All functions

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

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

extract_tax_data()

Extracts taxonomy info from vectors with regex

filter_obs

Filter observations with a list of conditions

filter_taxa

Filter taxa with a list of conditions

ranks() nms() ids()

Taxonomic filtering helpers

get_data

Get data in a taxmap object by name

get_data_frame

Get data in a taxonomy or taxmap object by name

get_dataset

Get a data set from a taxmap object

hierarchies()

Make a set of many hierarchy() class objects

hierarchy()

The Hierarchy class

highlight_taxon_ids()

Highlight taxon ID column

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

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_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-package

taxa

taxa()

A class for multiple taxon objects

taxmap()

Taxmap class

taxon()

Taxon class

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

taxonomy()

Taxonomy class

taxonomy_table

Convert taxonomy info to a table

transmute_obs

Replace columns in taxmap() objects