NEWS.md
In APCalign: Resolving Plant Taxon Names Using the Australian Plant Census

APCalign 1.1.3

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

Minor update to fix

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