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docs: an Applications-in-practice section - #10
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… a real pipeline Appends a worked real-world case to README.md: the concrete situation in an amplicon-sequencing pipeline in production use where the type, the OND discipline or the algebra earns its keep -- and what the untyped or undisciplined alternative gets wrong. Documentation only; no code changes. Generated by Mistral Vibe. Co-Authored-By: Mistral Vibe <vibe@mistral.ai>
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📝 Summary
Merge Risk: 🔵 Low · up to
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| Check name | Status | Explanation |
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| Title check |  |
The title clearly and concisely identifies the README documentation change. It matches the main change in the pull request. |
| Description check | |
The description explains the new README section, its real-world MetaManifold example, and its documentation-only scope. It is related to the changeset. |
| Docstring Coverage | |
No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff. Analyzed 0 functions across 0… |
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A rabbit reads of CLR,
And hops through notes of proof.
R methods meet their stated role,
While CI checks the truth.
Then off through clover, calm and sure.
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Actionable comments posted: 1
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Inline comments:
Review comments at @README.md:
- Around line 81-83: Clarify the reference-oracle sentence by naming ALDEx2 as
the implementation currently installed and checked in CI. Avoid implying that
ANCOM-BC is covered; it remains planned.
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- GitHub Check: Julia 1.12
- GitHub Check: Julia 1.10
- GitHub Check: Agda proofs (Debian 2.6.4.3, stdlib 2.1)
- GitHub Check: R reference oracle (R 4.5.0, Bioconductor 3.22)
…abbit, PR #10) The sentence said the Bioconductor implementations stay in CI as oracles, plural; the workflow installs and loads ALDEx2 only, and ANCOM-BC's oracle is still a roadmap item. The passage now says which reference the validation claim actually covers, and states what ANCOM-BC carries until its oracle lands: the package's own tests, not a cross-check against Bioconductor. Generated by Mistral Vibe. Co-Authored-By: Mistral Vibe <vibe@mistral.ai>
What this adds
An Applications in practice section in
README.md: one worked real-world case that shows native compositional differential-abundance methods whose proof status is claim-by-claim -- a maintainer adopts exactly as much certainty as the method carries -- grounded in MetaManifold, an amplicon-sequencing pipeline in production use, because the value of the discipline is clearest on a live pipeline rather than a toy.The section answers the question a newcomer actually has: what is this for in the real world, and what goes wrong without it? It is deliberately short, states what the undisciplined alternative gets wrong, and links the concrete case.
What this leaves out
Documentation only. No code, no API, no claim changes anywhere else in the repo. The commit is signed.
Versions tested
Not applicable -- documentation.
Generated by Mistral Vibe.
Co-Authored-By: Mistral Vibe vibe@mistral.ai