NEWS.md

In ALDEx3: Linear Models for Sequence Count Data

ALDEx3 1.4.0

Maintenance

• Made BLMM reject invalid or ill-conditioned raw anchor Hessians instead of ridge-regularising and inverting them. Draw-specific Newton updates are now checked against their profiled REML objective, and rejected draws fall back selectively to exact lme4 rather than returning pathological uncertainty.

ALDEx3 1.3.1

Maintenance

• Registered TMB native routines and disabled dynamic symbol lookup for portable compiled-code checks.
• Made the ALDEx2 compatibility regression test robust to the R 4.7.0 binomial RNG change by checking overall p-value agreement and matching significance decisions instead of a strict elementwise tolerance.

ALDEx3 1.3.0

User Facing Changes

• Harmonized independent scale-uncertainty inputs on standard deviations: sample.sm() now accepts s.sd, and coefficient.sm() now accepts c.sd.
• Added explicitly named s.cov and c.cov arguments for covariance matrices. The legacy s.var, s.cor, and c.cor arguments retain their original semantics with deprecation warnings until ALDEx3 2.0.0.
• Clarified that gamma is a standard deviation in clr.sm() and tss.sm(), and documented that sample-level and coefficient-level priors have different covariance structures even when their SD inputs are numerically equal.
• Added a two-group coefficient-scale example explaining how factor reference levels determine the sign of a group offset.

New Features

• Added method = "blmm": an ALDEx3-specific approximate mixed-effects engine using a batched profiled REML anchor fit per feature, draw-specific local covariance updates, and exact conditional GLS fixed-effect solves. Falls back to lme4 for features where the approximation cannot be evaluated cleanly.
• On small datasets (with S\approx 20) blmm is approximately 40x faster than lme4, that factor should increase substantially as S increases to more realistic levels.
• Added feature-level parallelism (n.cores) for method = "blmm" and method = "lme4".
• Added dedicated mixed-effects vignette covering model setup, BLMM formulation, validation guidance, and runtime comparison with exact lme4.

ALDEx3 1.0.3

User Facing Changes

• Added aldex.plot() for pairwise ALDEx3 model contrasts, with volcano, effect, MA, and waterfall plot modes.
• Added aldex.effect() for ALDEx2-inspired effect diagnostics on a single binary ALDEx3 contrast. The function reports the mean contrast estimate, mean pooled within-group standard deviation, mean Cohen's d, and an ALDEx2-style directional overlap diagnostic.
• Updated cohensd() documentation and preserved its legacy return value: a feature by Monte Carlo sample matrix of Cohen's d draws.
• Effect diagnostics and MA plots now use reconstructed log abundance, logComp + logScale, and clearly report that they require stored Monte Carlo arrays.
• Fixed the Quickstart vignette setup so package data such as gut_crohns_data is available during vignette rebuilds.

ALDEx3 0.1.1

User Facing Changes

• 1000x (approx) speed up in HC3 and HC0 standard error calculations. Note this was rate limiting before so this is a huge performance boost.
• Fixed error with how the streamsize variable was calibrated. Leads to massive improvement in memory management.

ALDEx3 documentation built on Oct. 20, 2026, 1:07 a.m.