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