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taxize v0.9.8

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@sckott sckott released this 28 Jun 16:38
· 350 commits to master since this release

NEW FEATURES

  • all get_* functions gain some new features (associated new fxns are taxon_last and taxon_clear): a) nicer messages printed to the console when iterating through taxa, and a summary at the end of what was done; and b) state is now saved when running get_* functions. That is, in an object external to the get_* function call we keep track of what happened, so that if an error is encountered, you can easily restart where you left off; this is especially useful when dealing with a large number of inputs to a get_* function. To utilize, pass the output of taxon_last() to a get_* function call. Associated with these changes are new package imports: R6, crayon and cli (#736) (#757)
  • gains a new function taxize_options() to set options when using taxize. the first reason for the function is to set two options for the above item for get_* functions: taxon_state_messages to allow taxon state tracking messages in get_* functions or not, and quiet=TRUE quiets output from the taxize_options() function itself

MINOR IMPROVEMENTS

  • in id2name() and worms_downstream() use worrms::wm_record instead of worrms::wm_record_ for newest version of worrms (#760)
  • many get_* functions and col_downstream() parameter verbose changed to messages to not conflict with a verbose curl options parameter passed in to crul

BUG FIXES

  • fix to http request processing for COL - sometimes errors, and gives a message in the response body, but DOES NOT give the appropriate error HTTP status code - need to always do a check for COL responses (#755) (#756) thanks @dougwyu
  • fix to gbif_downstream() - GBIF in some cases returns a rank of "unranked", which we hadn't accounted for in internal rank processing code (#758) thanks @ocstringham