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These functions include operations that will either return a transformed version of the input phyloseq object, a subset version, or extracted data on set parameters. In some cases the functions are practical rewrites of ones already available from phyloseq with additional features or a more efficient implementation with data.table for large datasets. Various functions include finding shared or exclusive taxa by treatments, agglomeration, factor handling, and filtering.

phylosmith: an R-package for reproducible and efficient microbiome analysis with phyloseq-objects