Dirichlet-Multinomial generative classifiers.

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.

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.

Author

Martin Morgan mailto:mtmorgan.xyz@gmail.com

Examples

## best fit for groups 'Lean' and 'Obese'; full example in vignette.
if (FALSE) bestgrp <- dmngroup(count, pheno, k=1:5, verbose=TRUE, 
                    mc.preschedule=FALSE)
 # \dontrun{}
data(bestgrp)
bestgrp
#> class: DMNGroup 
#> summary:
#>       k samples taxa       NLE   LogDet   Laplace       BIC       AIC
#> Lean  1      61  130  9065.657 162.3513  9027.371  9332.864  9195.657
#> Obese 3     193  130 26769.931 407.4130 26613.414 27801.418 27161.931
bestgrp[["Obese"]]
#> class: DMN 
#> k: 3 
#> samples x taxa: 193 x 130 
#> Laplace: 26613.41 BIC: 27801.42 AIC: 27161.93