# 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
