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 = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3

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

cpp

2.00 score 2 scripts 123 downloads 3 exports 16 dependencies

Last updated 2 years agofrom:d9d56eee60. Checks:OK: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 01 2024
R-4.5-linux-x86_64OKDec 01 2024

Exports:lnmbiclustlnmfaplnmfa

Dependencies:clicodetoolsforeachgluegtoolsiteratorslifecyclemagrittrMASSmclustpgmmRcpprlangstringistringrvctrs

lnmCluster

Rendered fromlnm-bicluster.Rmdusingknitr::rmarkdownon Dec 01 2024.

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