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taxa 0.2.1
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@zachary-foster zachary-foster released this 04 May 19:19
· 216 commits to master since this release
v0.2.1
3e88e29

Improvements

  • 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).

Changes

  • 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).

Bug fixes

  • 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).
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