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taxize v0.9.9
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@sckott sckott released this 17 Oct 20:13
· 306 commits to master since this release
v0.9.9
f6700c9

NEW FEATURES

  • update all EUBON functions to use their new API version; eubon_search() gains new params limit and page; other eubon functions have no pagination (#766)
  • change base url in ipni_search() from http to https, via (#773)

MINOR IMPROVEMENTS

  • change synonyms() to always return NA for name not found, and always return a zero row data.frame when name found BUT no synonyms found; updated docs to indicate better what's returned (#763) (#765)
  • COL sometimes returns control characters in the XML payload; these can't be parsed by the xml2 package, so we have to remove them using regex; we throw a message when we're doing this so the user knows (#768)
  • docs typos fixes (#770)
  • update classification() docs with a new EOL section discussing that EOL does not have good failure behavior, and what to expect from them (#775)
  • the following datasets are now available when the package is not loaded, so functions that use these datasets can now be called with package namespace like taxize::downstream(): rank_ref, theplantlist, apg_families, apg_orders (#777)
  • sci2comm() and comm2sci() improvements: for db="ncbi" we no longer stop with error when when there's no results for a query; instead we return character(0). In addition, now all data source options for both functions now return character(0) when there's no results for a query (#778)
  • id2name.uid() now actually passes on ... internally for curl options

BUG FIXES

  • fix get_nbnid(): was returning non-taxon entities, have ot add idxtype:TAXON to the fq query (#761)
  • fixes for as.eolid() and as.colid() - don't run through helper function that was raising error on HTTP 404/etc., dont want to fail (#762)
  • fix to class2tree(): set root node name to NA if it does not exist, ITIS does not set a root node (#767) (#769) work by @gpli
  • fix to ipni_search(): IPNI changed parameter names, fixes for that; and now returning tibble's instead of data.frame's (#773) thanks @joelnitta !
  • fix ncbi_children(): fixed regex that was supposed to flag ambiguous taxa only, it was supposed to flag sp. and spp., but was including subsp., which we didn't want included (#777)
  • another fix to ncbi_children(): when ID is passed rather than a name, we need to then set id=NULL after switching to the equivalent taxononmic name internally to avoid getting duplicate data back (#777)
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