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taxize v0.9.2
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@sckott sckott released this 07 Feb 20:15
· 626 commits to master since this release
v0.9.2
679ff43

Installation

Stalled on CRAN. Install like

install.packages("taxize", repos = c("http://packages.ropensci.org"))

OR

remotes::install_github("ropensci/taxize")
# OR
devtools::install_github("ropensci/taxize")

NEWS

NEW FEATURES

  • class2tree() gets a major overhaul thanks to @gedankenstuecke and @trvinh (!!). The function now takes unnamed ranks into account when clustering, which fixes problem where trees were unresolved for many splits as the named taxonomy levels were shared between them. Now it makes full use of the NCBI Taxonomy string, including the unnamed ranks, leading to higher resolution trees that have less multifurcations (#611) (#634)
  • Added support throughout package for use of NCBI Entrez API keys - NCBI now strongly encourages their use and you get a higher rate limit when you use one. See ?taxize-authentication for help. Importantly, note that API key names (both R options and environment variables) have changed. They are now the same for R options and env vars: TROPICOS_KEY, EOL_KEY, PLANTMINER_KEY, ENTREZ_KEY. You no longer need an API key for Plantminer. (#640) (#646)
  • New author Zebulun Arendsee (@arendsee)
  • New package dependencies: crul and zoo

MINOR IMPROVEMENTS

  • In downstream() we now pass on limit and start parameters to gbif_downstream(); we weren't doing that before; the two parameters control pagination (#638)
  • genbank2uid() now returns the correct ID when there are multiple possibilities and invalid IDs no longer make whole batches fail (#642) thanks @zachary-foster
  • children() outputs made more consistent for certain cases when no results found for searches (#648) (#649) thanks @arendsee
  • Improve downstream() by passing ... (additional parameters) down to ncbi_children() used internally. allows e.g., use of ambiguous parameter in ncbi_children() allows you to remove ambiguousl named nodes (#653) (#654) thanks @arendsee
  • swapped out use of httr for crul in EOL and Tropics functions - note that this won't affect you unless you're passing curl options. see package crul for help on curl options. Along with this change, the parameter verbose has changed to messages (for toggling printing of information messages)

DOCUMENTATION

  • Added additional text to the CONTRIBUTING.md file for how to contribute to the test suite (#635)

BUG FIXES

  • genbank2uid now returns the correct ID when there are multiple possibilities and invalid IDs no longer make whole batches fail.
  • Fix to downstream(): passing numeric taxon ids to the function while using db="ncbi" wasn't working (#641) thanks @arendsee
  • Fix to children(): passing numeric taxon ids to the function while using db="worms" wasn't working (#650) (#651) thanks @arendsee
  • synonyms_df() - that attemps to combine many outputs from the synonyms() function - now removes NA/NULL/empy outputs before attempting the combination (#636)
  • Fix to gnr_resolve(): before if preferred_data_sources was used, you would get the preferred data but only a few columns of the response. We now return all fields; however, we only return the preferred data part when that parameter is used (#656)
  • Fixes to children(). It was returning unexpected results for amgiguous taxonomic names (e.g., there's some insects that are returned when searching within Bacteria). It was also failing when one tried to get the children of a root taxon (e.g., the children of the NCBI id 131567). (#639) (#647) fixed via PR (#659) thanks @arendsee and @zachary-foster
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