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taxa v0.2.0
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@sckott sckott released this 20 Dec 00:19
· 304 commits to master since this release
v0.2.0
c0ba16c

Bug fixes

  • 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)

Improvements

  • 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)

Changes

  • 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".
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