# Linear Models for Sequence Count Data

## Documentation for package ‘ALDEx3’ version 1.2.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

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 | 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)
req | Test object contains elements
rLogDirichlet | Function for sampling Dirichlet random variables (base-2 normalized via log-sum-exp for stability)
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)