Taxize v0.6 is on CRAN


#1

hit CRAN last week

NEW FEATURES

  • Added a method for Catalogue of Life for the synonyms function to get
    name synonyms. (#430)
  • Added datasets apgFamilies and apgOrders. (#418)
  • col_search() gains parameters response to get a terse or full response, and
    ... to pass in curl options.
  • eol_dataobjects() gains parameter ... to pass in curl options, and parameter
    returntype renamed to asdf (for “as data.frame”).
  • ncb_get_taxon_summary() gains parameter ... to pass in curl options.
  • The children() function gains the rows parameter passed on to get_*() functions,
    supported for data sources ITIS and Catalogue of Life, but not for NCBI.
  • The upstream() function gains the rows parameter passed on to get_*() functions,
    supported for both data sources ITIS and Catalogue of Life.
  • The classification() function gains the rows parameter passed on to get_*()
    functions, for all sources used in the function.
  • The downstream() function gains the rows parameter passed on to get_*()
    functions, for all sources used in the function.
  • Nearly all taxonomic ID retrieveal functions (i.e., get_*()) gain new parameters to
    help filter results (e.g., division, phylum, class, family, parent, rank, etc.).
    These parameters allow direct matching or regex filters (e.g., .a to match any character
    followed by an a). (#410) (#385)
  • Nearly all taxonomic ID retrieveal functions (i.e., get_*()) now give back more
    information (mostly higher taxonomic data) to help in the interactive decision
    process. (#327)
  • New data source added to synonyms() function: Catalogue of Life. (#430)

MINOR IMPROVEMENTS

  • vegan package, used in class2tree() function, moved from Imports to Suggests. (#392)
  • Improved taxize_cite() a lot - get URLs and sometimes citation information
    for data sources available in taxize. (#270)
  • Fixed typo in apg_lookup() function. (#422)
  • Fixed documentation in apg_families() function. (#418)
  • Across many functions, fixed support for passing in curl options, and added
    examples of curl option use.
  • callopts parameter in eol_pages(), eol_search(), gnr_resolve(),
    tp_accnames(), tp_dist(), tp_search(), tp_summary(), tp_synonyms(),
    ubio_search() changed to ...
  • accepted parameter in get_tsn() changed to FALSE by default. (#425)
  • Default value of db parameter in resolve() changed to gnr as tnrs is
    often quite slow.
  • General code tidying across the package to make code easier to read.

BUG FIXES

  • Fixed encoding issues in tpl_families() and tpl_get(). (#424)

DEPRECATED AND DEFUNCT

  • The following functions that were deprecated are now defunct (no longer available):
    ncbi_getbyname(), ncbi_getbyid(), ncbi_search(), eol_invasive(),
    gisd_isinvasive(). These functions are available in the traits package. (#382)
  • phylomatic_tree() is deprecated, but will be defunct in a upcoming version.