R: Governance-First Predictive Modelling for 'Gazepoint' Research

# Governance-First Predictive Modelling for 'Gazepoint' Research

## Documentation for package ‘gp3ml’ version 0.3.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G I L N P R S T V W

## -- A --

apply_gazepoint_calibrator | Apply a fitted probability calibrator
apply_gazepoint_decision_rule | Apply a governed classification decision rule
assert_gp3ml_engine_available | Assert that a gp3ml engine is available
assert_gp3ml_use_case | Assert that a task is within the permitted gp3ml scope
assess_gazepoint_calibration | Calibration assessment with bootstrap uncertainty
assess_gazepoint_conformal_coverage | Assess conformal coverage
as_gp3ml_data | Extract model-ready data from a gp3ml handoff object
audit_gazepoint_abstention | Audit abstention decisions
audit_gazepoint_dataset_shift | Audit predictor distribution shift
audit_gazepoint_group_folds | Aggregate leakage audits across group-aware folds
audit_gazepoint_missingness_shift | Audit missingness shift
audit_gazepoint_ml_leakage | Audit leakage between predictive-analysis partitions
audit_gazepoint_model_robustness | Audit multiple robustness dimensions
audit_gazepoint_nested_resampling | Audit nested grouped resampling for outer-assessment leakage
audit_gazepoint_plan_deviations | Audit deviations from a locked analysis plan
audit_gazepoint_reproducibility | Audit generated artifacts for volatile output
audit_gp3ml_api_stability | Audit gp3ml API stability
audit_gp3ml_governance_profile | Audit a governance-evidence profile

## -- B --

bake_gazepoint_preprocessor | Apply a fitted preprocessing engine
bootstrap_gazepoint_metrics | Bootstrap uncertainty intervals for performance metrics
bootstrap_gazepoint_metrics_by_unit | Generalization-target-aligned bootstrap uncertainty

## -- C --

capture_gazepoint_environment | Capture a reproducibility environment record
collect_gazepoint_fold_predictions | Collect predictions from a grouped-fold evaluation
combine_gazepoint_handoffs | Combine validated cross-package handoffs
compare_gazepoint_environments | Compare two environment records
compare_gazepoint_models | Compare governed model candidates without selecting a winner
create_external_validation_report | Create an external-validation report object
create_gazepoint_decision_rule | Create a governed classification decision rule
create_gazepoint_feature_manifest | Create a Gazepoint feature-provenance manifest
create_gazepoint_group_folds | Create deterministic group-aware Gazepoint resampling folds
create_gazepoint_handoff | Create a lightweight cross-package Gazepoint handoff
create_gazepoint_model_artifact | Create a portable governed model artifact
create_gazepoint_model_card | Create a governance-focused model card
create_gazepoint_nested_folds | Create nested grouped resampling from mature outer folds
create_gazepoint_release_evidence | Create a release evidence manifest
create_gazepoint_release_model_card | Create a release-ready governed model card
create_gazepoint_reproducibility_report | Create a reproducibility report
create_gazepoint_synthetic_manifest | Create a synthetic governed feature manifest
create_gazepoint_synthetic_task | Create one of the governed synthetic demonstration tasks
create_gazepoint_tuning_grid | Create an explicit governed tuning grid
create_gp3ml_governance_profile | Create a governance-evidence profile

## -- D --

declare_gazepoint_analysis_plan | Declare a frozen-analysis-plan contract
declare_gazepoint_external_dataset | Declare an external dataset and its independence status
declare_gazepoint_task | Declare a governed Gazepoint prediction task
diagnose_gazepoint_group_folds | Diagnose group-aware Gazepoint resampling folds

## -- E --

evaluate_external_validation | Evaluate an independent external-validation dataset
evaluate_gazepoint_external_transportability | Evaluate external transportability and validation status
evaluate_gazepoint_feature_stability | Evaluate leave-one-feature-out stability
evaluate_gazepoint_group_folds | Evaluate a governed model specification across materialized grouped folds
evaluate_gazepoint_missingness_sensitivity | Evaluate named missingness-sensitivity scenarios
evaluate_gazepoint_nested_resampling | Evaluate nested grouped resampling with inner governed tuning
evaluate_gazepoint_seed_stability | Evaluate seed stability
evaluate_gazepoint_thresholds | Evaluate explicit classification thresholds
evaluate_gazepoint_threshold_stability | Evaluate threshold stability around the optimum

## -- F --

fit_gazepoint_calibrator | Fit a probability calibrator
fit_gazepoint_conformal | Fit target-aware split-conformal calibration
fit_gazepoint_deep_model | Fit an optional governed deep-learning model through keras3
fit_gazepoint_model | Fit a governed Gazepoint model
fit_gazepoint_preprocessor | Fit a fold-local preprocessing engine

## -- G --

gazepoint_classification_metrics | Binary classification metrics
gazepoint_performance_metrics | Task-aware performance metrics
gazepoint_regression_metrics | Regression metrics
gp3ml_api_contracts | gp3ml public API contracts
gp3ml_available_engines | List available model engines
gp3ml_engine_capabilities | Audit gp3ml model-engine capabilities
gp3ml_interop_contracts | Cross-package interoperability contracts
gp3ml_object_schema | Describe the schema of a gp3ml object
gp3ml_prohibited_uses | Prohibited gp3ml uses

## -- I --

integrate_black_box_model | Integrate a controlled black-box model engine

## -- L --

lock_gazepoint_analysis_plan | Lock an analysis plan using SHA-256

## -- N --

normalize_gazepoint_artifact_text | Normalize volatile text in generated research artifacts

## -- P --

plot.gp3ml_abstention_audit | Plot abstention audit
plot.gp3ml_api_stability_audit | Plot a gp3ml API stability audit
plot.gp3ml_conformal_coverage | Plot conformal coverage
plot.gp3ml_dataset_shift_audit | Plot a dataset shift audit
plot.gp3ml_engine_capabilities | Plot gp3ml engine availability
plot.gp3ml_environment_comparison | Plot an environment comparison
plot.gp3ml_governance_profile_audit | Plot a governance profile audit
plot.gp3ml_handoff_validation | Plot handoff validation checks
plot.gp3ml_model_artifact_validation | Plot model-artifact validation
plot.gp3ml_model_robustness_audit | Plot a robustness audit
plot.gp3ml_plan_deviation_audit | Plot analysis-plan deviations
plot.gp3ml_release_checksum_validation | Plot release checksum validation
plot.gp3ml_reproducibility_audit | Plot a reproducibility-hardening audit
plot.gp3ml_research_bundle_validation | Plot research-bundle validation
plot.gp3ml_ro_crate_validation | Plot RO-Crate validation
plot.gp3ml_threshold_evaluation | Plot threshold evaluation
predict.gp3ml_model | Predict from a gp3ml model
predict_gazepoint_interval | Predict conformal regression intervals
predict_gazepoint_set | Predict binary conformal prediction sets
print.gazepoint_feature_manifest_validation | Print feature-manifest validation
print.gazepoint_fold_diagnostics | Print Gazepoint fold diagnostics
print.gazepoint_fold_diagnostics_validation | Print Gazepoint fold-diagnostics validation
print.gazepoint_group_folds | Print group-aware Gazepoint resampling folds
print.gazepoint_group_folds_audit | Print aggregated group-fold leakage auditing
print.gazepoint_group_folds_validation | Print group-aware fold validation
print.gazepoint_ml_leakage_audit | Print a Gazepoint ML leakage audit
print.gazepoint_ml_split | Print a group-aware Gazepoint split
print.gazepoint_ml_split_validation | Print group-aware split validation
print.gp3ml_external_dataset_declaration | Declare an external dataset and its independence status
print.gp3ml_model_selection | Select a governed candidate using an explicit metric and direction
print.gp3ml_model_tuning | Evaluate every governed candidate on the same grouped folds
print.gp3ml_model_tuning_validation | Validate governed tuning results
print.gp3ml_nested_evaluation | Evaluate nested grouped resampling with inner governed tuning
print.gp3ml_nested_evaluation_validation | Validate a nested evaluation
print.gp3ml_nested_folds | Create nested grouped resampling from mature outer folds
print.gp3ml_nested_folds_validation | Validate nested grouped folds
print.gp3ml_nested_resampling_audit | Audit nested grouped resampling for outer-assessment leakage
print.gp3ml_release_evidence | Create a release evidence manifest
print.gp3ml_release_model_card | Create a release-ready governed model card
print.gp3ml_resample_evaluation | Evaluate a governed model specification across materialized grouped folds
print.gp3ml_resample_evaluation_validation | Validate a grouped-fold evaluation result
print.gp3ml_resample_performance_summary | Summarize repeated grouped-resampling performance
print.gp3ml_resample_uncertainty | Summarize uncertainty across folds or repeats
print.gp3ml_target_uncertainty | Generalization-target-aligned bootstrap uncertainty
print.gp3ml_transportability_report | Evaluate external transportability and validation status
print.gp3ml_transportability_validation | Validate an external transportability report
print.gp3ml_tuning_grid | Create an explicit governed tuning grid
print.gp3ml_uncertainty_validation | Validate target-aligned uncertainty metadata

## -- R --

restore_gazepoint_model_artifact | Restore a model artifact

## -- S --

select_gazepoint_model | Select a governed candidate using an explicit metric and direction
select_gazepoint_threshold | Select a threshold from a governed threshold evaluation
simulate_gazepoint_governed_data | Simulate governed synthetic Gazepoint-derived data
simulate_gazepoint_research_handoffs | Simulate realistic cross-package Gazepoint research handoffs
split_gazepoint_ml_data | Create a deterministic group-aware Gazepoint holdout split
summarize_gazepoint_resample_performance | Summarize repeated grouped-resampling performance
summarize_gazepoint_resample_uncertainty | Summarize uncertainty across folds or repeats
summarize_gazepoint_shift | Summarize dataset shift without collapsing it to one drift score

## -- T --

test_gazepoint_model_portability | Test model-artifact serialization and optional fresh-process prediction
train_gazepoint_classifier | Generic governed binary-classifier training wrapper
tune_gazepoint_model | Evaluate every governed candidate on the same grouped folds

## -- V --

validate_gazepoint_analysis_plan | Validate an analysis plan
validate_gazepoint_conformal | Validate a conformal fit
validate_gazepoint_decision_rule | Validate a governed decision rule
validate_gazepoint_environment | Validate the current environment against a reference record
validate_gazepoint_feature_manifest | Validate a Gazepoint feature-provenance manifest
validate_gazepoint_fold_diagnostics | Validate Gazepoint fold diagnostics
validate_gazepoint_group_folds | Validate group-aware Gazepoint resampling folds
validate_gazepoint_handoff | Validate a Gazepoint handoff
validate_gazepoint_ml_roles | Validate outcome, predictor, identifier, and grouping roles
validate_gazepoint_ml_split | Validate a group-aware Gazepoint holdout split
validate_gazepoint_model_artifact | Validate a model artifact
validate_gazepoint_model_tuning | Validate governed tuning results
validate_gazepoint_nested_evaluation | Validate a nested evaluation
validate_gazepoint_nested_folds | Validate nested grouped folds
validate_gazepoint_release_checksums | Validate SHA-256 release checksums
validate_gazepoint_resample_evaluation | Validate a grouped-fold evaluation result
validate_gazepoint_research_bundle | Validate a synthetic cross-package research bundle
validate_gazepoint_ro_crate | Validate a gp3ml RO-Crate-oriented export
validate_gazepoint_target_uncertainty | Validate target-aligned uncertainty metadata
validate_gazepoint_transportability | Validate an external transportability report
validate_gp3ml_object_contract | Validate an object against the gp3ml public-object contract

## -- W --

with_gazepoint_reproducible_output | Evaluate code with deterministic documentation-output settings
write_external_validation_report | Write an external-validation report
write_gazepoint_analysis_plan | Write an analysis plan
write_gazepoint_feature_manifest_csv | Write a Gazepoint feature manifest or validation table to CSV
write_gazepoint_fold_diagnostics_csv | Write Gazepoint fold diagnostics to CSV files
write_gazepoint_group_folds_csv | Write group-aware resampling tables to CSV
write_gazepoint_ml_leakage_audit_csv | Write a Gazepoint ML leakage-audit table to CSV
write_gazepoint_ml_split_csv | Write group-aware split tables to CSV
write_gazepoint_model_card | Write a model card
write_gazepoint_model_tuning | Write governed tuning and selection tables
write_gazepoint_nested_evaluation | Write nested-resampling evaluation tables
write_gazepoint_release_checksums | Write SHA-256 checksums for release artifacts
write_gazepoint_release_model_card | Write a release-ready governed model card
write_gazepoint_reproducibility_audit | Write a reproducibility-hardening audit
write_gazepoint_reproducibility_report | Write a reproducibility report
write_gazepoint_resample_evaluation | Write grouped-fold evaluation tables
write_gazepoint_ro_crate | Write a minimal RO-Crate-oriented research object
write_gazepoint_target_uncertainty | Write target-aligned uncertainty tables
write_gazepoint_transportability_report | Write an expanded transportability report
write_gp3ml_api_contracts | Write gp3ml API contracts
write_gp3ml_governance_profile | Write a governance profile audit