Taxa

The taxa R package provides a set of tools for defining and manipulating
taxonomic data. The recent and widespread application of DNA sequencing to
community composition studies is making large data sets with taxonomic
information commonplace. However, compared to typical tabular data, this
information is encoded in many different ways and the hierarchical nature of
taxonomic classifications makes it difficult to work with. There are many R
packages that use taxonomic data to varying degrees but there is currently no
cross-package standard for how this information is encoded and manipulated. We
developed the R package taxa to provide a robust and flexible solution to storing
and manipulating taxonomic data in R and any application-specific information
associated with it. Taxa provides parsers that can read common sources of
taxonomic information (taxon IDs, sequence IDs, taxon names, and classifications)
from nearly any format while preserving associated data. Once parsed, the
taxonomic data and any associated data can be manipulated using a cohesive set of
functions modeled after the popular R package dplyr. These functions take into
account the hierarchical nature of taxa and can modify the taxonomy or associated
data in such a way that both are kept in sync. Taxa is currently being used by
the metacoder and taxize packages, which provide broadly useful functionality
that we hope will speed adoption by users and developers.

Taxa: An R package implementing data standards and methods for taxonomic data.

Taxa is an R tool containing classes that can store, define and manipulate taxonomic data. The Taxa tool includes a parser that can read most taxonomic information sources, including taxon IDs, sequence IDs, taxon names, and classifications. The Taxa algorithm allows modification of taxonomy and associated data and keeps both synchronized.

Taxa

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