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Changelog

Source: NEWS.md

APCalign 2.0.0

CRAN release: 2026-03-27

  • standardise_names() no longer rewrites affinis to aff. when it is the species epithet of an infraspecific name — that is, when the next word is a rank marker (subsp., var., f., ser., cv. and their unabbreviated or unpunctuated variants). Previously Gomphrena affinis subsp. pilbarensis became Gomphrena aff. subsp. pilbarensis, a name that exists nowhere, so it could only ever align to genus rank. Eight APC/APNI names were affected, three of them currently accepted; all now align at their own rank. A trailing affinis (Acacia affinis) was already left alone and still is. Two hybrid formulas of the form Genus affinis x Genus epithet are still rewritten, and are left for a follow-up.
  • Fix malformed aligned_reason text for fuzzy genus-level aff./affinis matches (match_06b/06c/06d), which previously appended the date without a separating (.
  • align_taxa(full = TRUE) no longer leaks the internal identifier_string, identifier_string2 and aligned_name_tmp columns when every name is aligned before the last match step runs. The output is now the documented set of columns in all cases.
  • Internal refactor of match_taxa(): the ~54 match steps now share helper functions rather than repeating the same block of code. Alignment output is unchanged.
  • native_anywhere_in_australia() now checks for missing taxonomic resources before building the state-origin matrix, so an offline call reports the problem once instead of once per function that gives up. Its native/introduced test also now reads only the state columns, so a taxon whose name contains “native” (e.g. the nativitatis epithets) can no longer be misclassified.
  • 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