{
  "schema_version": "pollenomics-v5-scoped-study-report.v1",
  "status": "scoped_development_report_with_external_source_blockers",
  "as_of": "2026-09-30",
  "confirmatory_result": false,
  "outcome_access_for_report": "previously exposed outcomes scored after frozen country predictions; no untouched confirmatory outcome",
  "primary_prediction_cohort": {
    "source": "previously opened English author-prepared pollen counts",
    "site_count": 17,
    "taxon_count": 31,
    "grouping": "whole author site IDs; cross-database alias closure unreviewed",
    "fold_count": 3,
    "attempted_site_bins": 184,
    "common_scored_site_bins": 174,
    "outcomes_used_for_development_selection": true
  },
  "selected_development_candidate": {
    "candidate_id": "clr_rbf_q25_ridge_0.1",
    "method": "clr_wgs84_rbf_ridge",
    "distance_quantile": 0.25,
    "ridge_penalty": 0.1,
    "training_zero_policy": "half-count per taxon for CLR fit only",
    "selection_rule": "minimum common-support site-macro MAE among candidates with at least 80 percent own scored-bin coverage; ties prefer greater own coverage then candidate ID",
    "scoring": "original observed counts; site-macro MAE and Hellinger distance",
    "status": "exploratory_prior_exposed_development_evidence"
  },
  "excluded_claims": [
    "Nordic LRA and independent vegetation accuracy: no admitted inputs for those claims; DK/FI/NO direct-pollen results are exploratory, prior-exposed subcomposition predictions only",
    "The 31-author-target Nordic pollen response has a different axis and denominator from the 16-label response; their MAE values are not a paired method-improvement comparison",
    "Independent vegetation accuracy: no eligible measured pairs",
    "HYDE-assisted pollen covariate effect: not evaluated; source country cropland and seven selected CE-label native grid reconciliations are modeled context, not measured vegetation",
    "Whole-paper historical reproduction: source inputs, chronology, rights and PFT mapping unresolved",
    "Untouched confirmatory prediction skill: all author pollen outcomes were previously exposed",
    "Swedish LRA prediction: no fold run because time-matched basin geometry and parameterized count denominator remain unresolved",
    "The Swedish 31-author-target all-bin denominator differs from the 39-common-bin parameter screen and the prior 16-label observed-pollen response"
  ],
  "producer_and_source_identities": {
    "author_development_design": "docs/report/pollen-reconstruction/author-development-design.json",
    "author_development_source_manifest_sha256": "48d853468f979a04636642c6c757e9d05edf708d799b29cbae4d2286a9ac0acb",
    "swedish_direct_pollen_producer": "bijux_pollenomics_dev.source_completion.swedish_direct_pollen",
    "swedish_direct_pollen_configuration": "docs/report/pollen-reconstruction/swedish-direct-pollen/config.json",
    "swedish_direct_pollen_input_manifest": "docs/report/pollen-reconstruction/swedish-direct-pollen/input-manifest.json",
    "swedish_direct_pollen_source_files": {
      "part-004.json": "d96046c88b497ba07082120e446fecacad0d9b5533d8960bdbc03811976ea435",
      "part-008.json": "9cdcb2d394bc8ef23bf2b4b5e3f1f3ae5916aae16db71542c58f4b80a2dd1134"
    },
    "paper_correspondence": "reports/science/publication-correspondence.md",
    "swedish_source_questions": "docs/report/pollen-reconstruction/swedish-source-questions.csv",
    "nordic_direct_pollen_producer": "bijux_pollenomics_dev.source_completion.nordic_direct_pollen",
    "nordic_direct_pollen_report": "docs/report/regions/nordic/direct-pollen/RESULTS.md",
    "nordic_direct_pollen_manifest": "docs/report/regions/nordic/direct-pollen/manifest.json",
    "nordic_direct_pollen_source_snapshot": "sha256:b2bcb99157e10b0c9f13c228acc12eabcb39d96a1f39c86ec25e34aacd78c791",
    "nordic_direct_pollen_relational_build": "sha256:92dd52619837f3641d004a1a5dbe38f9ab6023a79f61989314bb90e612eb58e1",
    "nordic_direct_pollen_scored_rows": 6172,
    "nordic_direct_pollen_prediction_rows": {
      "DK": 96,
      "FI": 1740,
      "NO": 4336
    },
    "delivery_commits": [
      "21fa4ae8",
      "907c948f",
      "20ecd351"
    ],
    "final_development_suite": "1,097 passed before final cache guard failure; 3 opt-in skipped; guard rechecked in a 10-test managed selection",
    "focused_delivery_verification": "10 passed; read set unchanged; Ruff check/format and mypy passed",
    "isolated_package_build": "passed; wheel and sdist built; not published",
    "rootsi_source_review": "docs/public/pollenomics-data/sources/landclim.md",
    "author_source_custody": "docs/report/pollen-reconstruction/author-source-custody.json",
    "author_private_source_store_relative_path": "landclim/author-reference"
  },
  "scientific_acceptance": "not_evaluated_for_full_nordic_lra_objective; exploratory_direct_pollen_results_available_for_DK_FI_NO",
  "program_delivery_acceptance": "s9_test_selection_1097_passed_before_cache_guard_failure; focused_guard_rerun_passed; isolated_package_build_passed; full_scientific_objective_incomplete_due_to_external_source_blockers",
  "additional_exploratory_prediction_cohort": {
    "source": "EPD native Neotoma pollen datasets 19913/13338 (Abborrtj\u00e4rnen), 53995/28869 (Bussj\u00f6sj\u00f6n), and 54001/28872 (B\u00f6kesj\u00f6n)",
    "site_count": 3,
    "source_sample_rows": 228,
    "taxon_count": 16,
    "age_support": "sample-owned calibrated radiocarbon years BP; bounds absent; exploratory 500-year bins",
    "folds": "whole physical site held out; target coordinates allowed; target pollen withheld until frozen prediction scoring",
    "attempted_site_bins_per_candidate": 39,
    "common_bins": 13,
    "candidates": [
      "training_mean",
      "nearest_site",
      "inverse_distance_squared",
      "clr_rbf_ridge"
    ],
    "outcomes_previously_exposed": true,
    "status": "exploratory_prior_exposed_swedish_direct_observed_pollen_prediction"
  },
  "nordic_direct_pollen_country_holdout": {
    "source": "Neotoma/EPD datasets from retained relational build",
    "target_countries": [
      "DK",
      "FI",
      "NO"
    ],
    "screen_candidates": {
      "DK": {
        "samples": 91,
        "sites": 1
      },
      "FI": {
        "samples": 1797,
        "sites": 28
      },
      "NO": {
        "samples": 3544,
        "sites": 52
      }
    },
    "scored_site_bins": {
      "DK": 24,
      "FI": 435,
      "NO": 1084
    },
    "scored_sites": {
      "DK": 1,
      "FI": 28,
      "NO": 52
    },
    "unsupported_or_empty_bins": {
      "DK": 0,
      "FI": 0,
      "NO": 94
    },
    "prediction_rows": {
      "DK": 96,
      "FI": 1740,
      "NO": 4336
    },
    "methods": [
      "training_mean",
      "nearest_site",
      "inverse_distance_squared",
      "clr_rbf_ridge"
    ],
    "outcomes_previously_exposed": true,
    "response": "fixed 16 exact-label direct-pollen subcomposition",
    "status": "exploratory_prior_exposed_country_held_out_direct_observed_pollen_prediction",
    "excluded_claims": [
      "measured vegetation accuracy",
      "LRA skill",
      "all-Nordic population-level skill",
      "between-site Danish skill"
    ]
  },
  "author_lra_development": {
    "source": "private LandClim II author-prepared TW5 window, previously exposed",
    "eligible_sites": 15,
    "taxa": 31,
    "pollen_counts": 20732,
    "requested_folds": 15,
    "requested_method_predictions": 45,
    "generated_method_predictions": 0,
    "failed_folds": 15,
    "local_cover_rows_with_negative_fractions": 54,
    "local_cover_rows": 54,
    "status": "exploratory_numerical_refusal_under_declared_geometry_assumptions",
    "report": "reports/science/english-analytical-love/report.json",
    "ring_rows_with_zero_local_positive_regional": 42,
    "zero_local_positive_regional_taxon_cells": 134,
    "equation_max_abs_residual": 2.6645352591003757e-15
  },
  "author_lra_forward_radius_sensitivity": {
    "source": "previously exposed English author TW5 constrained LOVE predictions",
    "report": "docs/report/pollen-reconstruction/author-lra-constrained/radius-sensitivity/scored/report.json",
    "prediction_freeze_sha256": "ca244e33f47ac9768dab60b3e62e59ea06e524cdd0e3d7e21477cb61bb592c44",
    "modeled_radius_factors": [0.8, 1.0, 1.2],
    "eligible_sites": 15,
    "scored_sites": 14,
    "prediction_rows": 126,
    "paired_report": "docs/report/pollen-reconstruction/author-lra-constrained/radius-sensitivity/paired/report.json",
    "paired_rows": 126,
    "aggregate_direct_lower_all_nine": true,
    "claim": "fixed_LRA_vegetation_target_basin_forward_pollen_sensitivity_only"
  },
  "nordic_selected_pollen_transfer": {
    "source_report": "docs/report/regions/nordic/selected-pollen-transfer/report.json",
    "freeze_sha256": "785148abb60b1b76a9568f3e723af1c449150534e2352d005dd8fe8864adae72",
    "paired_scores_sha256": "6946b25a779d47954958b7fa965d5d98b56362c54c68f02a8c067cea0366f31d",
    "paired_scored_site_bins": 1543,
    "site_macro_selected_minus_idw_mae": {
      "DK": 0.0,
      "FI": 0.000496306435025834,
      "NO": 0.006930021467741869
    },
    "status": "prior_exposed_development; selected RBF worse than IDW in FI and NO"
  },
  "nordic_author_target_pollen": {
    "report": "docs/report/regions/nordic/author-target-pollen/report.json",
    "input_manifest_sha256": "86645e8d2f29f60c6c206cb9b594030e7ec01d6b568009eb1e6dec3fc3481500",
    "author_target_taxa": 31,
    "paired_scored_site_bins": 1543,
    "fixed_method_score_rows": 4629,
    "norwegian_training_support_refusals": 94,
    "status": "prior_exposed_observed_pollen_subcomposition; no LRA or measured vegetation claim"
  },
  "hyde_modeled_country_context": {
    "country_result": "docs/report/regions/nordic/hyde-country-cropland/report.json",
    "grid_result": "docs/report/regions/nordic/hyde-country-cropland/grid-conservation/report.json",
    "source_country_values": 84,
    "conserved_country_year_scenario_pairs": 84,
    "pollen_ablation": "not_run; release rights, formal CRS and historical time support remain unresolved"
  },
  "swedish_author_target_pollen": {
    "report": "docs/report/regions/nordic/swedish-author-target-pollen/report.json",
    "input_manifest_sha256": "e6359b4c14cea325c5cecb8d7ff57b5f5b26c17593a1cc3f94e9591edb3fb7f6",
    "author_target_taxa": 31,
    "attempted_site_bins": 54,
    "scored_site_bins": 51,
    "fixed_method_score_rows": 153,
    "training_support_refusals": 3,
    "status": "prior_exposed_observed_pollen_subcomposition; no LRA or measured vegetation claim"
  },
  "swedish_neotoma_holdout": {
    "report": "docs/report/regions/nordic/swedish-neotoma-holdout/report.json",
    "protocol": "docs/report/regions/nordic/swedish-neotoma-holdout/protocol.json",
    "prediction_freeze": "docs/report/regions/nordic/swedish-neotoma-holdout/prediction-freeze.json",
    "physical_core_sites": 1,
    "selected_samples": 77,
    "excluded_parallel_dataset_samples": 77,
    "candidate_and_scored_site_bins": 22,
    "fixed_method_score_rows": 66,
    "native_pollen_nisp": 35767,
    "author_assigned_nisp": 35505,
    "status": "additional_prior_exposed_development_transfer; no LRA, vegetation or country-wide claim"
  },
  "swedish_lake_transfer": {
    "report": "docs/report/regions/nordic/swedish-lake-transfer/report.json",
    "protocol": "docs/report/regions/nordic/swedish-lake-transfer/protocol.json",
    "prediction_freeze": "docs/report/regions/nordic/swedish-lake-transfer/prediction-freeze.json",
    "prediction_freeze_sha256": "3aa60965e7d79b02674a0a61d8806e267bc04a7e2d37df711feb003ef289f18a",
    "physical_lake_sites": 3,
    "selected_samples": 268,
    "excluded_source_samples": 5,
    "candidate_and_scored_site_bins": 63,
    "fixed_method_score_rows": 189,
    "native_pollen_nisp": 238797,
    "author_assigned_nisp": 231115,
    "status": "additional_prior_exposed_development_transfer; no LRA, vegetation or country-wide claim"
  },
  "pft_uncertainty_bounds": {
    "report": "reports/science/publication-correspondence/pft-crosswalk/uncertainty-bounds/report.json",
    "groups": 5,
    "grid_window_rows_per_group": 10500,
    "necessary_bound_violations": 0,
    "same_draw_covariance_aggregation_verified": false
  },
  "author_example_site_mean_holdout": {
    "report": "docs/report/pollen-reconstruction/author-example-site-mean-holdout/report.json",
    "source_revision": "57ead2e2fcc493d099be4e5a3092fc396e1c3d3a",
    "site_count": 17,
    "attempted_site_bins": 184,
    "scored_site_bins": 177,
    "refused_no_training_site_bins": 7,
    "site_macro_mae_fraction": 0.01894855574145571,
    "site_macro_total_variation": 0.29370261399256353,
    "status": "prior_exposed_development_baseline_not_confirmatory"
  },
  "author_buffered_spatial_pollen": {
    "directory": "docs/report/pollen-reconstruction/author-buffered-pollen",
    "private_source_manifest_sha256": "48d853468f979a04636642c6c757e9d05edf708d799b29cbae4d2286a9ac0acb",
    "observed_site_bins": 184,
    "fixed_baseline_scored_bins": 148,
    "four_method_common_scored_bins": 140,
    "fitted_site_macro_mae_fraction": 0.040564201040558065,
    "training_mean_common_site_macro_mae_fraction": 0.025298319144157262,
    "status": "prior_exposed_english_direct_pollen_development_diagnostic"
  },
  "publication_input_inventory": {
    "directory": "docs/report/publication-replay/landclim-study-inputs",
    "publication_metadata_records": 1128,
    "refusal_ledger_records": 4512,
    "reproduction_ready_records": 0,
    "status": "metadata_only_no_authenticated_historical_primary_input_closure"
  },
  "publication_correspondence": {
    "author_example": {
      "directory": "docs/report/publication-replay/landclim-author-example-correspondence",
      "compared_values": 14074,
      "unit": "fraction",
      "status": "bounded_exact_author_R_parity"
    },
    "published_window": {
      "directory": "docs/report/publication-replay/landclim-published-window-correspondence",
      "shared_grid_taxon_keys": 62,
      "window": "100-350 BP",
      "unit": "percentage_cover",
      "status": "descriptive_cross_revision_difference_without_pass_tolerance"
    },
    "three_way_provenance": {
      "directory": "docs/report/publication-replay/landclim-published-window-provenance",
      "paired_mean_se_values": 124,
      "unit": "percentage_cover",
      "status": "author_R_and_installed_python_agree_archive_difference_is_cross_revision"
    },
    "uncertainty_envelopes": {
      "directory": "docs/report/publication-replay/landclim-published-window-uncertainty",
      "taxon_envelopes": 62,
      "disjoint_one_se_envelopes": 0,
      "status": "descriptive_overlap_without_inferential_test"
    },
    "window_alignment": {
      "directory": "docs/report/publication-replay/landclim-window-alignment",
      "compared_windows": 25,
      "exact_tw_indices": ["2"],
      "status": "only_TW2_has_exact_shared_bounds"
    }
  },
  "swedish_training_scope": {
    "report": "docs/report/regions/nordic/swedish-training-scope/report.json",
    "source_response": "31-author-target closed observed-pollen composition",
    "target_sites": 3,
    "candidate_site_bins": 54,
    "common_scored_site_bins": 39,
    "prediction_freeze_sha256": "8ff7979c370465762b0903ed1551f1b78161dade7fda60e2ed5f2ceea3182f8b",
    "sweden_only_training_sites_per_fold": 2,
    "four_country_training_sites_per_fold": 83,
    "sweden_only_support_refusals": 15,
    "paired_method_scores": 117,
    "status": "prior_exposed_matched_whole_site_observed_pollen_development; no temporal displacement, LRA or measured vegetation claim"
  },
  "swedish_support_sensitivity": {
    "report": "docs/report/regions/nordic/swedish-support-sensitivity/report.json",
    "source_response": "31-author-target closed observed-pollen composition",
    "target_sites": 3,
    "candidate_site_bins": 54,
    "age_bin_width_bp": 500,
    "nominal_shift_bins": [
      -1,
      0,
      1
    ],
    "spatial_support_policies": [
      "all",
      "nearest_five",
      "beyond_100_km"
    ],
    "attempted_site_policy_bins": 486,
    "predicted_site_policy_bins": 473,
    "refused_site_policy_bins": 13,
    "prediction_freeze_sha256": "db5bd39b7e9630b48def3ea5082ad1d93358e1e2de75c297b75933584c8a08ed",
    "status": "prior_exposed_whole_site_observed_pollen_sensitivity; nominal bin shifts and center distances, no age posterior, LRA or measured vegetation claim"
  },
  "bjaresjo_context_screen": {
    "report": "reports/science/bjaresjo-context/report.json",
    "official_lake_registry_id": "614958-137018",
    "candidate_neotoma_site_id": "28871",
    "nearby_sead_display_interval_features": 371,
    "nearby_sead_sites": 13,
    "published_window_count": 25,
    "status": "modern_lake_and_display_context_bound; physical_core_and_ecological_event_join_refused"
  },
  "sambosjon_contained_age_support": {
    "report": "docs/report/regions/nordic/sambosjon-direct-pollen/interval-support/report.json",
    "producer": "packages/bijux-pollenomics-dev/src/bijux_pollenomics_dev/source_completion/pollen_age_support/sambosjon.py",
    "source_samples": 111,
    "contained_samples": 53,
    "boundary_crossing_samples": 58,
    "candidate_bins": 22,
    "scored_common_bins": 21,
    "refused_bins": 1,
    "primary_method": "inverse_distance_squared",
    "status": "one_site_exposed_direct_pollen_development_sensitivity",
    "confirmatory_result": false,
    "independent_vegetation_comparison": false
  }
}