cols=None, mad_multiplier=8, flatline_tolerance=1e-06, flatline_min_run=5, wall_abs_change=None, output_prefix='mad')

format_gazepoint_biometrics_feature_inventory

format_gazepoint_biometrics_feature_inventory(inventory=None, include_internal=False, sort=True)

impute_gazepoint_missing

impute_gazepoint_missing(data, method='linear', cols=None, time_col=None, group_cols=None, max_gap=inf, fill_edges=True, constant_value=0, add_flags=True, treat_infinite_as_missing=True)

pipeline_comparison_dashboard

pipeline_comparison_dashboard(data, participant_col=None, session_col=None, grouping_cols=None, missingness_col=None, quality_col=None, qc_status_col=None, failed_rules_col=None, excluded_col=None, notes_col=None)

plot_gazepoint_biometric_quality

plot_gazepoint_biometric_quality(data, quality_cols=None, signal_cols=None, time_col=None, group_col=None, dropout_prefix='biometric_dropout', max_points=5000, main=None, plot=True, **kwargs)

plot_gazepoint_biometric_report_dashboard

plot_gazepoint_biometric_report_dashboard(data=None, signal_activity=None, time_resets=None, signal_cols=None, group_cols=None, time_col=None, include_signal_activity=True, include_time_resets=True, max_groups=30, continue_on_error=True, title_prefix='Gazepoint biometric QC')

plot_gazepoint_export_profile

plot_gazepoint_export_profile(profile, type='files', top_n=20)

plot_gazepoint_missingness

plot_gazepoint_missingness(data, cols=None, time_col=None, id_col=None, max_points=5000)

plot_gazepoint_signal_quality

plot_gazepoint_signal_quality(quality, metric='prop_missing', x=None, colour=None, facet=None)

prepare_gazepoint_artifact_svm_features

prepare_gazepoint_artifact_svm_features(dat, eda_col='GSR_US', time_col=None, group_cols=None, segment_seconds=5, samples_per_segment=None, sampling_rate=None)

profile_gazepoint_export_folder

profile_gazepoint_export_folder(path, pattern='\\.csv$', recursive=False, max_files=inf, max_rows=inf, na_strings=('', 'NA', 'NaN'))

recommend_gazepoint_biometric_exclusions

recommend_gazepoint_biometric_exclusions(data, group_columns=None, data_is_window_summary=False, participant_column=None, gsr_min_usable_pct=50, hr_min_usable_pct=50, dial_min_usable_pct=50, require_gsr=True, require_hr=True, require_dial=False)

report_gazepoint_cluster_permutation

report_gazepoint_cluster_permutation(result, cluster_alpha=0.05, digits=3, include_assumptions=True)

report_gazepoint_data_quality

report_gazepoint_data_quality(data, output_dir=None, report_name='gazepoint_data_quality', formats=('html', 'csv'), max_plot_columns=6, open=False)

run_gazepoint_biometrics_real_data_readiness

run_gazepoint_biometrics_real_data_readiness(data=None, workflow_result=None, min_rows=100, min_active_signal_count=1, max_missing_prop=0.5, required_signal_cols=None, require_gsr_us_preferred=True, require_ibi_for_hrv=False, time_col=None, ttl_cols=None)

simulate_gazepoint_artifact

simulate_gazepoint_artifact(data, signal_cols, artifact=('missing_run', 'flatline', 'spike'), n_artifacts=1, artifact_length=5, magnitude=None, seed=None, suffix='_artifact', overwrite=False)

summarise_gazepoint_biometrics_feature_inventory

summarise_gazepoint_biometrics_feature_inventory(formatted_inventory=None)

summarise_gazepoint_decision_log

summarise_gazepoint_decision_log(log)

summarize_gazepoint_audit_trail

summarize_gazepoint_audit_trail(audit_index, by=None)

summarize_gazepoint_missingness

summarize_gazepoint_missingness(data, signal_cols=None, time_col=None, group_cols=None, long_gap_s=None, count_nonfinite=True)

summarize_gazepoint_nonwear

summarize_gazepoint_nonwear(nonwear, by='signal')

summarize_gazepoint_preregistration_readiness

summarize_gazepoint_preregistration_readiness(audit, by=None)

summarize_gazepoint_signal_quality

summarize_gazepoint_signal_quality(quality, by='signal')

validate_gazepoint_biometrics

validate_gazepoint_biometrics(data, require_active_signal=False)

validate_gazepoint_format

validate_gazepoint_format(data, required_cols=None, optional_cols=None, expected_modalities=None, standardize=False, strict=False, **kwargs)

validate_gazepoint_metadata

validate_gazepoint_metadata(data, required_cols=(), expected_cols=(), id_cols=None, time_col=None, unique_cols=None, allow_missing_ids=False)

write_gazepoint_biometrics_report_tables

write_gazepoint_biometrics_report_tables(tables, output_dir, prefix='gazepoint_biometrics', overwrite=True, include_empty_message_tables=False)

write_gazepoint_decision_log

write_gazepoint_decision_log(log, path, summary_path=None, overwrite=False)

write_gazepoint_export_profile

write_gazepoint_export_profile(profile, path, prefix='gazepoint_export_profile', overwrite=False)