diff --git a/ROADMAP.md b/ROADMAP.md index bc98c01c..4b4beb7f 100644 --- a/ROADMAP.md +++ b/ROADMAP.md @@ -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. diff --git a/docs/statistics/zero-handling.md b/docs/statistics/zero-handling.md index 66095019..49486999 100644 --- a/docs/statistics/zero-handling.md +++ b/docs/statistics/zero-handling.md @@ -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