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taxa 0.4.3

Fixing minor CRAN check issues.

taxa 0.4.2

  • Experimenting with using '' instead of NA for missing values at the suggestion of Davis Vaughan (issue #212).
  • Fix failing CRAN tests due to vctrs update.

taxa 0.4.1

Minor update

  • Fixed taxonomy printing error
  • Removed default.stringsAsFactors since it is depreciated.

taxa 0.4.0

LARGE CHANGES:

The beginning of a complete rewrite of the taxa package to make the more basic component classes more like base R vectors. The taxmap class is not yet reimplemented, but will be similar to the class in the previous versions of taxa. The old version of taxa has been incorporated into the metacoder package until this version of taxa is mature, at which time metacoder will also use this version.

taxa 0.3.4

Bug fixes

  • Fixed bug in n_obs that would cause an error when used on an object with tables with columns named by numbers.
  • Various minor bug fixes

taxa 0.3.3

Bug fixes

  • Numeric column names in tables in taxmap are now supported
  • Various small bug fixes

taxa 0.3.2

Bug fixes

  • Parsers now correclty handle zero-length inputs (issue #185).
  • taxonomy_table option add_id_col now works (issue #191).

Improvements

  • The parse_tax_data option class_col now accepts negative column indexes, meaning "all other columns".

taxa 0.3.1

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.

taxa 0.2.1

Improvements

  • parse_tax_data can now incorporate 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 misspelled 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 associated 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).

taxa 0.2.0

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 variable (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".

taxa 0.1.0

NEW FEATURES

  • Released to CRAN.