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)
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Co-authored-by: Elizabeth Wenk <[email protected]>
Co-authored-by: Fonti Kar <[email protected]>
Co-authored-by: Daniel Falster <[email protected]>
Co-authored-by: Will Cornwell <[email protected]>