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taxize v0.9.91
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@sckott sckott released this 15 Nov 00:12
· 282 commits to master since this release
v0.9.91
aa258b0

NEW FEATURES

  • get_ids() gains a new parameter suppress (default:FALSE) to toggle pakage cli messages stating which database is being worked on (#719)

MINOR IMPROVEMENTS

  • 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) (#781)
  • add new documentation site url (https://docs.ropensci.org/taxize/) to DESCRITPION file (#774) (@jeroen)
  • fix links in README to issues label of new potential data sources (#782) (@katrinleinweber)
  • more or less all functions that take as input the output of get_* functions have S3 methods that dispatch on those get_* output classes. however, you can still pass in a db parameter, which is IGNORED when dispatching on the input class. the db parameter is used (not ignored) when passing in a taxon id as character/numeric/etc. now these functions (children, classification, comm2sci, sci2comm, downstream, id2name, synonyms, upstream) warn when the user passes a db value which will be ignored (#780)
  • The NCBI Entrez API often throws errors for users of this and other packages related to HTTP version used by the client; we now hard code the http version to HTTP/1.1 via the curl option http_version=2L across all Entrez requests (#783)

BUG FIXES

  • fixes to col_search(): COL now does rate limiting (if you make too many requests within a time period they will stop allowing requests from your IP address/your computer); documented rate limiting, what I know at least; changed checklist parameter behavior: years 2014 and back dont provide JSON, so we return xml_document objects now for those years that the user can parse themselves (#786)
  • tax_rank somehow (my bad) had two .default methods. previous behavior is the same as current behavior (this version) (#784)
  • 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) (#781)
  • 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) (#781)
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