fix: add acceptedUsageKey and acceptedScientificName to name_backbone…

[jhnwllr]

#824

[Copilot]

Pull request overview

This pull request adds support for returning acceptedUsageKey and acceptedScientificName fields from the name_backbone function to handle taxonomic synonyms. When the GBIF API returns a synonym, these fields provide information about the accepted/valid name for the taxon. This addresses issue #824.

• Extracts acceptedUsage data from the GBIF species match API v2 response
• Adds test coverage for the new fields using a synonym example (Anastrophyllum minutum)
• Increments package version from 3.8.4.1 to 3.8.4.2

Reviewed changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 2 comments.

File	Description
R/name_backbone.r	Adds processing logic to extract acceptedUsageKey and acceptedScientificName from API response
tests/testthat/test-name_backbone.r	Adds test to verify the new fields are returned
tests/fixtures/name_backbone_acceptedUsageKey.yml	Provides VCR cassette with API response containing synonym and acceptedUsage data
DESCRIPTION	Bumps version to 3.8.4.2

---

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

[Copilot]

The test verifies that the columns exist but doesn't check their actual values. Based on the fixture data, the test should verify that acceptedUsageKey is "2689422" and acceptedScientificName is "Sphenolobus minutus (Schreb. ex Cranz) Berggr." to ensure the function correctly extracts these values from the API response.

[Copilot]

The acceptedUsage processing subsets only the "key" and "name" fields, which is inconsistent with how the usage object is processed (lines 231-235). The usage processing converts the entire object to a tibble and then renames specific columns. Consider following the same pattern here: convert the entire acceptedUsage object to a tibble first, then rename the columns, to maintain consistency and allow any additional fields from the API to be included.

Suggested change

	a <- tibble::as_tibble(tt$acceptedUsage)[c("key","name")]
	colnames(a)[colnames(a) == "key"] <- "acceptedUsageKey"
	colnames(a)[colnames(a) == "name"] <- "acceptedScientificName"
	a <- tibble::as_tibble(tt$acceptedUsage)
	if ("key" %in% colnames(a)) colnames(a)[colnames(a) == "key"] <- "acceptedUsageKey"
	if ("name" %in% colnames(a)) colnames(a)[colnames(a) == "name"] <- "acceptedScientificName"