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:
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')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 years agofrom:d9d56eee60. Checks:OK: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 01 2024 |
| R-4.5-linux-x86_64 | OK | Nov 01 2024 |
Exports:lnmbiclustlnmfaplnmfa
Dependencies:clicodetoolsforeachgluegtoolsiteratorslifecyclemagrittrMASSmclustpgmmRcpprlangstringistringrvctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Gives default initial guesses for logistic-normal multinomial biclustering algorithm. | initial_variational_gaussian |
| Gives default initial guesses for penalized logistic-normal multinomial Factor analyzer algorithm. | initial_variational_lasso |
| Gives default initial guesses for logistic-normal multinomial Factor analyzer algorithm. | initial_variational_PGMM |
| Logistic Normal Multinomial Biclustering algorithm | lnmbiclust |
| Logistic Normal Multinomial factor analyzer algorithm | lnmfa |
| run main microbiome bicluster algorithm. | Mico_bi_jensens |
| Penalized Logistic Normal Multinomial factor analyzer main estimation process | Mico_bi_lasso |
| run main microbiome Factor Analyzer algorithm. | Mico_bi_PGMM |
| Model selections for 'lnmbicluster' | model_selection |
| Model selections for 'plnmfa' | model_selection_lasso |
| Model selections for 'lnmfa' | model_selection_PGMM |
| Penalized Logistic Normal Multinomial factor analyzer algorithm | plnmfa |