aldex                   ALDEx3 Linear Models
aldex.effect            ALDEx3 Effect Diagnostics
aldex.lm.sim.clr        Simulation function soley for testing and
                        exploring ALDEx3, Truth is in CLR Coordinates.
aldex.mem.sim           Simulation for testing mixed effects models.
aldex.plot              Plot Method for ALDEx3 objects with pairwise
                        comparisons
aldex.pvals             Calculate p-values adjusting for changes in
                        sign as described by Nixon et al. (2024) in
                        Beyond Normalization: Incorporating Scale
                        Uncertainty in Microbiome and Gene Expression
                        Analysis (internal only)
blmm                    Fast approximate mixed-effects engine for
                        ALDEx3.
clr.sm                  CLR-based scale model
coefficient.sm          Scale model using prior information about
                        groups or treatments
cohensd                 Cohen's D
combine.streams         Combine output from aldex streams (internal
                        only)
fflm                    Freaking Fask Linear Models
gut_crohns_data         Gut Crohn's microbiome dataset (list)
miniclo                 Closure operation
oral_mouthwash_data     Oral microbiome perturbation dataset (list)
rLogDirichlet           Function for sampling Dirichlet random
                        variables (base-2 normalized via log-sum-exp
                        for stability)
req                     Test object contains elements
sample.sm               Per-sample scale model using external
                        information
sr.mem                  Implementation of SR-MEM: scale-reliant mixed
                        effects models.
summary.aldex           Summary Method for ALDEx3 Objects
tss.sm                  TSS-centered scale model
