NEWS.md
make_taxonomicCoverage() now accepts authority arguments of length == 1 rather than requiring a length equal to taxa.clean (@atn38, #46).make_taxonomicCoverage() was failing when taxa.clean = NA. This has been fixed.resolve_sci_taxa(). This fixes EMLassemblyline issue #89
taxize::gnr_datasources(). The fix uses data source IDs rather than titles so no related issues are expected unless the IDs change.make_taxonomicCoverage() with the authority and authority.id arguments. Values for these args will be listed in the return object “as is” and should correspond to the authority home page URL/URI and the taxon’s ID within that authority system, respectively. Additionally, users can now manually define the taxon’s rank. NOTE: These new methods don’t facilitate expansion of a taxon resolved in an unsupported system to the full classification hierarchy that is currently available when using ITIS, WORMS, or GBIF. That will require additional effort. Furthermore, methods for supported authorities are more clearly defined in function docs. The enhancement partially addresses EMLassemblyline issue #50.Annotation: Authority system and taxon identifier are now listed for each taxonomicClassification node (taxonomic rank) created via make_taxonomicCoverage() or get_classification(). Fixes issue #28
Common names: All common names are listed, when available, for each taxonomicClassification node (taxonomic rank) created via make_taxonomicCoverage() or get_classification(). Fixes issue #14
taxize::get_tsn_() resulted in resolve_comm_taxa() unable to fetch data. This issue has been fixed. Thanks @srearl!taxize::classification() was throwing errors. Thanks for the fix @srearl !make_taxonomicCoverage() now uses schema version 2.2.0. Note: Annotation has not yet been implemented.make_taxonomicCoverage() now works with EML v.2.0.0 and outputs the taxonomicCoverage node as a list object and/or an .xml file written to path. The argument write.file has been added to enable use of taxa_map.csv without writing to file. These changes are based on a pull request by @srearl.taxize. The taxize package changed to tibble outputs and taxonomyCleanr was expecting data frames. Inputs from taxize are now converted to data frames prior to processing. Thanks for reporting this issue @srearl!