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Oct 15, 2026
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docs: an Applications-in-practice section #10

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docs: an Applications-in-practice section -- the discipline earned on…
hyperpolymath Oct 15, 2026
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docs: name ALDEx2 as the CI oracle; ANCOM-BC's remains planned (CodeR…
hyperpolymath Oct 15, 2026
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Expand Up @@ -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.
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