# Taxonomic Classes

## Documentation for package ‘taxa’ version 0.3.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

taxa-package | taxa
all_names | Return names of data in 'taxonomy()' or 'taxmap()'
arrange_obs | Sort user data in 'taxmap()' objects
arrange_taxa | Sort the edge list of 'taxmap()' objects
branches | Get "branch" taxa
classifications | Get classifications of taxa
database_list | Database list
extract_tax_data | Extracts taxonomy info from vectors with regex
ex_hierarchies | An example hierarchies object
ex_hierarchy1 | An example Hierarchy object
ex_hierarchy2 | An example Hierarchy object
ex_hierarchy3 | An example Hierarchy object
ex_taxmap | An example taxmap object
ex_taxonomy | An example Taxonomy object
filtering-helpers | Taxonomic filtering helpers
filter_obs | Filter observations with a list of conditions
filter_taxa | Filter taxa with a list of conditions
get_data | Get data in a taxmap object by name
get_dataset | Get a data set from a taxmap object
get_data_frame | Get data in a taxonomy or taxmap object by name
hierarchies | Make a set of many 'hierarchy()' class objects
hierarchy | The Hierarchy class
highlight_taxon_ids | Highlight taxon ID column
ids | Taxonomic filtering helpers
id_classifications | Get ID classifications of taxa
internodes | Get "internode" taxa
is_branch | Test if taxa are branches
is_internode | Test if taxa are "internodes"
is_leaf | Test if taxa are leaves
is_root | Test if taxa are roots
is_stem | Test if taxa are stems
leaves | Get leaf taxa
leaves_apply | Apply function to leaves of each taxon
lookup_tax_data | Convert one or more data sets to taxmap
map_data | Create a mapping between two variables
map_data_ | Create a mapping without NSE
mutate_obs | Add columns to 'taxmap()' objects
nms | Taxonomic filtering helpers
n_leaves | Get number of leaves
n_leaves_1 | Get number of leaves
n_obs | Count observations in 'taxmap()'
n_obs_1 | Count observation assigned in 'taxmap()'
n_subtaxa | Get number of subtaxa
n_subtaxa_1 | Get number of subtaxa
n_supertaxa | Get number of supertaxa
n_supertaxa_1 | Get number of supertaxa
obs | Get data indexes associated with taxa
obs_apply | Apply function to observations per taxon
parse_dataset | Parse options specifying datasets
parse_edge_list | Convert a table with an edge list to taxmap
parse_tax_data | Convert one or more data sets to taxmap
pick | Pick taxa
pop | Pop taxa out
print_tree | Print a text tree
ranks | Taxonomic filtering helpers
ranks_ref | Lookup-table for IDs of taxonomic ranks
remove_redundant_names | Remove redundant parts of taxon names
replace_taxon_ids | Replace taxon ids
roots | Get root taxa
sample_frac_obs | Sample a proportion of observations from 'taxmap()'
sample_frac_taxa | Sample a proportion of taxa from 'taxonomy()' or 'taxmap()'
sample_n_obs | Sample n observations from 'taxmap()'
sample_n_taxa | Sample n taxa from 'taxonomy()' or 'taxmap()'
select_obs | Subset columns in a 'taxmap()' object
span | Span taxa
stems | Get stem taxa
subtaxa | Get subtaxa
subtaxa_apply | Apply function to subtaxa of each taxon
supertaxa | Get all supertaxa of a taxon
supertaxa_apply | Apply function to supertaxa of each taxon
taxa | A class for multiple taxon objects
taxmap | Taxmap class
taxon | Taxon class
taxonomy | Taxonomy class
taxonomy_table | Convert taxonomy info to a table
taxon_database | Taxonomy database class
taxon_id | Taxon ID class
taxon_ids | Get taxon IDs
taxon_indexes | Get taxon indexes
taxon_name | Taxon name class
taxon_names | Get taxon names
taxon_rank | Taxon rank class
taxon_ranks | Get taxon ranks
transmute_obs | Replace columns in 'taxmap()' objects