lnmCluster

MaRDI QIDQ101519CRANFDO

Authors Wangshu Tu, Sanjeena Dang, Yuan Fang, Sanjeena Subedi

Last update 28 August 2026

Copyright license GNU General Public License, version 2.0, GNU General Public License, version 3.0

Software version identifier 0.3.1, PACKAGES.rds, 1.0.0

Description

An implementation of logistic normal multinomial (LNM) clustering. It is an extension of LNM mixture model proposed by Fang and Subedi (2020) <doi:10.1038/s41598-023-41318-8>, 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 (2023) <doi:10.1007/s00357-023-09452-0> and Tu and Subedi (2022) <doi:10.3329/jsr.v56i2.67469>. It also include a Biclustering algorithm that applies to multivariate normal data: Tu and Subedi (2022) <doi:10.1002/sam.11555>.

Cites work

• A family of mixture models for biclustering
• Clustering microbiome data using mixtures of logistic normal multinomial models
• Logistic Normal Multinomial Factor Analyzers for Clustering Microbiome Data
• Penalized logistic normal multinomial factor analyzers for high dimensional compositional data

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