Table 1. Primary functions found in metacoder.

Function	Description
extract_taxonomy	Parses taxonomic data from arbitrary text and returns a taxmap object containing a table with rows corresponding to inputs (i.e. observations) and a table with rows corresponding to taxa.
heat_tree	Makes tree-based plots of data stored in taxmap objects. Color, size, and labels of tree components can be mapped to arbitrary data. The output is a ggplot2 object.
primersearch	Executes the EMBOSS program primersearch on sequence data stored in a taxmap object. Results are parsed, added to the input taxmap object and returned.
mutate_taxa mutate_obs transmute_taxa transmute_obs	Modify or add columns of taxon or observation data in taxmap objects. mutate_* adds columns and transmute_* returns only new columns.
select_taxa select_obs	Subset columns of taxon or observation data in taxmap objects.
filter_taxa filter_obs	Subset rows of taxon or observation 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 rows of taxon or observation data in taxmap objects.
sample_n_taxa sample_n_obs sample_frac_taxa sample_frac_obs	Randomly subsample rows of taxon or observation data in taxmap objects. Weights can be applied that take into account the taxonomic hierarchy and associated observations. Hierarchical relationships among taxa and mappings between taxa and observations are taken into account.
subtaxa supertaxa observations roots	Returns the indices of rows in taxon or observation data in taxmap objects. Used to map taxa to related taxa and observations.