- A logic issue in the original implementation of v1.6.3 is now fixed (@RobLBaker, #49).
- A syntax error introduced to the DESCRIPTION file in v1.6.3 is now fixed (@pendragon1998, #48).
make_taxonomicCoverage()now acceptsauthorityarguments of length == 1 rather than requiring a length equal totaxa.clean(@atn38, #46).
- Remove EDIutils dependency (take 3). Was still listed in the package DESCRIPTION
- Remove EDIutils dependency
- Integrated some EDIutils functions and removed the package dependency
- make_taxonomicCoverage():
make_taxonomicCoverage()was failing whentaxa.clean = NA. This has been fixed.
- Fix unexpected responses: Some taxa known to be in an authority were not found by
resolve_sci_taxa(). This fixes EMLassemblyline issue #89
- Match selection: Select first match when more than one is found.
- ITIS title change: Resolving to ITIS began failing due to a change in title (from "ITIS" to "Integrated Taxonomic Information SystemITIS" listed in the return from
taxize::gnr_datasources(). The fix uses data source IDs rather than titles so no related issues are expected unless the IDs change.
- Improve handling of unsupported authorities: Methods have been improved for unsupported authorities (i.e. authorities other than "ITIS", "WORMS", "GBIF"). Users can now annotate outputs of
make_taxonomicCoverage()with theauthorityandauthority.idarguments. 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'srank. 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.
- get_classification(): Was throwing errors for unresolvable taxa. No long doing this.
-
Annotation: Authority system and taxon identifier are now listed for each taxonomicClassification node (taxonomic rank) created via
make_taxonomicCoverage()orget_classification(). Fixes issue #28 -
Common names: All common names are listed, when available, for each taxonomicClassification node (taxonomic rank) created via
make_taxonomicCoverage()orget_classification(). Fixes issue #14
- Resolve common taxa: Changes in
taxize::get_tsn_()resulted inresolve_comm_taxa()unable to fetch data. This issue has been fixed. Thanks @srearl!
- get_classification(): A deprecated argument in
taxize::classification()was throwing errors. Thanks for the fix @srearl !
- Support unresolved taxa: Taxa that could not be resolved to an authority system are now included in EML outputs with an accompanied taxonomic rank value of "unknown".
- EML 2.2.0: EML output from
make_taxonomicCoverage()now uses schema version 2.2.0. Note: Annotation has not yet been implemented.
These enhancements focus on making the resolve functions more robust and efficient, specifically:
- Warn if an authority can't be reached
- Don't try resolving taxa that have already been resolved
- Return results even if the connection to the authority fails
- New table readers: Old table readers were inaccurately reading data (e.g. dropping quote characters). This has been fixed.
- tibble input: Tibbles are now an accepted input taxonomyCleanr functions.
- Invalid taxonomicCoverage EML: Invalid taxonomicCoverage EML was being created due to incorrectly nested list objects names. This issue has been fixed.
- Missing taxonomicClassification: The taxonomicClassification element was missing from the taxonomicCoverage top-level list producing invalid EML. This issue has been fixed.
- EML v2.0.0:
make_taxonomicCoverage()now works withEMLv.2.0.0 and outputs the taxonomicCoverage node as a list object and/or an .xml file written to path. The argumentwrite.filehas been added to enable use of taxa_map.csv without writing to file. These changes are based on a pull request by @srearl.
- Invalid input: Refactor calls to
taxize. Thetaxizepackage 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!
- Demo vignette: Clean up demonstration vignette.
- Project website: Build project website with
pkgdown. - Change log: Add change log!