ALDEx3 1.2.0

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) 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.