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Changelog

Source: NEWS.md

APCalign 1.0.1

CRAN release: 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