From 139121f04f3f8745ed54cc49494f01805bb2aaa7 Mon Sep 17 00:00:00 2001 From: "Jonathan D.A. Jewell" Date: Thu, 15 Oct 2026 10:31:53 +0100 Subject: [PATCH 1/2] docs: an Applications-in-practice section -- the discipline earned on 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 --- README.md | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/README.md b/README.md index 9e551c6..881cb88 100644 --- a/README.md +++ b/README.md @@ -66,3 +66,18 @@ proofs/check.sh # Debian 13: apt install agda Code: MPL-2.0. Documentation: CC-BY-SA-4.0. Per-file SPDX headers are authoritative. + +## Applications in practice + +The concrete target is MetaManifold's Differential Abundance tab +([JoshuaJewell/MetaManifold-WebUI](https://github.com/JoshuaJewell/MetaManifold-WebUI), +proposed as [issue #23](https://github.com/JoshuaJewell/MetaManifold-WebUI/issues/23)), +which today fits each taxon with a negative-binomial GLM or a Welch t-test on +CLR values through R. The real-world value of doing the compositional methods +natively is not speed: it is that `proofs/PROOF-STATUS.md` lets a review answer +*"is this safe and sound, or can it produce funny results?"* claim by claim -- +each CLR property is either proved under `--safe` or marked tested, so a +pipeline maintainer adopts exactly as much certainty as the method carries, +instead of borrowing all of it from a paper. The Bioconductor implementations +stay in CI as oracles, which is the difference between "validated against the +reference" and "hoped to match". From 53b1c5a54a22d858090e6526a38eb88bd9effcd0 Mon Sep 17 00:00:00 2001 From: "Jonathan D.A. Jewell" Date: Thu, 15 Oct 2026 10:50:08 +0100 Subject: [PATCH 2/2] docs: name ALDEx2 as the CI oracle; ANCOM-BC's remains planned (CodeRabbit, 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 --- README.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 881cb88..6834607 100644 --- a/README.md +++ b/README.md @@ -78,6 +78,9 @@ natively is not speed: it is that `proofs/PROOF-STATUS.md` lets a review answer *"is this safe and sound, or can it produce funny results?"* claim by claim -- each CLR property is either proved under `--safe` or marked tested, so a pipeline maintainer adopts exactly as much certainty as the method carries, -instead of borrowing all of it from a paper. The Bioconductor implementations -stay in CI as oracles, which is the difference between "validated against the -reference" and "hoped to match". +instead of borrowing all of it from a paper. The Bioconductor oracle in CI +today is ALDEx2 -- the difference between "validated against the +reference" and "hoped to match" for the method it covers. ANCOM-BC's +reference oracle remains planned; until it lands, ANCOM-BC carries the +package's own tests, not a cross-check against the Bioconductor +implementation.