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taxize v0.7.0

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@sckott sckott released this 01 Dec 15:18
· 989 commits to master since this release

NEW FEATURES

  • Now requires R >= 3.2.1. Good idea to update your R installation anyway (#476)
  • New function ion() for obtaining data from Index of Organism Names (#345)
  • New function eubon() for obtaining data from EU (European Union) BON
    taxonomy (#466) Note that you may onloy get partial results for some requests
    as paging isn't implemented yet in the EU BON API (#481)
  • New suite of functions, with prefix fg_*() for obtaining data from Index
    Fungorum. More work has to be done yet on this data source, but these initial
    functions allow some Index Fungorum data access (#471)
  • New function gbif_downstream() for obtaining downstream names from
    GBIF's backbone taxonomy. Also available in downstream(), where you can
    request downstream names from GBIF, along with other data sources (#414)

MINOR IMPROVEMENTS

  • Note added in docs for all db parameters to warn users that if they
    provide the wrong db value for the given taxon ID, they can get data
    back, but it would be wrong. That is, all taxonomic data sources available
    in taxize use their own unique IDs, so a single ID value can be in multiple
    data sources, even though the ID refers to different taxa in each data source.
    There is no way we can think of to prevent this from happening, so be cautious.
    (#465)
  • A note added to all IUCN functions to warn users that sometimes incorrect
    data is returned. This is beyond our control, as sometimes IUCN itself gives
    back incorrect data, and sometimes EOL/Global Names (which we use in some of
    the IUCN functions) give back incorrect data. (#468) (#473) (#174) (472) (#475)

BUG FIXES

  • Fix to gnr_resolve() to by default capitalize first name of a name string
    passed to the function. GNR is case sensitive, so case matters (#469)

DEFUNCT

  • phylomatic_tree() and phylomatic_format() are defunct. They were deprecated
    in recent versions, but are now gone. See the new package brranching for
    Phylomatic data (#479)