Current

parse_tax_data can now incorperate rank information which can be accessed by result$taxon_ranks() (issue #113).
taxmap print methods now have more information and color (issue #124).
Added leaves_apply function that works like subtaxa_apply, but on leaves (issue #126).
Functions with a value option now return named taxon indexes by default, instead of unnamed taxon indexes (issue #128).
lookup_tax_data and extract_tax_data can now use “fuzzy” matching when looking up taxon names, so taxon names can be mispelled and still be founds.
lookup_tax_data and extract_tax_data now only look up unique sequence IDs, improving download speed.
filter_obs now can filter out observations in non-target data sets that are assocaited with taxa that are removed when drop_taxa = TRUE (issue #143). This is done using filter_taxa, so the supertaxa, subtaxa, and reassign_obs options are now available to filter_obs to control how taxon removal is done.
lookup_tax_data and extract_tax_data now have progress bars instead of printing lots of text when downloading information.
mutate_obs now creates new vector/tables if the data set specified does not exist (issue #121).
Add filter_taxa option keep_order that preserves input taxon order. It is TRUE by default, which changes how it used to work. Set to FALSE for old behavior.
Using NSE with an ambiguous name (appears in multiple datasets) now produces a warning (issue #153).

The simplify option in many functions is now always handled the same way: If all vectors in a list are names, then unique key-value pairs are returned. Otherwise, names are ignored and unique values are returned.
The leaves option now behaves like subtaxa, returning all leaves for each taxon. The old behavior can be replicated by setting the new simplify option to TRUE (issue #127).

filter_taxa now has better error messages for invalid inputs (issue #117).
Fix a bug that caused an error in filter_taxa when no taxa pass filter (issue #116).
Fixed a bug in parse_tax_data when class_key was not named (issue #131).
Fixed bug in hierarchy print method with taxon_id class was not used (issue #138).
Fixed bug in parse_tax_data when all classification data is NA.
Fixed bug in taxmap print method when printing zero-length lists and vectors (issue #148).

taxa 0.2.0

Fixed a few problems with using duplicated inputs to subset (issue #88, issue #89)
Fixed a bug that caused an error when using unnamed vectors (issue #86)
Fixed a bug that prevents using sequence accession numbers (issue #85)
Fixed bug in lookup_tax_data and extract_tax_data that caused an error when one of the queries failed too download.
Fixed bug that caused “data” argument of obs_apply to not work when passed as a varaible (issue #97)

Added map_data_ for mapping without using NSE.
Make default dataset for n_obs and n_obs_1 and make them available for NSE (issue #91
parse_tax_data/extract_tax_data can now parse things like phylum;Nitrosopumilales;order;Nitrosopumilaceae;family; and split out the rank and taxon names by using multiple matches to the class_regex when class_sep is NULL.
extract_tax_data now gives warnings if a regex does not match.
Added n_supertaxa_1 function to get number of immediate supertaxa (always 1 or 0).
Added branches function to go with roots, leaves, and stems. (issue #56)
Added internodes and is_internode functions to go with roots, leaves, branches, and stems. USeful for removing uninformative taxonomic ranks/taxa.
Started to incorporate ability for taxon, taxon_name, taxon_id, taxon_rank, and taxa to handle NULL inputs as first class citizens to handle cases when you have essentially a blank taxon (use case comes from taxize package) #95 #107
data parsers: Put long, often unused columns last (issue #93)
When parsing classifications that have per-taxon info add input id column (issue #92)
New function classification as an abstraction to get either hierarchy of taxon indexes, names, or ids (issue #57)
New function get_data_frame for both Taxonomy and Taxmap objects that wraps around get_data to coerce into a data.frame. (issue #58) (PR #105)

In the output of the taxmap parsing functions like parse_tax_data, I moved “taxon_id” and “input_index” columns to front and “input” to rear. Also “tax_data” now comes before “class_data”.