Table 1. Primary classes and functions found in taxa.

Function	Description
•    taxon	A class that combines the classes containing the name, rank, and ID for a taxon.
•    taxa	A simple list of taxon objects in an arbitrary order.
•    hierarchy	A class that stores a list of nested taxa constituting a classification.
•    hierarchies	A simple list of hierarchy objects in an arbitrary order.
•    taxonomy	A class that stores a list of unique taxon objects and a tree structure.
•    taxmap	A class that combines a taxonomy with user-defined, tables, lists, or vectors associated with taxa in the taxonomy. The taxonomic tree and the associated data can then be manipulated such that the two remain in sync.
•    supertaxa     •    subtaxa	A "supertaxon" is a taxon of a coarser rank that encompasses the taxon of interest (e.g. Homo is a supertaxon of Homo sapiens). The "subtaxa" of a taxon are all those of a finer rank encompassed by that taxon. For example, Homo sapiens is a subtaxon of Homo. The supertaxa/subtaxa function returns the supertaxa/subtaxa of all or a subset of the taxa in a taxonomy object. By default, these functions return taxon IDs, but they can also return any data associated with taxa.
•    roots     •    leaves     •    stems     •    branches	Roots are taxa that lack a supertaxon. Likewise, leaves are taxa that lack a subtaxon. Stems are those taxa from the roots to the first split in the tree. Branches are taxa with exactly one supertaxon and one subtaxon. In general, stems and branches can be filtered out without changing the relative relationship between the remaining taxa. By default, these functions return taxon IDs, but they can also return any data associated with taxa.
•    obs	Returns the information about every observation from an user-defined data set for each taxon and their subtaxa. By default, indices of a list, vector, or table mapped to taxa are returned.
•    filter_taxa     •    filter_obs	Subset taxa or associated data in taxmap objects based on arbitrary conditions. Hierarchical relationships among taxa and mappings between taxa and observations are taken into account.
•    arrange_taxa     •    arrange_obs	Order taxon or observation data in taxmap objects.
•    sample_n_taxa     •    sample_n_obs     •    sample_frac_taxa     •    sample_frac_obs	Randomly sample taxa or observation data in taxmap objects. Weights can be applied that take into account the taxonomic hierarchy and associated data. Hierarchical relationships among taxa and mappings between taxa and associated data are taken into account.