bioconductor-dirichletmultinomial

name	bioconductor-dirichletmultinomial
description	Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed fu
when_to_use	Use when: Fitting Dirichlet-Multinomial models to microbial metagenomic count data using dmn().; Identifying the optimal number of Dirichlet components (clusters) by comparing laplace(), AIC(), or BIC() scores.; Building generative classifiers for phenotypic groups using dmngroup().; Assigning new samples to classes using predict().. Not for: For continuous covariate modeling, use alternative regression frameworks because dmngroup() is designed for discrete phenotypic categories (e.g., 'Lean', 'Obese').
user-invocable	false

DirichletMultinomial

Dependencies & Environment

Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.

• Version: 1.54.0 · Bioconductor: 3.23 · R: ≥ 4.6
• Depends: S4Vectors, IRanges
• Imports: BiocGenerics
• System requirements: gsl
• Install: BiocManager::install("DirichletMultinomial")

When to Use

• Fitting Dirichlet-Multinomial models to microbial metagenomic count data using dmn().
• Identifying the optimal number of Dirichlet components (clusters) by comparing laplace(), AIC(), or BIC() scores.
• Building generative classifiers for phenotypic groups using dmngroup().
• Assigning new samples to classes using predict().

When NOT to Use

• For continuous covariate modeling, use alternative regression frameworks because dmngroup() is designed for discrete phenotypic categories (e.g., 'Lean', 'Obese').

Data Requirements

• A matrix of raw integer counts (samples in rows, taxa in columns).
• Phenotypic information as a factor for classification.

Key Parameters

• count (default): The matrix of samples by taxa counts provided to dmn() or dmngroup().
• k (default): The number of Dirichlet components to model in dmn() or dmngroup().
• assign (FALSE): Set to TRUE in predict() or mixture() to return the component/class with the maximum value.
• scale (FALSE): Set to TRUE in fitted() to scale the posterior mean difference by theta.

Best Practices

• Fit models across a range of components (e.g., k=1:7) and select the best fit using which.min(lplc) on the Laplace scores.
• Use cvdmngroup() to perform cross-validation and assess classifier performance via ROC curves.
• Use heatmapdmn() to visualize samples arranged by their dominant Dirichlet component.

Common Pitfalls

• Cross-validation with cvdmngroup() is computationally expensive; fix this by using mc.preschedule=FALSE and running it on multiple cores via the parallel package.
• Passing non-integer or normalized data to dmn() violates the multinomial assumption; fix this by ensuring the input is a raw count matrix.

Alternatives

• vegan: For standard distance-based clustering and ordination rather than generative mixture modeling.
• phyloseq: For general microbiome data manipulation and visualization.

Citations

• Holmes et al., 2012, PLoS ONE 7(2): 1-15. https://doi.org/10.1371/journal.pone.0030126

References

• Homepage: https://bioconductor.org/packages/DirichletMultinomial
• Vignette: https://bioconductor.org/packages/release/bioc/vignettes/DirichletMultinomial/inst/doc/DirichletMultinomial.pdf

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