model_selection_lasso

fit several models for plnmfa along with 3 criteria values: AIC BIC and ICL

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>.

Wangshu Tu

lnmCluster

Perform Logistic Normal Multinomial Clustering for Microbiome
Compositional Data

Sanjeena Dang

Yuan Fang

model_selection_lasso function

<dl><dt>W_count</dt>
<dd>The microbiome count matrix that you want to analyze.</dd>
<dt>K</dt>
<dd>A specific number of component</dd>
<dt>Q_K</dt>
<dd>A specific number of latent dimension.</dd>
<dt>model</dt>
<dd>A specific model name, UUU or GUU</dd>
<dt>range_tuning</dt>
<dd>A range of tuning parameters specified, ranged from 0-1.</dd>
<dt>iter</dt>
<dd>Max iterations, defaul is 150.</dd>
<dt>const</dt>
<dd>Constant permutation term in multinomial distribution.</dd>
<dt>X</dt>
<dd>The regression covariates matrix, which generates from model.matrix.</dd></dl>

Arguments

Model selections for plnmfa — model_selection_lasso

<dl>

<dt>W_count</dt>
<dd>The microbiome count matrix that you want to analyze.</dd>


<dt>K</dt>
<dd>A specific number of component</dd>


<dt>Q_K</dt>
<dd>A specific number of latent dimension.</dd>


<dt>model</dt>
<dd>A specific model name, UUU or GUU</dd>


<dt>range_tuning</dt>
<dd>A range of tuning parameters specified, ranged from 0-1.</dd>


<dt>iter</dt>
<dd>Max iterations, defaul is 150.</dd>


<dt>const</dt>
<dd>Constant permutation term in multinomial distribution.</dd>


<dt>X</dt>
<dd>The regression covariates matrix, which generates from model.matrix.</dd>

</dl>

model_selection_lasso: Model selections for `plnmfa`

Description

Usage

Value

Arguments