Package: lnmCluster 0.3.1

Wangshu Tu

lnmCluster: Perform Logistic Normal Multinomial Clustering for Microbiome Compositional Data

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>.

Authors:Wangshu Tu [aut, cre], Sanjeena Dang [aut], Yuan Fang [aut]

lnmCluster_0.3.1.tar.gz
lnmCluster_0.3.1.tar.gz(r-4.5-noble)lnmCluster_0.3.1.tar.gz(r-4.4-noble)
lnmCluster_0.3.1.tgz(r-4.4-emscripten)lnmCluster_0.3.1.tgz(r-4.3-emscripten)
lnmCluster.pdf |lnmCluster.html✨
lnmCluster/json (API)

# Install 'lnmCluster' in R:
install.packages('lnmCluster', repos = 'https://cloud.r-project.org')
Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

cpp

2.00 score 121 downloads 3 exports 16 dependencies

Last updated 3 years agofrom:d9d56eee60. Checks:3 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 31 2025
R-4.5-linux-x86_64OKMar 31 2025
R-4.4-linux-x86_64OKMar 31 2025

Exports:lnmbiclustlnmfaplnmfa

Dependencies:clicodetoolsforeachgluegtoolsiteratorslifecyclemagrittrMASSmclustpgmmRcpprlangstringistringrvctrs

lnmCluster

Rendered fromlnm-bicluster.Rmdusingknitr::rmarkdownon Mar 31 2025.

Last update: 2022-07-20
Started: 2022-07-20

Citation

To cite package ‘lnmCluster’ in publications use:

Tu W, Dang S, Fang Y (2022). lnmCluster: Perform Logistic Normal Multinomial Clustering for Microbiome Compositional Data. R package version 0.3.1, https://CRAN.R-project.org/package=lnmCluster.

Corresponding BibTeX entry: 

  @Manual{,
    title = {lnmCluster: Perform Logistic Normal Multinomial Clustering
      for Microbiome Compositional Data},
    author = {Wangshu Tu and Sanjeena Dang and Yuan Fang},
    year = {2022},
    note = {R package version 0.3.1},
    url = {https://CRAN.R-project.org/package=lnmCluster},
  }