DirichletMultinomial: Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data

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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 This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed further in the man page for this package, ?DirichletMultinomial.

Author
Martin Morgan <martin.morgan@roswellpark.org>
Date of publication
None
Maintainer
Martin Morgan <martin.morgan@roswellpark.org>
License
LGPL-3
Version
1.16.0

View on Bioconductor

Man pages

cvdmngroup
Cross-validation on Dirichlet-Multinomial classifiers.
dataobjects
Data objects used for examples and the vignette
DirichletMultinomial-package
Dirichlet-Multinomial Mixture Model Machine Learning for...
dmn
Fit Dirichlet-Multinomial models to count data.
DMN-class
Class '"DMN"'
dmngroup
Dirichlet-Multinomial generative classifiers.
DMNGroup-class
Class '"DMNGroup"'
fitted
Access model components.
heatmapdmn
Heatmap representation of samples assigned to Dirichlet...
roc
Summarize receiver-operator characteristics
util
Helpful utility functions

Files in this package

DirichletMultinomial/DESCRIPTION
DirichletMultinomial/NAMESPACE
DirichletMultinomial/R
DirichletMultinomial/R/AllGenerics.R
DirichletMultinomial/R/dmn.R
DirichletMultinomial/R/dmngroup.R
DirichletMultinomial/R/roc.R
DirichletMultinomial/R/util.R
DirichletMultinomial/build
DirichletMultinomial/build/vignette.rds
DirichletMultinomial/data
DirichletMultinomial/data/bestgrp.rda
DirichletMultinomial/data/fit.rda
DirichletMultinomial/data/xval.rda
DirichletMultinomial/inst
DirichletMultinomial/inst/doc
DirichletMultinomial/inst/doc/DirichletMultinomial.R
DirichletMultinomial/inst/doc/DirichletMultinomial.Rnw
DirichletMultinomial/inst/doc/DirichletMultinomial.pdf
DirichletMultinomial/inst/extdata
DirichletMultinomial/inst/extdata/TwinStudy.t
DirichletMultinomial/inst/extdata/Twins.csv
DirichletMultinomial/man
DirichletMultinomial/man/DMN-class.Rd
DirichletMultinomial/man/DMNGroup-class.Rd
DirichletMultinomial/man/DirichletMultinomial-package.Rd
DirichletMultinomial/man/cvdmngroup.Rd
DirichletMultinomial/man/dataobjects.Rd
DirichletMultinomial/man/dmn.Rd
DirichletMultinomial/man/dmngroup.Rd
DirichletMultinomial/man/fitted.Rd
DirichletMultinomial/man/heatmapdmn.Rd
DirichletMultinomial/man/roc.Rd
DirichletMultinomial/man/util.Rd
DirichletMultinomial/src
DirichletMultinomial/src/Makevars
DirichletMultinomial/src/Makevars.win
DirichletMultinomial/src/R_init_DirichletMultinomial.c
DirichletMultinomial/src/dirichlet_fit.c
DirichletMultinomial/src/dirichlet_fit.h
DirichletMultinomial/src/dirichlet_fit_main.c
DirichletMultinomial/src/dirichlet_fit_main.h
DirichletMultinomial/vignettes
DirichletMultinomial/vignettes/DirichletMultinomial.Rnw
DirichletMultinomial/vignettes/References.bib