NEWS.md

In EDIorg/taxonomyCleanr: A workflow and set of functions to clean taxonomy data using R

taxonomyCleanr 1.6.5

• A logic issue in the original implementation of v1.6.3 is now fixed (@RobLBaker, #49).

taxonomyCleanr 1.6.4

• A syntax error introduced to the DESCRIPTION file in v1.6.3 is now fixed (@pendragon1998, #48).

taxonomyCleanr 1.6.3

• make_taxonomicCoverage() now accepts authority arguments of length == 1 rather than requiring a length equal to taxa.clean (@atn38, #46).

taxonomyCleanr 1.6.2

• Remove EDIutils dependency (take 3). Was still listed in the package DESCRIPTION

taxonomyCleanr 1.6.1

• Remove EDIutils dependency

taxonomyCleanr 1.6.0

• Integrated some EDIutils functions and removed the package dependency

taxonomyCleanr 1.5.4

Bug fix

• make_taxonomicCoverage(): make_taxonomicCoverage() was failing when taxa.clean = NA. This has been fixed.

taxonomyCleanr 1.5.3

Bug fix

• Fix unexpected responses: Some taxa known to be in an authority were not found by resolve_sci_taxa(). This fixes EMLassemblyline issue #89

taxonomyCleanr 1.5.2

Bug fix

• Match selection: Select first match when more than one is found.

taxonomyCleanr 1.5.1

Bug fix

• 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.

taxonomyCleanr 1.5.0

Enhancement

• 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 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.

taxonomyCleanr 1.4.1

Bug fix

• get_classification(): Was throwing errors for unresolvable taxa. No long doing this.

taxonomyCleanr 1.4.0

Enhancement

• 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

taxonomyCleanr 1.3.2

Bug fix

• Resolve common taxa: Changes in taxize::get_tsn_() resulted in resolve_comm_taxa() unable to fetch data. This issue has been fixed. Thanks @srearl!

taxonomyCleanr 1.3.1

Bug fix

• get_classification(): A deprecated argument in taxize::classification() was throwing errors. Thanks for the fix @srearl !

taxonomyCleanr 1.3.0

Enhancements

• 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.

taxonomyCleanr 1.2.0

Enhancements

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

taxonomyCleanr 1.1.3

Bug fixes

• New table readers: Old table readers were inaccurately reading data (e.g. dropping quote characters). This has been fixed.

Enhancements

• tibble input: Tibbles are now an accepted input taxonomyCleanr functions.

taxonomyCleanr 1.1.2

Bug fixes

• Invalid taxonomicCoverage EML: Invalid taxonomicCoverage EML was being created due to incorrectly nested list objects names. This issue has been fixed.

taxonomyCleanr 1.1.1

Bug fixes

• Missing taxonomicClassification: The taxonomicClassification element was missing from the taxonomicCoverage top-level list producing invalid EML. This issue has been fixed.

taxonomyCleanr 1.1.0

Enhancements

• EML v2.0.0: 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.

taxonomyCleanr 1.0.1

Bug fixes

• Invalid input: Refactor calls to 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!

taxonomyCleanr 1.0.0

Enhancements

• Demo vignette: Clean up demonstration vignette.
• Project website: Build project website with pkgdown.
• Change log: Add change log!

EDIorg/taxonomyCleanr documentation built on April 9, 2023, 2:43 a.m.