Package: lnmCluster
Type: Package
Title: Perform Logistic Normal Multinomial Clustering for Microbiome
        Compositional Data
Version: 0.3.1
Authors@R: c(
    person("Wangshu","Tu",email="wangshu.tu@carleton.ca",role=c("aut","cre")),
    person("Sanjeena","Dang",email="sanjeena.dang@carleton.ca",role=c("aut")), 
    person("Yuan","Fang",email="yuanf@bu.edu",role=c("aut")))
Maintainer: Wangshu Tu <wangshu.tu@carleton.ca>
Description: An implementation of logistic normal multinomial (LNM) clustering. It is an extension of LNM mixture model proposed by Fang and Subedi (2020) <arXiv:2011.06682>, and is designed for clustering compositional data. The package includes 3 extended models: LNM Factor Analyzer (LNM-FA), LNM Bicluster Mixture Model (LNM-BMM) and Penalized LNM Factor Analyzer (LNM-FA). There are several advantages of LNM models: 1. LNM provides more flexible covariance structure; 2. Factor analyzer can reduce the number of parameters to estimate; 3. Bicluster can simultaneously cluster subjects and taxa, and provides significant biological insights; 4. Penalty term allows sparse estimation in the covariance matrix. Details for model assumptions and interpretation can be found in papers: Tu and Subedi (2021) <arXiv:2101.01871> and Tu and Subedi (2022) <doi:10.1002/sam.11555>.  
License: GPL (>= 2)
Encoding: UTF-8
RoxygenNote: 7.1.2
Imports: mclust, foreach, MASS, stringr, gtools, pgmm, utils
Suggests: knitr, rmarkdown, testthat, mvtnorm
VignetteBuilder: knitr
Depends: R (>= 3.50)
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2022-07-19 19:53:07 UTC; wangshutu
Author: Wangshu Tu [aut, cre],
  Sanjeena Dang [aut],
  Yuan Fang [aut]
Repository: CRAN
Date/Publication: 2022-07-20 17:50:02 UTC
Built: R 4.6.0; aarch64-apple-darwin23; 2026-04-26 04:04:57 UTC; unix
Archs: lnmCluster.so.dSYM
