aldex                   ALDEx3 Linear Models
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.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)
clr.sm                  Default CLR-based scale model (with optional
                        scale uncertainty)
coefficient.sm          Coefficient-based scale model with
                        user-specified prior on fixed effects
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               Sample-specific scale model with user-specified
                        mean and variance/covariance
sr.mem                  Implementation of SR-MEM: scale-reliant mixed
                        effects models.
summary.aldex           Summary Method for ALDEx3 Objects
tss.sm                  TSS-centered scale model (with optional scale
                        uncertainty)
