Package: MicrobiomeStat
Type: Package
Title: Statistical Methods for Microbiome Compositional Data
Version: 1.4
Date: 2026-03-03
Authors@R: c(
              person("Xianyang", "Zhang", role = "aut", email = "zhangxiany@stat.tamu.edu"),
              person("Jun", "Chen", role = c("aut", "cre"),
                     email = "chen.jun2@mayo.edu"),
              person("Huijuan", "Zhou", role = "ctb"),
              person("Linsui", "Deng", role = "ctb"))
Author: Xianyang Zhang [aut],
  Jun Chen [aut, cre],
  Huijuan Zhou [ctb],
  Linsui Deng [ctb]
Maintainer: Jun Chen <chen.jun2@mayo.edu>
Description: A suite of methods for powerful and robust microbiome data analysis addressing zero-inflation, phylogenetic structure and compositional effects. Includes the LinDA method for differential abundance analysis (Zhou et al. (2022)<doi:10.1186/s13059-022-02655-5>), the BMDD (Bimodal Dirichlet Distribution) method for accurate modeling and imputation of zero-inflated microbiome sequencing data (Zhou et al. (2025)<doi:10.1371/journal.pcbi.1013124>) and compositional sparse CCA methods for microbiome multi-omics data integration (Deng et al. (2024) <doi: 10.3389/fgene.2024.1489694>). 
Depends: R (>= 3.5.0)
Imports: ggplot2, matrixStats, parallel, stats, utils, Matrix, statmod,
        MASS, ggrepel, lmerTest, foreach, modeest, dplyr, Rcpp, mlr3,
        mlr3mbo, bbotk, paradox
LinkingTo: Rcpp, RcppArmadillo
Suggests: DiceKriging, randomForest
NeedsCompilation: yes
SystemRequirements: NLopt library (optional, for high-performance BMDD
        mode)
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.3
Packaged: 2026-03-03 20:47:26 UTC; chen.jun2
Repository: CRAN
Date/Publication: 2026-03-03 21:40:02 UTC
Built: R 4.6.0; x86_64-apple-darwin20; 2026-04-29 04:56:22 UTC; unix
Archs: MicrobiomeStat.so.dSYM
