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taxa v0.3.1

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@zachary-foster zachary-foster released this 20 Aug 19:32
· 182 commits to master since this release

New features

  • Added the taxonomy_table function that converts the information in a taxmap or taxonomy object into a table with taxa as rows and ranks as columns.
  • Added the print_tree function that prints text-based trees of taxmap or taxonomy objects (issue #173).
  • Added get_dataset function to get a single data set from taxmap objects. Useful for piping with %>%.
  • filter_taxa and filter_obs can now subset anything that has names, length, and can be subset, not just tables, lists, and vectors. For example, DNAbin objects from the ape package can now be used in taxmap objects (issue #178).

Improvements

  • Parsers are somewhat faster and use less RAM (issue #177).
  • taxmap and taxonomy parsers now treat taxa with the same name and same place in the taxonomy, but different ranks, database IDs, or authorities, as different taxa.
  • filter_obs can now filter multiple datasets at once if they are the same length (issue #179).
  • select_obs and arrange_obs can now work on multiple datasets at once.

Bug fixes

  • Made the "taxon_rank" value for the class_key options work with extract_tax_data.
  • Fixed bug in taxmap print method when printing tables with only a taxon ID column (issue #181).

Changes

  • Option target in many functions renamed to data to make it more intuitive.