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7 changes: 6 additions & 1 deletion ROADMAP.md
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Expand Up @@ -6,7 +6,12 @@ occupancy work. The GitHub Wiki roadmap still needs a synchronized update; see

## Available now

- `nb_glm` and `clr_welch` remain the existing differential methods.
- The differential-abundance config offers four per-taxon count models
(`nb_glm`, `clr_welch`, `zinb`, `hurdle_nb`) and five compositional models
(`ancom_bc`, `aldex2`, `songbird`, `multinomial`, `dirichlet_multinomial`);
see [the differential-abundance section](README.md#differential-abundance).
`songbird` and `multinomial` are two implementations of the same
baseline-category multinomial model.
- `zinb` and `hurdle_nb` are available in the differential-abundance config and
UI. They report the count effect and zero/occurrence effect and test group
effects jointly. The UI surfaces model cautions; BH adjustment remains on.
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4 changes: 4 additions & 0 deletions docs/statistics/zero-handling.md
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Expand Up @@ -105,6 +105,10 @@ there is no silent fallback to another estimator.
valid observations under that model.
- Raise `min_prevalence` when rare taxa would make imputed values dominate the
composition. The result reports median and maximum imputed mass per sample.
- Use `multinomial` or `dirichlet_multinomial` when the whole composition is the
unit of inference: a zero count is part of the likelihood, no size factor is
fitted, and conditioning on each sample's read total makes every effect a log
ratio against a reference taxon rather than an absolute abundance.
- Consider an occupancy/observation model when detection itself is the object of
inference, or a zero-inflated or hurdle model when structural and sampling
zeros must be separated. Those models are not implemented by `clr_welch`, and
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