Changelog

Source: NEWS.md

APCalign 2.0.0

• New function synonyms_for_accepted_names() to list synonyms for currently accepted taxon names.
• load_taxonomic_resources() now caches results in memory for the duration of the R session, so repeated calls with the same version return immediately without re-downloading or re-processing data.
• New function clear_cached_resources() to remove the session cache and force a reload.
• load_taxonomic_resources() now works offline when parquet files have been previously downloaded; default_version() falls back to the most recently cached local version when no internet connection is available.
• Internal taxonomic resource tables renamed to snake_case; family column added to resource tables.
• Functions create_species_state_origin_matrix() and state_diversity_counts() now includes the parameter include_infrataxa, allowing users to select whether just species-rank taxa or species and infra-specific taxa are output in the table. When create_species_state_origin_matrix() is called by native_anywhere_in_australia(), include_infrataxa = TRUE is set as the default, so infrataxa can also be checked by this function.

APCalign 1.1.6

• Fix issue #262: filter to accepted species only in genus-family lookup
• Skip problematic tests on CRAN
• Update maintainer to Elizabeth Wenk, reflecting her leading role in writing the core of the package algorithms and maintaining it going forward.

APCalign 1.1.3

CRAN release: 2025-02-11

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

APCalign 1.1.2

CRAN release: 2025-01-28

• Added get_versions()

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

APCalign 1.0.2

CRAN release: 2024-08-17

Minor update to fix issues

• 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

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