A suite of methods for powerful and robust microbiome data analysis including data normalization, data simulation, community-level association testing and differential abundance analysis. It implements generalized UniFrac distances,  Geometric Mean of Pairwise Ratios (GMPR) normalization, semiparametric data simulator, distance-based statistical methods, and feature-based statistical methods. The distance-based statistical methods include three extensions of PERMANOVA: (1) PERMANOVA using the Freedman-Lane permutation scheme, (2) PERMANOVA omnibus test using multiple matrices, and  (3) analytical approach to approximating PERMANOVA p-value. Feature-based statistical methods include linear model-based methods for differential abundance analysis of zero-inflated high-dimensional compositional data.
Rcpp (>= 0.12.13), vegan, ggplot2, matrixStats, Matrix, ape,
parallel, stats, utils, statmod, rmutil, dirmult, MASS,
ggrepel, lmerTest, foreach, modeest

Rcpp (>= 0.12.13), vegan, ggplot2, matrixStats, Matrix, ape,
parallel, stats, utils, statmod, rmutil, dirmult, MASS,
ggrepel, foreach, modeest

Perform Stationary Global Vector Autoregression Estimation and
Inference
Perform the estimation and inference of stationary Global Vector Autoregression model (GVAR) of Pesaran, Schuermann and Weiner (2004) <DOI:10.1198/073500104000000019> and Dees, di Mauro, Pesaran and Smith (2007) <DOI:10.1002/jae.932>.
lmtest, lubridate, urca, sandwich, strucchange

Perform Global Vector Autoregression Estimation and Inference
Perform the estimation and inference of Global Vector Autoregression model (GVAR) of Pesaran, Schuermann and Weiner (2004) <DOI:10.1198/073500104000000019> and Dees, di Mauro, Pesaran and Smith (2007) <DOI:10.1002/jae.932>.
lmtest, lubridate, urca, sandwich, strucchange, tsDyn

Genome-Wide Association analyses with Family data
Ming-Huei Chen <mhchen@bu.edu> and Qiong Yang <qyang@bu.edu>
Functions to test genetic association between SNPs and a
continuous/dichotomous trait using family data, and to make
genome-wide p-value plot and QQ plot.