Package index • popgenVCF

All functions

new_popgen_vcf_analysis() is_popgen_vcf_analysis() validate_analysis() set_analysis_result() get_analysis_result() print(<PopgenVCFAnalysis>) summary(<PopgenVCFAnalysis>): Canonical popgenVCF analysis state
run_admixture_cv(): Run ADMIXTURE Cross-Validation
align_ancestry_replicate(): Align ancestry Q matrices across label permutations
amova_module_spec(): Construct the AMOVA analysis module descriptor
new_analysis_artifact() validate_analysis_artifact() new_artifact_manifest() register_artifact() validate_artifact_manifest() artifact_manifest_table(): Canonical analysis artifacts and manifests
publication_analysis_citations() publication_analysis_narratives() write_publication_bibliography(): Analysis-specific publication narratives
new_analysis_registry() register_analysis() list_analyses() resolve_analysis_order() execute_analysis_registry() default_analysis_registry(): Dependency-aware analysis registry
new_ancestry_backend() new_ancestry_backend_registry() register_ancestry_backend() ancestry_backend_status() default_ancestry_backend_registry() run_ancestry(): Unified ancestry backend plugins and execution
select_ancestry_k() validate_ancestry_k_selection() ancestry_k_selection_text(): Select ancestry K from fit metrics and replicate stability
new_ancestry_replicate() validate_ancestry_replicate() new_ancestry_result() validate_ancestry_result() ancestry_result_table() ancestry_q_table(): Canonical ancestry result contracts
approve_canonical_ancestry_three_backend_evidence(): Approve proposed canonical ancestry three-backend evidence
approve_scientific_concordance_record(): Approve a proposed scientific concordance record
new_lineage_execution() new_lineage_artifact() new_artifact_lineage() validate_artifact_lineage() lineage_execution_table() lineage_artifact_table() artifact_lineage_dag() verify_artifact_lineage() write_artifact_lineage() set_project_artifact_lineage(): Immutable artifact lineage
artifact_lineage_from_manifest(): Convert an artifact manifest to immutable lineage
new_attempt_ledger() validate_attempt_ledger() write_attempt_ledger() read_attempt_ledger(): Attempt ledger integrity persistence
new_benchmark_dataset_entry() validate_benchmark_dataset_entry() new_benchmark_dataset_catalogue() register_benchmark_dataset() list_benchmark_datasets() benchmark_dataset_cache_dir() verify_benchmark_dataset() resolve_benchmark_dataset() benchmark_dataset_from_entry() default_benchmark_dataset_catalogue(): Benchmark dataset catalogue and cache
new_benchmark_dataset() new_benchmark_spec() new_benchmark_registry() register_benchmark() list_benchmarks() run_benchmark() run_benchmark_suite() benchmark_suite_table() save_benchmark_suite() read_benchmark_suite() print(<PopgenVCFBenchmarkSuite>): Canonical scientific benchmark registry and execution engine
benchmark_stage() synthetic_genotypes(): Deterministic performance benchmarking helpers
bottleneck_module_spec(): Construct the site frequency spectrum and bottleneck-screen module descriptor
new_canonical_real_data_baseline_snapshot() validate_canonical_real_data_baseline_snapshot() read_canonical_real_data_baseline_snapshot() approve_canonical_real_data_baseline_snapshot() write_canonical_real_data_baseline_snapshot(): Canonical real-data baseline snapshots
canonical_1000g_chr22_source(): Describe the approved 1000 Genomes Phase 3 chromosome 22 source
canonical_1000g_chrY_source() validate_canonical_source() verify_canonical_source() canonical_dataset_from_source() approved_1000g_chrY_registry() write_approved_canonical_source_evidence(): Approved 1000 Genomes chromosome Y canonical dataset
new_canonical_baseline_metric() validate_canonical_baseline_metric() new_canonical_baseline_registry() register_canonical_baseline_metric() validate_canonical_baseline_registry() compare_canonical_baseline_metric() evaluate_canonical_baselines() canonical_baseline_table() write_canonical_baseline_evidence() canonical_baseline_validation() canonical_baseline_coverage(): Canonical quantitative baseline metrics
new_canonical_change_request() new_canonical_change_registry() register_canonical_change_request() set_canonical_change_status() reconcile_canonical_changes() canonical_change_summary() write_canonical_change_evidence(): Canonical Scientific Change Approval
new_canonical_drift_profile() new_canonical_baseline_snapshot() assess_canonical_baseline_drift() canonical_drift_table() canonical_drift_history() canonical_drift_summary() write_canonical_drift_evidence(): Canonical baseline drift detection
new_canonical_dataset() validate_canonical_dataset() verify_canonical_dataset() materialize_canonical_dataset() compare_external_results() write_canonical_validation_evidence(): Canonical real-data validation contracts
new_canonical_release_gate_policy() evaluate_canonical_release_gate() canonical_release_gate_table() canonical_release_certificate() write_canonical_release_gate_evidence(): Canonical scientific release gate
canonical_validation_dataset_report(): Render a canonical validation dataset report
new_canonical_validation_suite() register_canonical_validation() validate_canonical_validation_suite() run_canonical_validation_suite() canonical_validation_suite_table() canonical_validation_coverage() write_canonical_validation_suite(): Canonical validation suites
classify_runtime_schema(): Classify an execution-runtime schema version
cli_main(): Command-Line Entry Point
clonality_module_spec(): Construct the multilocus genotype and clonal diversity analysis module descriptor
compare_runtime_api_manifests(): Compare runtime API manifests
compute_ibs_mds(): Compute deterministic classical MDS coordinates from an IBS distance matrix
default_config() read_config() validate_config(): Create, Read, and Validate Configuration
consensus_ancestry() validate_ancestry_consensus() ancestry_consensus_table(): Build and validate consensus ancestry estimates
new_release_performance_budget() validate_release_performance_budget() new_continuous_benchmark_observation() validate_continuous_benchmark_observation() compare_continuous_release_benchmark() validate_continuous_benchmark_comparison() write_continuous_benchmark_evidence(): Continuous release benchmarking
new_core_result() validate_core_result() new_pca_result() new_ibs_result() new_tree_result() new_diversity_result() new_fst_result() new_amova_result() new_dapc_result() new_ibd_result() as_core_result() core_result_table() save_core_result() read_core_result() print(<PopgenVCFCoreResult>): Canonical core analysis result objects
dapc_module_spec(): Construct the DAPC analysis module descriptor
execute_public_analysis(): Execute a Canonical Public Analysis Request
new_persisted_execution_ledger() validate_execution_ledger() write_execution_ledger() read_execution_ledger(): Persist and validate execution ledgers
new_execution_cancellation_token() print(<PopgenVCFExecutionCancellationToken>) request_execution_cancellation() validate_execution_cancellation_token() execute_analysis_plan_with_cancellation() execute_analysis_registry_with_cancellation(): Deterministic cooperative execution cancellation
new_execution_checkpoint() validate_execution_checkpoint() write_execution_checkpoint() read_execution_checkpoint() resume_analysis_execution(): Deterministic analysis execution checkpoints
new_execution_engine() print(<PopgenVCFExecutionEngine>) plan_analysis_execution() print(<PopgenVCFExecutionPlan>) execute_analysis_plan(): Unified deterministic analysis execution engine
new_execution_resource_policy() new_module_resource_requirements() admit_execution_resources(): Execution resource policies and deterministic admission
new_execution_retry_policy() print(<PopgenVCFExecutionRetryPolicy>) execute_analysis_plan_with_retries() execute_analysis_registry_with_retries(): Deterministic execution retry and recovery orchestration
new_execution_timeout_policy() print(<PopgenVCFExecutionTimeoutPolicy>) execute_analysis_plan_with_timeouts() execute_analysis_registry_with_timeouts(): Deterministic execution timeout policies
new_external_command() validate_external_command() print(<PopgenVCFExternalCommand>) run_external_command() print(<PopgenVCFExternalProcessResult>): Canonical external-process execution
start_supervised_external_command() poll_supervised_external_command() read_supervised_external_output() finalize_supervised_external_command() validate_external_process_handle() print(<PopgenVCFExternalProcessHandle>): Asynchronous supervised external-process control
validate_external_process_result() write_external_process_result() read_external_process_result(): External process result integrity persistence
new_external_process_supervision_policy() print(<PopgenVCFExternalProcessSupervisionPolicy>) run_supervised_external_command(): Timeout and resource-aware external-process supervision
new_external_process_workspace_policy() print(<PopgenVCFExternalProcessWorkspacePolicy>) run_supervised_external_command_in_workspace(): Deterministic external-process workspaces
new_external_process_workspace() validate_external_process_workspace() write_external_process_workspace() read_external_process_workspace(): External-process workspace integrity persistence
new_external_reference_spec() validate_external_reference_spec() compare_external_reference() run_external_reference() external_reference_table() external_reference_benchmark_spec(): Systematic external-reference scientific validation
new_fair_creator() fair_identifier() new_fair_metadata() validate_fair_metadata() fair_documents() write_fair_bundle() validate_fair_bundle() set_project_fair_metadata(): FAIR research-object metadata and exports
fst_module_spec(): Construct the FST analysis module descriptor
genome_scan_module_spec(): Construct the sliding-window genome scan analysis module descriptor
get_canonical_dataset(): Get a registered canonical dataset
new_golden_spec() new_golden_entry() new_golden_store() register_golden_entry() validate_golden_entry() compare_golden_outputs() golden_output_table() write_golden_store() read_golden_store() verify_golden_store(): Golden-output scientific regression framework
new_graphical_abstract() validate_graphical_abstract() write_graphical_abstract(): Deterministic graphical abstract specifications
ibd_module_spec(): Construct the isolation-by-distance analysis module descriptor
ibs_module_spec(): Construct the IBS/MDS analysis module descriptor
inspect_public_result(): Inspect a Canonical Public Scientific Result
new_journal_profile() validate_journal_profile() generic_journal_profile() journal_profile() apply_journal_profile() validate_journal_submission() render_journal_profile() write_journal_profile(): Deterministic journal submission profiles
kinship_module_spec(): Construct the kinship/relatedness analysis module descriptor
ld_decay_module_spec(): Construct the linkage-disequilibrium decay analysis module descriptor
list_canonical_datasets(): List registered canonical datasets
new_citation_profile() validate_citation_profile() set_manuscript_citation_profile() manuscript_citation_keys(): Configure reproducible manuscript citation metadata
manuscript_cross_reference_table(): Build the manuscript artifact cross-reference table
new_manuscript() validate_manuscript() render_manuscript_markdown() write_manuscript(): Automatic manuscript generation
render_manuscript_jats() write_manuscript_jats() validate_manuscript_jats(): Generate deterministic JATS manuscript XML
pandoc_status() pandoc_render_arguments() render_manuscript() validate_manuscript_render(): Render canonical manuscripts with Pandoc
new_manuscript_regeneration_verification() manuscript_regeneration_verification_table() validate_manuscript_regeneration_verification() render_manuscript_regeneration_verification() write_manuscript_regeneration_verification(): Deterministic manuscript regeneration verification records
submission_package_plan() write_submission_package() verify_submission_package(): Deterministic manuscript submission packages
manuscript_regeneration_execution_table(): Return the canonical regeneration execution table
new_manuscript_regeneration_plan() manuscript_regeneration_table() validate_manuscript_regeneration_plan() render_manuscript_regeneration_plan() write_manuscript_regeneration_plan(): Manuscript regeneration plans
new_manuscript_revision() validate_manuscript_revision() compare_manuscript_revisions() render_manuscript_revision_diff() write_manuscript_revision_diff(): Deterministic manuscript revision records and diff reports
materialize_registered_canonical_dataset(): Materialize an approved registered canonical dataset
ml_tree_module_spec(): Construct the maximum-likelihood tree module descriptor
validate_module_result(): Validate an analysis-module result
ne_ld_module_spec(): Construct the LD-based effective population size analysis module descriptor
new_analysis_module_spec() register_analysis_module() print(<PopgenVCFModuleSpec>): Create and register self-contained analysis module descriptors
new_ancestry_backend_evidence(): Create ancestry backend evidence for one backend's K sweep
new_ancestry_cross_backend_comparison(): Create a cross-backend Q-matrix comparison record
new_canonical_ancestry_three_backend_evidence(): Create canonical ancestry three-backend release evidence
new_canonical_dataset_registry(): Create a canonical dataset registry
new_canonical_validation_dataset(): Create a canonical validation dataset specification
new_execution_plan(): Create a canonical module execution plan
new_execution_transition(): Create an execution state-transition record
new_manuscript_regeneration_execution(): Create a deterministic manuscript regeneration execution record
new_module_execution_integration_record(): Create a unified module execution integration record
new_module_execution_integration_request(): Create a unified module execution request
new_module_plugin(): Canonical module plugin descriptor
new_phase9_builtin_fixture(): Construct a deterministic built-in Phase 9 module fixture
new_phase9_builtin_run(): Construct a first built-in Phase 9 runtime run record
new_phase9_builtin_verification(): Construct deterministic equivalence verification for built-in executions
new_phase9_cache_decision(): Construct a deterministic Phase 9 cache decision
new_phase9_cutover_readiness(): Construct a portfolio cutover-readiness record
new_phase9_migration_registry_entry(): Construct a production-module migration registry entry
new_phase9_migration_verification(): Construct a production-module migration verification record
new_phase9_module_migration(): Construct a Phase 9 production-module migration record
new_phase9_module_migration_registry(): Construct a deterministic production-module migration registry
new_phase9_runtime_adapter(): Construct a Phase 9 to Phase 8 runtime adapter record
new_phase9_vertical_slice(): Construct a Phase 9 executable vertical-slice record
new_publication_amova_output(): Create a deterministic publication AMOVA output
new_publication_amova_spec(): Create a publication AMOVA specification
new_publication_ancestry_output(): Create a deterministic publication ancestry output
new_publication_ancestry_spec(): Create a publication ancestry specification
new_publication_diversity_output(): Create a deterministic publication diversity output
new_publication_diversity_spec(): Create a publication diversity specification
new_publication_fst_output(): Create deterministic publication FST output
new_publication_fst_spec(): Create a publication FST specification
new_publication_ibd_output(): Create a deterministic publication IBD output
new_publication_ibd_spec(): Create a publication isolation-by-distance specification
new_publication_spatial_output(): Create a deterministic publication spatial-genetics output
new_publication_spatial_spec(): Create a publication spatial-genetics specification
new_runtime_integrity_envelope(): Create a versioned runtime integrity envelope
new_runtime_schema_metadata(): Create canonical runtime schema metadata
new_scheduler_metadata(): Create canonical scheduler metadata
new_schema_descriptor(): Create a canonical schema descriptor
new_schema_registry(): Create a canonical schema registry
new_scientific_cache_key(): Construct a canonical scientific cache key
new_scientific_cache_manifest(): Construct an immutable scientific cache manifest
pca_eigen_residuals(): Validate PCA Eigenvectors Against a Covariance Matrix
pca_module_spec(): Construct the PCA analysis module descriptor
pcadapt_module_spec(): Construct the pcadapt outlier scan module descriptor
performance_environment_fingerprint() new_performance_benchmark_spec() run_performance_benchmark() compare_performance_baseline() performance_benchmark_table() save_performance_baseline() read_performance_baseline(): Performance and resource regression benchmarking
phase10_1_public_surface_manifest() phase10_1_audit_public_surface() phase10_1_closure_evidence() phase10_1_closure_report(): Audit and close the Phase 10.1 public API milestone
phase10_2_audit_compatibility_closure(): Audit the completed Phase 10.2 compatibility evidence chain
phase10_2_closure_evidence(): Assemble deterministic Phase 10.2 closure evidence
phase10_2_closure_report(): Render a deterministic Phase 10.2 closure report
compare_phase10_api_descriptors() validate_phase10_api_compatibility() phase10_api_compatibility_report(): Phase 10 Public API Compatibility Contracts
phase10_api_evolution_policy() new_phase10_migration_guidance() new_phase10_api_migration_plan() validate_phase10_api_migration_plan() phase10_api_migration_report(): Phase 10 Public API Evolution and Migration Planning
phase10_api_descriptor() phase10_api_operations() new_public_analysis_request() new_public_analysis_response() validate_phase10_api_descriptor() validate_public_analysis_request() validate_public_analysis_response() inspect_public_analysis_response() write_public_api_record() read_public_api_record() phase10_public_fingerprint(): Canonical Phase 10 public analysis and artifact API
list_public_artifacts() inspect_public_provenance(): Phase 10 Public Artifact and Provenance Adapters
new_phase10_release_identity() new_phase10_release_conformance() validate_phase10_release_conformance() assert_phase10_release_conformance() phase10_release_conformance_report(): Phase 10 public API release conformance
popgenVCF popgenVCF-package: Population Genomics Toolkit for VCF Data
new_project_rng() new_popgenvcf_project() validate_popgenvcf_project() project_table() write_popgenvcf_project() verify_popgenvcf_project() read_popgenvcf_project() compare_popgenvcf_projects(): Create, bundle, reopen, and compare reproducible popgenVCF projects
population_assignment_module_spec(): Construct the population assignment test analysis module descriptor
build_dashboard_summary() calculate_scientific_quality() write_population_genomics_dashboard(): Interactive population-genomics dashboard
build_population_genomics_report_plan() validate_population_genomics_report_plan() write_population_genomics_report() print(<PopgenVCFReportPlan>): Build and render unified population-genomics reports
align_cluster_labels() compare_q_matrices() structure_reproducibility() select_structure_k() run_faststructure() run_snmf() run_population_structure_validation(): Population-structure comparison and validation tools
population_tree_module_spec(): Construct the population-level genetic distance and tree analysis module descriptor
prepare_vcf_input(): Prepare and Index a VCF Input
print(<PopgenVCFExecutionCheckpoint>): Print an execution checkpoint
new_provenance_node() new_provenance_edge() new_provenance_dag() add_provenance_node() add_provenance_edge() provenance_node_table() provenance_edge_table() provenance_topological_order() provenance_ancestors() provenance_descendants() validate_provenance_dag() new_sample_identity() validate_sample_identity() sample_identity_table() resolve_sample_identity() sample_identity_groups(): Provenance DAGs and canonical sample identity
publication_style() new_publication_bundle() validate_publication_bundle() generate_publication_bundle() set_project_publication_bundle(): Publication companion bundles
new_publication_figure_style_profile() validate_publication_figure_style_profile() publication_figure_style_profile() bind_publication_figure_style() validate_publication_figure_style_binding() publication_figure_parameters() publication_figure_accessibility_audit(): Deterministic Accessible Publication Figure Styles
new_publication_layout_profile() validate_publication_layout_profile() publication_layout_profile() bind_publication_layout() validate_publication_layout_binding() publication_layout_parameters() publication_layout_report(): Deterministic journal-oriented publication layouts
new_publication_submission_package_spec() validate_publication_submission_package_spec() new_publication_supplementary_index() validate_publication_supplementary_index() new_publication_submission_package_manifest() validate_publication_submission_package_manifest() publication_submission_package_report(): Deterministic publication submission packages
publication_amova_caption(): Create a deterministic publication AMOVA caption
publication_amova_report(): Render a deterministic publication AMOVA report
publication_ancestry_caption(): Create a deterministic publication ancestry caption
publication_ancestry_report(): Render a deterministic publication ancestry report
new_publication_dapc_spec() validate_publication_dapc_spec() new_publication_dapc_output() validate_publication_dapc_output() publication_dapc_caption() publication_dapc_report(): Deterministic publication DAPC outputs
publication_diversity_caption(): Create a deterministic publication diversity caption
publication_diversity_report(): Render a deterministic publication diversity report
publication_fst_caption(): Create a deterministic publication FST caption
publication_fst_report(): Render a deterministic publication FST report
publication_ibd_caption(): Create a deterministic publication IBD caption
publication_ibd_report(): Render a deterministic publication IBD report
new_publication_ordination_spec() validate_publication_ordination_spec() new_publication_ordination_output() validate_publication_ordination_output() publication_ordination_caption() publication_ordination_report(): Deterministic publication PCA and ordination outputs
new_publication_report_renderer() validate_publication_report_renderer() quarto_publication_report_renderer() execute_publication_report_plan() validate_publication_report_execution() publication_report_execution_report(): Publication report renderer adapters and execution records
new_publication_report_spec() validate_publication_report_spec() new_publication_report_plan() validate_publication_report_plan() new_publication_report_output_manifest() validate_publication_report_output_manifest() publication_report_plan_report(): Deterministic publication report rendering contracts
publication_spatial_caption(): Create a deterministic publication spatial-genetics caption
publication_spatial_report(): Render a deterministic publication spatial-genetics report
quickstart_dataset_paths(): Locate the bundled real quickstart example dataset
read_canonical_ancestry_three_backend_evidence(): Read canonical ancestry three-backend release evidence
read_scheduler_metadata(): Read and verify scheduler metadata
read_scientific_concordance_suite(): Read a scientific concordance suite
new_reference_adapter() validate_reference_adapter() reference_adapter_status() reference_adapter_spec() default_reference_adapter_registry() run_reference_adapters(): Established external-reference benchmark adapters
register_analysis_artifacts(): Declare Required Artifacts for a Registered Analysis
register_canonical_dataset(): Register a canonical dataset
register_schema(): Register a schema descriptor
new_release_benchmark_record() validate_release_benchmark_record() new_benchmark_archive() register_release_benchmark() get_release_benchmark() benchmark_archive_table() write_benchmark_archive() read_benchmark_archive() verify_benchmark_archive(): Scientific Regression Archive
compare_release_benchmarks() release_comparison_table() latest_release_benchmark() write_regression_report(): Compare archived releases and generate regression reports
diversity_module_spec() tree_module_spec() admixture_module_spec() faststructure_module_spec() snmf_module_spec() chromosome_module_spec(): Construct built-in analysis module descriptors
render_manuscript_regeneration_execution(): Render a manuscript regeneration execution record as Markdown
render_public_report(): Render a Canonical Public Population-Genomics Report
render_report(): Render a Population Genomics Report
new_reporting_checklist() validate_reporting_checklist() generic_reporting_checklist() validate_reporting_checklist_responses() render_reporting_checklist() write_reporting_checklist(): Deterministic reporting checklists
resolve_schema(): Resolve a schema from the registry
new_reviewer_response() validate_reviewer_response() reviewer_response_table() reviewer_response_report() render_reviewer_response() write_reviewer_response(): Deterministic reviewer-response records and bundles
roh_module_spec(): Construct the runs-of-homozygosity (ROH) analysis module descriptor
run_pipeline(): Run the Population Genomics Pipeline
run_pipeline_resume(): Resume a popgenVCF analysis pipeline from its last execution checkpoint
runtime_integrity_payload(): Extract a validated runtime payload
new_runtime_migration_registry() register_runtime_migration() runtime_migration_path() migrate_runtime_integrity_envelope(): Explicit deterministic runtime schema migration
runtime_payload_digest(): Compute a deterministic runtime payload digest
new_runtime_replay_bundle() verify_runtime_replay(): Create and verify deterministic runtime replay bundles
runtime_schema_versions(): Return supported execution-runtime schema versions
runtime_state_transition_matrix() validate_runtime_state_transition() validate_runtime_state_history() assemble_runtime_replay_from_envelopes(): Validate runtime state transitions and assemble migrated replay bundles
new_scientific_concordance_record() validate_scientific_concordance_record() new_scientific_concordance_suite() validate_scientific_concordance_suite() scientific_concordance_table() write_scientific_concordance_evidence(): Canonical external-tool scientific concordance
new_scientific_release_bundle() scientific_release_bundle_table() validate_scientific_release_bundle() render_scientific_release_bundle() write_scientific_release_bundle(): Deterministic scientific release bundles
validation_tolerances() validation_statistics() align_pca_signs() compare_validation_values() manual_ibs_matrix() compare_pca_subspaces() manual_population_diversity() run_scientific_validation(): Scientific validation utilities
sex_check_module_spec(): Construct the sex-check analysis module descriptor
sexbias_module_spec(): Construct the sex-biased dispersal test module descriptor
spatial_autocorrelation_module_spec(): Construct the spatial autocorrelation analysis module descriptor
new_submission_companions() validate_submission_companions() write_submission_companions(): Deterministic submission companion documents
validate_ancestry_backend_evidence(): Validate ancestry backend evidence
validate_ancestry_cross_backend_comparison(): Validate a cross-backend Q-matrix comparison record
validate_canonical_ancestry_three_backend_evidence(): Validate canonical ancestry three-backend release evidence
validate_canonical_dataset_registry(): Validate a canonical dataset registry
validate_canonical_validation_dataset(): Validate a canonical validation dataset specification
validate_concurrency_stress_invariants(): Validate scheduler concurrency invariants
validate_execution_plan(): Validate a module execution plan
validate_manuscript_regeneration_execution(): Validate a manuscript regeneration execution record or bundle
validate_manuscript_revision_diff_bundle(): Validate a written manuscript revision diff bundle
validate_module_execution_integration_request(): Validate a unified module execution request
validate_module_plugin(): Validate a module plugin descriptor
validate_phase9_builtin_fixture(): Validate a deterministic built-in Phase 9 module fixture
validate_phase9_builtin_run(): Validate a first built-in Phase 9 runtime run record
validate_phase9_builtin_verification(): Validate built-in execution equivalence verification
validate_phase9_cache_decision(): Validate a deterministic Phase 9 cache decision
validate_phase9_cutover_readiness(): Validate a portfolio cutover-readiness record
validate_phase9_migration_registry_entry(): Validate a production-module migration registry entry
validate_phase9_migration_transition(): Validate a migration lifecycle transition
validate_phase9_migration_verification(): Validate a production-module migration verification record
validate_phase9_module_migration(): Validate a Phase 9 production-module migration record
validate_phase9_module_migration_registry(): Validate a production-module migration registry
validate_phase9_runtime_adapter(): Validate a Phase 9 runtime adapter record
validate_phase9_vertical_slice(): Validate a Phase 9 executable vertical-slice record
validate_publication_amova_output(): Validate a publication AMOVA output
validate_publication_amova_spec(): Validate a publication AMOVA specification
validate_publication_ancestry_output(): Validate a publication ancestry output
validate_publication_ancestry_spec(): Validate a publication ancestry specification
validate_publication_diversity_output(): Validate a publication diversity output
validate_publication_diversity_spec(): Validate a publication diversity specification
validate_publication_fst_output(): Validate a publication FST output
validate_publication_fst_spec(): Validate a publication FST specification
validate_publication_ibd_output(): Validate a publication IBD output
validate_publication_ibd_spec(): Validate a publication IBD specification
validate_publication_spatial_output(): Validate a publication spatial-genetics output
validate_publication_spatial_spec(): Validate a publication spatial-genetics specification
validate_runtime_api_manifest(): Validate a runtime API manifest
validate_runtime_integrity_envelope(): Validate a runtime integrity envelope
validate_runtime_schema(): Validate an execution-runtime schema version
validate_scheduler_metadata(): Validate scheduler metadata
validate_schema_object(): Validate an object against a registered schema
validate_scientific_cache_manifest(): Validate a scientific cache manifest
verify_cross_backend_replay_equivalence(): Verify deterministic replay equivalence across execution backends
verify_runtime_recovery_equivalence(): Verify recovery equivalence against an uninterrupted execution
write_ancestry_publication_artifacts(): Write publication-ready ancestry artifacts
write_canonical_ancestry_three_backend_evidence(): Write canonical ancestry three-backend evidence
write_canonical_dataset_registry(): Write canonical dataset registry evidence
write_ibs_publication_artifacts(): Write publication-ready IBS and MDS artifacts
write_manuscript_regeneration_execution(): Write a deterministic manuscript regeneration execution bundle
write_pca_publication_artifacts(): Write Publication-Ready PCA Artifacts
write_scheduler_metadata(): Write scheduler metadata