NEWS.md

In APCalign: Resolving Plant Taxon Names Using the Australian Plant Census

APCalign 2.0.1

• fuzzy_match() no longer confirms a fuzzy match against a candidate that drops an aff./cf./x qualifier present in the query. Its check_match() confirmation step only compared word positions up to the shorter of query/candidate, so Acacia aff. aneura ("resembles Acacia aneura, not confidently identified") could fuzzy-match past its qualifier to the unrelated accepted species Acacia aptaneura instead of being capped at genus rank. A query containing aff, cf, or x as a standalone word now requires the candidate to contain that same token, or the candidate is rejected outright before the coarser word-position check runs; genuine aff./cf.-qualified synonyms and named hybrids that still need fuzzy matching to fix a typo are unaffected.
• standardise_taxon_rank() no longer corrupts rank values that are already English, or that merely contain a Latin rank term as a substring. sectio is a literal prefix of its own translation (section) and forma sits inside informal, so replacing either anywhere in the input silently mangled section/subsection/zoosection into sectionn/subsectionn/zoosectionn, and informal/informal group into informl/informl group. Both terms are now matched only as the last word of the value, which still translates the prefixed ranks that need it (subsectio, subforma). APC/APNI rank values are unaffected — the fix changes output only for the zoological and DwC vocabularies, where it was found (traitecoevo/taxonAlign#11).
• 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.
• 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.
• 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.
• Internal refactor: the duplicated gsub()-wrapper helper in standardise_names(), strip_names() and strip_names_extra() is now a single shared gsub_perl(), and a redundant nested copy of relevel_taxonomic_status_preferred_order() inside synonyms_for_accepted_names() has been removed in favour of the existing top-level function. Behaviour is unchanged.

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

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

APCalign 1.1.2

• Added get_versions()

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

APCalign 1.0.2

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

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

APCalign documentation built on Sept. 9, 2026, 9:07 a.m.