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feat(analysis): add two-part count models and occupancy fitter - #196
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📝 Summary
Merge Risk: 🟡 Moderate · up to
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| Check name | Status | Explanation |
|---|---|---|
| Title check |  |
The title clearly summarises the main changes: two-part count models and an occupancy fitter. |
| Description check | |
The description clearly explains the changes, motivation, scope limitations, related issue, and validation results. It omits the template headings for “Change and reason” and “Scope”, and it does not … |
| Docstring Coverage | |
Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 3 functions across 6 files. (6 skipped: 6 … |
| Linked Issues check | |
Check skipped because no linked issues were found for this pull request. |
| Out of Scope Changes check | |
Check skipped because no linked issues were found for this pull request. |
Full details: Description check
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Explanation
The description clearly explains the changes, motivation, scope limitations, related issue, and validation results. It omits the template headings for “Change and reason” and “Scope”, and it does not include the contribution checklist, but the required information is mostly present.
Full details: Docstring Coverage
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Explanation
Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 3 functions across 6 files. (6 skipped: 6 unsupported.)
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Actionable comments posted: 4
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Inline comments:
Review comments at @docs/occupancy-models.md:
- Around line 41-47: Update the `fit_occupancy` documentation to state that
`psi_reference` is the estimate for `levels[1]` and `psi_contrast` is the
estimate for `levels[2]`, replacing the vague statement that ψ is returned for
each group.
Review comments at @src/analysis/differential.jl:
- Line 530: Rename the `g` parameter in `da_tp_nll` to `grp` so it cannot
partially match `optim`’s `gr` formal. Update the `b1*g` and `z1*g` expressions
in the function body and the `g` arguments in both `optim` calls to use `grp`.
- Line 632: Rename the `g` parameter in `da_occ_nll` to avoid `optim`
partial-matching it to `gr`; use the new name in the `b0+b1*g` occupancy
calculation and in the `g` argument supplied by both `optim` calls. Preserve the
likelihood behaviour while ensuring the group data reaches it.
Review comments at @test/unit/test_differential.jl:
- Line 696: Update the row-count assertion for the result returned by
fit_occupancy to compare nrow(fitted) with length(taxa), reflecting the
one-row-per-taxon output.
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📒 Files selected for processing: 12
README.mdconfig/defaults/pipeline.ymldocs/occupancy-models.mdfrontend/src/api/types.tsfrontend/src/components/DifferentialPanel.tsxfrontend/src/components/PipelineStages.test.tsfrontend/src/components/PipelineStages.tsxfrontend/src/components/differentialTable.test.tsfrontend/src/components/differentialTable.tssrc/analysis/differential.jlsrc/server/routes/config.jltest/unit/test_differential.jl
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📜 Review details
⏰ Context from checks skipped due to timeout: 6
- GitHub Check: Occupancy relevance
- GitHub Check: Code relevance
- GitHub Check: semgrep-cloud-platform/scan
- GitHub Check: DOI relevance
- GitHub Check: Analyze (javascript-typescript)
- GitHub Check: Analyze (actions)
🧰 Additional context used
🪛 LanguageTool
docs/occupancy-models.md
[uncategorized] ~78-~78: Do not mix variants of the same word (‘modelling’ and ‘modeling’) within a single text.
Context: ...gy: improving ecological inference by modelling the source of zero observations. *Ecolo...
(EN_EXACT_COHERENCY_RULE)
README.md
[uncategorized] ~264-~264: Loose punctuation mark.
Context: ... (default) orrlescaling. -zinb`: a zero-inflated negative-binomial model...
(UNLIKELY_OPENING_PUNCTUATION)
[uncategorized] ~267-~267: Loose punctuation mark.
Context: ...o test, and BH correction. - hurdle_nb: a logistic occurrence model plus zero-t...
(UNLIKELY_OPENING_PUNCTUATION)
[uncategorized] ~279-~279: Loose punctuation mark.
Context: ...ocs/occupancy-models.md). - clr_welch: Welch's t-test on centred log-ratios af...
(UNLIKELY_OPENING_PUNCTUATION)
🔇 Additional comments: 9
frontend/src/api/types.ts: 1
416-421: LGTM!config/defaults/pipeline.yml: 1
350-358: LGTM!frontend/src/components/PipelineStages.tsx: 1
153-154: LGTM!Also applies to: 254-254
src/server/routes/config.jl: 1
200-201: LGTM!frontend/src/components/PipelineStages.test.ts: 1
10-16: LGTM!README.md: 1
264-284: LGTM!frontend/src/components/DifferentialPanel.tsx: 1
141-147: LGTM!Also applies to: 162-163, 175-176
frontend/src/components/differentialTable.ts: 1
7-7: LGTM!Also applies to: 30-30, 51-51
frontend/src/components/differentialTable.test.ts: 1
41-43: LGTM!
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Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> Signed-off-by: Jonathan D.A. Jewell <6759885+hyperpolymath@users.noreply.github.com>
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hyperpolymath
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Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>
Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>
Signed-off-by: Jonathan D.A. Jewell <6759885+hyperpolymath@users.noreply.github.com>
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This was referenced Oct 23, 2026
hyperpolymath
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…s main lost Rebased onto main (c978994, which includes #208/#211/#213) so this is only the part main still gets wrong. Package loading — `using MetaManifold` fails on main: - src/core/doi.jl declared `module DOI` twice (lines 4 and 21) with one terminator, a ParseError at EOF before any test can run. The declaration after the header comment is kept. - src/MetaManifold.jl included analysis/clade_cumulus.jl twice and never included analysis/compositional.jl, which Differential imports CompositionalModels from (UndefVarError as soon as it is loaded). Both corrected in place. - src/server/server.jl never included routes/cladistics.jl, so the study-level Cladistics tab the frontend calls returns 404 while the route file sits unused. Included after clade_cumulus.jl; no path or helper clashes. Test registration: - test/runtests.jl listed test_clade_cumulus.jl twice and had lost test_evidence.jl and test_evidence_routes.jl, which #201 added. 49 files, each once, and every file in test/unit is registered. Statistics tests that contradicted their own sources: - test_exact_summaries.jl expected 0/1 proportions for a zero-read sample, but `_summarise` fills those with `nothing` (a proportion is undefined, not zero, when a sample has no reads) and stores null. Test realigned to the source. - test_high_precision.jl expected UnsupportedRepresentationError for a numeric policy of the wrong mode; `assert_mode` raises ArgumentError for that. Test realigned, with the reason stated inline. Docs main lost in the #196 merge: - docs/statistics/zero-handling.md is back to the full treatment (replacement policies, delta semantics, what the Bayesian posterior does and does not claim, warnings and references) instead of the 60-line summary. - README regains the Evidence Mode section and the differential-abundance method guidance (why a count model rather than a t-test, choosing the reference taxon, overdispersion, which model to use), documents all nine methods and settings, and the config sample lists every differential key. Verified: tree-sitter parses every touched Julia file; no file is included twice; YAML parses with the expected differential keys; `npx tsc --noEmit` clean; `bun test src` 85/85. Julia itself is not available here, so the suite's first real run is CI. Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>
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…in lost (#209) Rebased onto `main` (c978994, which now carries #208/#211/#213), so this PR is only the part `main` still gets wrong — and `main` still cannot load the package. ## 1. `using MetaManifold` fails | File | Defect | Effect | |---|---|---| | `src/core/doi.jl` | `module DOI` declared twice (lines 4 and 21) with one terminator | `ParseError` at EOF, before a single test runs | | `src/MetaManifold.jl` | `analysis/clade_cumulus.jl` included twice; `analysis/compositional.jl` never included | module redefined; `UndefVarError: CompositionalModels` when `differential.jl` loads | | `src/server/server.jl` | `routes/cladistics.jl` never included | the Cladistics tab calls endpoints that return 404 while the route file sits unused | Each is a one-line fix in place. `cladistics.jl` is included after `clade_cumulus.jl`; it shares no route path or helper name with the other route files. ## 2. Test registration `test/runtests.jl` listed `test_clade_cumulus.jl` twice and had lost `test_evidence.jl` and `test_evidence_routes.jl`, which #201 added. Now 49 files, each once, and every file in `test/unit` is registered. ## 3. Two statistics tests that contradicted their own sources Both came from a branch whose tests were written against different source behaviour: - `test_exact_summaries.jl` expected `0/1` proportions for a zero-read sample. `_summarise` fills them with `nothing` and stores null, because a proportion is undefined — not zero — when a sample has no reads. The test is realigned to the source; the source is not weakened to the test. - `test_high_precision.jl` expected `UnsupportedRepresentationError` for a policy of the wrong numeric mode. `assert_mode` raises `ArgumentError` for that (a caller error, not an unrepresentable value). Realigned, with the reason stated inline. ## 4. Documentation main lost in the #196 merge - `docs/statistics/zero-handling.md` is back to the full treatment — replacement policies and their exact `cmultRepl` calls, `delta` semantics, what the Bayesian posterior parameterisation does and does **not** claim, warnings, and references — instead of the 60-line summary. - `README.md` regains the Evidence Mode section and the differential-abundance method guidance (why a count model rather than a t-test, choosing the reference taxon, overdispersion, which model to use), documents all nine methods and their settings, and the config sample lists every differential key including the multinomial optimiser budget. ## Validation Julia is not available in my environment, so the Julia side is static: tree-sitter parses every touched file, no file is included twice, every `test/unit` file is registered exactly once, and the YAML parses with the expected differential keys. Frontend: `npx tsc --noEmit` clean, `bun test src` 85/85, `npm run build` succeeds. CI is the first real execution of the Julia suite, and I will follow it and fix what it reports. Co-authored-by: Arena Agent <agent@arena.ai> Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>
hyperpolymath
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…tegration repair (#214) ## Why This branch carries the fork-side resolution of **#193** and, because the squash merges of #196–#207 left `main` unable to build the frontend or load the Julia package, the integration repair needed to land anything at all. A file-by-file audit (every squash commit matched its PR-head tree exactly) traced the breakage to PR-branch conflict resolutions overwriting each other: - #200 dropped `include("analysis/compositional.jl")` while `differential.jl` requires `..CompositionalModels`. - #207 duplicated the clade-cumulus include/panel import, dropped the cladistics client imports, and replaced `routes/cladistics.jl` with `routes/clade_cumulus.jl`. - #206 then #196 overwrote the differential method/config union: `DifferentialConfig` referenced undefined `mn_*`/`dm_*`/`max_*` names, the ancom_bc/aldex2/songbird and multinomial dispatch branches were unreachable, and `_differential_settings_error` called an undefined `keys_`. ## What **#193** (`ad7f5f2`): `bench/null_calibration/` extracts the production NB R block and measures Wald/LRT null rejection (WebR + genuine MASS 7.3-65 reduced run executed; full grid + `wald_trend`/glmGamPoi QL/edgeR committed unrun — `REPORT.md` bounds exactly what ran). `nb_glm` results carry `diagnostics.calibration_caveat` (every `ml` result, scaled by the smaller group; `glmGamPoi` through 12/group), surfaced in the panel and CSV header. No p-value or default changes. **Merge** (no-ff, by request): current `main` merged in; conflicts resolved onto main-side structure with the #193 changes reapplied. **Integration repair** (`1335ccd`): nine-method registry/config/dispatch union, compositional + cladistics/clade-cumulus routes restored, frontend type/config/CSV unions, panel import disambiguated, stale test pins updated to the union. ## Verification - Frontend: `tsc` clean, `bun test` 87/87, production build passes. - Julia: no runtime in the authoring sandbox — CI is the evidence; this PR stays open until it is green. Refs #193 (fork-side bench + warning per maintainer decision; upstream default remains the upstream maintainer's call — draft in `bench/null_calibration/UPSTREAM_DRAFT.md`). --------- Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>
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Summary
Related to #18. This is a partial implementation, not a close of #18: occupancy remains a lower-level API (not selectable in AnalysisConfig or the single-sample UI), and detection covariates/formula editors, Vuong/residual diagnostics, performance benchmarks, and corresponding schema/provenance work remain outstanding. The issue should stay open until those acceptance criteria are completed.
Validation