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APCalign 1.0.1

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

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.