Linear Models for Sequence Count Data

Documentation for package ‘ALDEx3’ version 1.0.0

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)
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)