align_taxa {APCalign}R Documentation

Find taxonomic alignments for a list of names to a version of the Australian Plant Census (APC) through standardizing formatting and checking for spelling issues

Description

This function uses Australian Plant Census (APC) & the Australian Plant Name Index (APNI) to find taxonomic alignments for a list of names. It uses the internal function match_taxa to attempt to match input strings to taxon names in the APC/APNI. It sequentially searches for matches against more than 20 different string patterns, prioritising exact matches (to accepted names as well as synonyms, orthographic variants) over fuzzy matches. It prioritises matches to taxa in the APC over names in the APNI. It identifies string patterns in input names that suggest a name can only be aligned to a genus (hybrids that are not in the APC/ANI; graded species; taxa not identified to species), and indicates these names only have a genus-rank match.

Usage

align_taxa(
  original_name,
  output = NULL,
  full = FALSE,
  resources = load_taxonomic_resources(),
  fuzzy_abs_dist = 3,
  fuzzy_rel_dist = 0.2,
  fuzzy_matches = TRUE,
  imprecise_fuzzy_matches = FALSE,
  APNI_matches = TRUE,
  identifier = NA_character_
)

Arguments

original_name

A list of names to query for taxonomic alignments.

output

(optional) The name of the file to save the results to.

full

Parameter to determine how many columns are output

resources

the taxonomic resources used to align the taxa names. Loading this can be slow, so call load_taxonomic_resources separately to greatly speed this function up and pass the resources in.

fuzzy_abs_dist

The number of characters allowed to be different for a fuzzy match.

fuzzy_rel_dist

The proportion of characters allowed to be different for a fuzzy match.

fuzzy_matches

Fuzzy matches are turned on as a default. The relative and absolute distances allowed for fuzzy matches to species and infraspecific taxon names are defined by the parameters fuzzy_abs_dist and fuzzy_rel_dist

imprecise_fuzzy_matches

Imprecise fuzzy matches are turned off as a default.

APNI_matches

Name matches to the APNI (Australian Plant Names Index) are turned off as a default.

identifier

A dataset, location or other identifier, which defaults to NA.

Value

A tibble with columns that include original_name, aligned_name, taxonomic_dataset, taxon_rank, aligned_reason, alignment_code.

See Also

load_taxonomic_resources

Other taxonomic alignment functions: create_taxonomic_update_lookup(), update_taxonomy()

Examples

align_taxa(c("Poa annua", "Abies alba"))


[Package APCalign version 0.1.3 Index]