diff --git a/README.md b/README.md index 9e551c6..6834607 100644 --- a/README.md +++ b/README.md @@ -66,3 +66,21 @@ 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 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.