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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

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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