R: Dirichlet-Multinomial generative classifiers.

dmngroup {DirichletMultinomial}

R Documentation

Dirichlet-Multinomial generative classifiers.

Description

Fit Dirichlet-Multinomial generative classifiers to groups (rows) within a sample x taxon count matrix.

Usage


dmngroup(count, group, k, ..., simplify = TRUE,
    .lapply = parallel::mclapply)

Arguments

`count`	`matrix()` of sample x taxon counts.
`group`	`factor()` or vector to be coerced to a factor, with as many elements as there are rows in `count`, indicating the group to which the corresponding sample belongs.
`k`	`integer()`, the number(s) of Dirichlet components to fit.
`...`	Additional arguments, passed to `dmn`.
`simplify`	Return only the best-fit model for each group?
`.lapply`	An `lapply`-like function for application of group x k fits.

Details

This function divided count into groups defined by group, creates all combinations of group x k, and evaluates each using dmn. When simplify=TRUE, the best (Laplace) fit is selected for each group.

Value

An object of class dmngroup, a list of fitted models of class dmn. When simplify=TRUE, elements are named by the group to which they correspond.

Author(s)

Martin Morgan mailto:mtmorgan@fhcrc.org

References

Holmes I, Harris K, Quince C, 2012 Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics. PLoS ONE 7(2): e30126. doi:10.1371/journal.pone.0030126.

Examples

## best fit for groups 'Lean' and 'Obese'; full example in vignette.
## Not run: bestgrp <- dmngroup(count, pheno, k=1:5, verbose=TRUE, 
                    mc.preschedule=FALSE)

## End(Not run)
data(bestgrp)
bestgrp
bestgrp[["Obese"]]

[Package DirichletMultinomial version 1.30.0 Index]