# Generalized UniFrac Distances, Distance-Based Multivariate Methods and Feature-Based Univariate Methods for Microbiome Data Analysis

## Documentation for package ‘GUniFrac’ version 1.9

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

adonis3 | Permutational Multivariate Analysis of Variance Using Distance Matrices (Freedman-Lane permutation)
dICC | Distance-based Intra-Class Correlation Coefficient
dICC.SE.asympt | Asymptotic Standard Error of Distance-based Intra-Class Correlation Coefficient
dICC.SE.bt | Bootstrap Standard Error of Distance-based Intra-Class Correlation Coefficient
dmanova | Distance-based Multivariate Analysis of Variance (Analytical P-value Calculation)
GMPR | Geometric Mean of Pairwise Ratios (GMPR) Normalization for Zero-inflated Count Data
GUniFrac | Generalized UniFrac distances for comparing microbial communities.
PermanovaG | Permutational Multivariate Analysis of Variance Using Multiple Distance Matrices
PermanovaG2 | Permutational Multivariate Analysis of Variance Using Multiple Distance Matrices(Freedman-Lane Permutation)
Rarefy | Rarefy a Count Table to Equal Sequencing Depth
SimulateMSeq | A Semiparametric Model-based Microbiome Sequencing Data Simulator for Cross-sectional and Case-control Studies
SimulateMSeqC | A Semiparametric Model-based Microbiome Sequencing Data Simulator for Longitudinal, Matched-pair, and Replicate Sampling Designs
stool.otu.tab | Stool Microbiome OTU Count Table
throat.meta | Throat Microbiome Meta Data
throat.otu.tab | Throat Microbiome OTU Count Table
throat.tree | UPGMA Tree of Throat Microbiome OTUs
vaginal.otu.tab | Vaginal Microbiome OTU Count Table
ZicoSeq | A linear Model-based Permutation Test for Differential Abundance Analysis of Microbiome Data and Other Omics Data
ZicoSeq.plot | A Plot Function for Visualizing the ZicoSeq Results