NEWS

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APCalign 1.1.3

• Failing gracefully for the edge case when the internet is up generally but github is down for a few seconds

APCalign 1.1.2 (2025-01-28)

• Added get_versions()

• Create a genus->family lookup from the specified APC release

APCalign 1.0.2 (2024-08-17)

Minor update to fix

• Deal with the vignette issues that emerged on CRAN
• Improve "graceful failing", based on issues that have come up on github CI
• minor formatting

APCalign 1.0.1 (2024-05-30)

First major release of APCalign. A preprint is available at https://www.biorxiv.org/content/10.1101/2024.02.02.578715v1. Article has been accepted for publication at Australian journal of Botany.

Following review, a number of changes have been implemented. These have sped & streamlined the package.

• Update function documentation
• Speed up extract_genus
• Write a replacement function for stringr::word that is much faster.
• Additional speed up and accuracy of fuzzy_match function by
  • Restricting reference list to names with the same first letter as input string.
  • Switch from using utils::adist to stringdist::stringdist(method = "dl")
• Rework standardise_names to remove punctuation from the start of the string
• Rework strip_names_extra (previously strip_names_2) to just perform additional functions to strip_names, rather than repeating those performed by strip_names.
• Avoid importing entire packages by using package::function format throughout and removing functions from @import
• Add fuzzy match arguments to create_taxonomic_update_lookup
• Add 3 additional family-level APC matches to match_taxa.
• Refine tests
• Make messages to console optional
• Fix issue with fails when github is down (https://github.com/traitecoevo/APCalign/issues/205)
• Update installation instructions
• Added how to cite and version APCalign as an article
• Exported default_version
• Add citing method for R package
• Update GitHub Actions
• Improved family alignments
• Added standardise_taxon_rank
• Improved messaging during alignment