# Case 21: Dietary diversity and gut community composition

## Case details

| Field | Value |
|---|---|
| Case ID | `case21` |
| Case title | Dietary diversity and gut community composition |
| Case folder | `cases/case21/` |
| Product / feature | AIPOCH Open-Science research conversation, Plan, Notebook, automatic review and session export |
| Author | mumumm |
| Submitter | mumumm |
| Created / updated | 2026-10-08 / 2026-10-08 |
| Status | draft |
| Case type | evaluation |
| Product / model version | OpenScience 0.35.1 per review record; model gpt-6-astra; backend codex:builtin-codex-isolated; reasoning medium |

## Goal and context

Assess reported plant-type categories and gut microbial community composition in historical American Gut data, with geography and questionnaire-missingness sensitivity.

This submission selects attempt `20261008-light-3`, not the first run. The selected export is named `21-2-2026-10-08.science`; filename numbering is not the native attempt number. The new analysis uses 600 participants, processed 100-nt features and Lingoes-corrected Bray–Curtis geometry. It is not a wording-only repair or an exact replication of the first attempt. Permitted Plan review and operator follow-ups are preserved and do not themselves constitute a failure.

## Inputs and sources

The unchanged [session.science](session.science) export preserves the exact user-role request sequence.

Source: American Gut commit `68fd6d4b2fa6aeb5b4f5272c6f1006defe5b160e`, a May 2015-or-earlier data/survey snapshot. The captured files are:

- [AG_100nt.biom](https://raw.githubusercontent.com/biocore/American-Gut/68fd6d4b2fa6aeb5b4f5272c6f1006defe5b160e/data/AG/AG_100nt.biom): SHA-256 `35e474a374acb6bbf53ba7c2d1ba750b5e3c579eed0b8fc325e63f309cb503bb`.
- [AG_100nt.txt](https://raw.githubusercontent.com/biocore/American-Gut/68fd6d4b2fa6aeb5b4f5272c6f1006defe5b160e/data/AG/AG_100nt.txt): SHA-256 `e37d1c5b2e17f62c194da231e499611a391bea76e4d15fe2d1a5b55166fcea4b`.
- [README.md](https://raw.githubusercontent.com/biocore/American-Gut/68fd6d4b2fa6aeb5b4f5272c6f1006defe5b160e/README.md): SHA-256 `a01016dba296950fb798c0dcb577676d9b776bbfa4d6ba06567cbc9030c0d30f`.
- [metadata_charts.json](https://raw.githubusercontent.com/biocore/American-Gut/68fd6d4b2fa6aeb5b4f5272c6f1006defe5b160e/latex/metadata_charts.json): SHA-256 `e13dd86e7c20635eafe12c84ea3f582067614a96b71c8c75ffe34968d440bc01`.

Historical acquisition occurred during the 2026-10-08 original run; the saved download manifest does not record per-file timestamps. The source README describes open-access/deidentified data, but a specific redistribution license was not established from the inspected records. Preserve attribution and verify applicable source terms before redistribution. No new source retrieval or license verification was performed during preparation; the repository license does not relicense third-party inputs.

Export completed **2026-10-08T16:58:25.760000+08:00**, Asia/Shanghai. Source filename `21-2-2026-10-08.science`, size 30,806,918 bytes, SHA-256 `ec457ca8f832735c9e7b3414c3145fd472f48c4bad7dbb1d439ffbdb29df5672`. Archive validation does not independently certify sensitive-content screening.

### Runtime and prerequisites

Recorded Python: 3.12.3 (tags/v3.12.3:f6650f9, Apr  9 2024, 14:05:25) [MSC v.1938 64 bit (AMD64)]. Libraries: numpy 2.4.6, pandas 3.0.5, scipy 1.17.0, matplotlib 3.8.4, h5py 3.16.0, threadpoolctl 3.6.0. Pillow is also used for image metadata; its exact version is not recorded in this validation file. A compatible existing runtime is required; the interpreter and a full environment lock are not bundled. No installation or product changes were performed.

## Reproduction steps

1. Import `session.science` into a compatible OpenScience version. Fresh import was not performed during preparation.
2. Inspect the Plan, `analysis_rules.md`, `study_report.md` and `plant_diversity_reproducible.zip`.
3. Extract the bundle into a new directory. Keep `ag_analysis/` captured inputs and `reference_results/` intact.
4. With the recorded dependencies already available, run from the extracted directory:

```text
python analysis.py
```

With provided inputs this needs no network; the script can download missing files from pinned URLs, so retain and checksum-check all included inputs for an offline replay. It writes `ag_results/` and refuses an existing output directory. A fresh alternative directory can be selected through `AG_OUTPUT_DIR`.

Compare model/cohort/feature/input-hash outputs at recorded tolerances rtol=1e-10 and atol=1e-12. Eigenvector signs may change between numerical libraries; compare reconstructed distances or coordinate Gram matrices rather than signs. The displayed two-axis ordination is not the full inferential geometry. This command was documented, not executed during packaging; prior Notebook replay is distinct from a new replay or native Reproduction.

### Exact prompt or request

See the [session history](session.science). Original session messages are preserved verbatim; automatic-review messages are labeled separately. The later checking branch is documented below, not merged into the research session.

## Expected result and acceptance criteria

| Criterion | How to check | Pass condition |
|---|---|---|
| Bounded analysis | Request, Plan, input manifests and cohort audit | Specified data, local methods and sample scope respected |
| Numerical consistency | Report, saved tables and code | Correct denominators, transformations, estimates, uncertainty and multiple-testing treatment |
| Interpretation | Report opening, methods, limitations and conclusion | Claims limited to observational evidence and measured quantities |
| Inspectable delivery | Session inventory and offline bundle | Captured inputs, code, provenance, report, tables and standalone figures agree |
| Reproduction | Authorized offline replay | Regenerated outputs agree with saved results under recorded tolerances |

## Actual result

The source contains 4,827 matching samples and 22,742 features. Eligibility and participant deduplication leave 2,719 participants, from whom a fixed-seed country-proportional sample of 600 was selected. Main analysis includes 564 respondents with known country; 479 complete cases, 540 US respondents and a 300-person eight-state subset support sensitivity analyses.

All 9,089 nonzero cohort features were retained. Bray–Curtis geometry had 259 materially negative eigenvalues; Lingoes correction yielded 598 retained coordinate dimensions. All dimensions were used for inference; display axes explain 4.40% and 2.47% of corrected inertia.

The primary country-adjusted association has incremental R² **0.0080399356 (0.804%)**, partial R² **0.0081978586 (0.820%)**, pseudo-F **1.1344562**, and permutation **p=.004** using 999 permutations. This is a small association in corrected geometry, not the fraction of raw-count biological variance explained or a causal benefit. Multiplicity-adjusted complete-case and regional sensitivity tests are less conclusive.

The new mean centroid distances decrease from **0.840916** to **0.808207** across increasing plant categories; “More than 30” is correctly identified as the minimum. The previous attempt's range defect is absent. Dispersion F is **2.3986004**, with saved permutation p=.046; unequal dispersion limits a pure centroid interpretation.

Artifacts inside the package: `analysis_rules.md`, `analysis.py`, `study_report.md`, `plant_diversity_reproducible.zip`, `ordination.png`, and `sensitivity_missingness.png`. The bundle additionally includes captured inputs, model/cohort/missingness/geometry tables, PDF figures and replay records.

| Criterion | Result (pass / fail / not-run) | Evidence and limitation |
|---|---|---|
| Numerical spot-checks | pass in checked scope | Five review groups plus operator counts, model arithmetic, Holm and dispersion calculations agree |
| Interpretation | pass in checked scope | No confirmed overclaim in inspected report; old descriptive defect absent |
| Delivered-copy consistency | pass | Exported artifact objects hash-verified; six registered scientific files match reviewed local delivery; report/code/rules/PNGs match bundle copies; four captured inputs match manifest hashes |
| Complete historical lineage | not-run / unable to verify | Original/replay execution history not fully linked or accessible; no stale content demonstrated |
| New full replay / fresh application import | not-run | Preparation verified retained evidence and bytes, not the full computation |

### Limitations and review context

This observational historical cohort is heavily US-dominated. Survey recall interval, self-report, identity-key validity, upstream processing and confounding limit generalization. Missingness tests do not establish missing-at-random or equivalence. Dispersion, multiplicity, absent effect-size confidence intervals and the substantial geometry correction remain disclosed.

No confirmed scientific defect was found in this bounded review. Underlying abundance-to-geometry calculations and original permutation generation were not independently rerun; complete supersession history remains unverified. The saved replay record lacks originating execution IDs.

Native review autoReview `cmuzap9je000lx4zojrlqavk1` completed/pass with `verificationUnavailable=true` and legacy-unverified bindings. Its pass traces bounded findings to recorded outputs, not independent validation of the entire study. The review record is kept separate from the original session; no original scientific contents were edited during packaging.

### Package-to-review correspondence

| Item | Identifier |
|---|---|
| Original package | `21-2-2026-10-08.science` |
| Native attempt | `20261008-light-3` |
| Checking report | `case21-20261008-attempt3.md` |
| Checking report SHA-256 | `069e79d4c34714b4bd0166cf07074be88052f129695716c409f619f417d4cf01` |
| Project | `cmuz9gqyu000fx4zor7gdf33r` |
| Original session | `01a11a94-934c-7b41-a60e-d2720d505494` |
| Review-only branch | `01a11aaf-927b-7f73-b6db-e833d0b64c92` |
| Review run | `99c95953-6235-4b53-8174-c065a813bb77` |
| Reviewed report version | `b967c3d0-46bc-4ed6-8e98-7c2ce9777608` |
| Reviewed bundle version | `7c7bfebf-4247-413d-a1dc-a026f739cb0a` |

Full review and evidence remain outside this two-file submission. The preparation index records their paths and hashes.

## Review

- Reviewer: unassigned for repository acceptance.
- Review date: pending; external bounded checking completed 2026-10-08.
- Decision: pending.
- Notes and next actions: no scientific correction recommended by the bounded review. Fresh import and complete historical lineage remain unverified. Prepared for HF submission on 2026-10-08; Feishu is not updated by this upload.