Match collection to IUCN Red List of Threatened Species via taxonomic name

Usage

match_collection_to_iucnRedlist(
  collection,
  iucnRedlist,
  taxon_name_column = "TaxonName",
  taxon_name_full_column = NA,
  taxon_author_column = NA,
  typo_method = "All",
  do_add_split = TRUE,
  do_fix_hybrid = TRUE,
  do_rm_autonym = TRUE,
  ...,
  enrich_taxon_name_column = "scientific_name",
  enrich_taxon_authors_column = "sanitise_author",
  enrich_display_in_message_column = "taxonid",
  enrich_plant_identifier_column = "taxonid",
  matching_criterion = BGSmartR::no_additional_matching,
  try_hybrid = FALSE
)

Arguments

collection: A data frame containing a collection.
iucnRedlist: IUCN Red List of Threatened Species database, obtained using the function XXXX.
taxon_name_column: The name of the column in the collection corresponding to taxonomic names.
taxon_name_full_column: The name of the column in the collection corresponding to joined taxonomic names and authors.
taxon_author_column: The name of the column in the collection corresponding to the authors of the taxonomic names.
typo_method: Either 'All', 'Data frame only','Data frame + common', detailing the level of typo finding required.
do_add_split: Flag (TRUE/FALSE) for whether we search for missing f./var./subsp.
do_fix_hybrid: Flag (TRUE/FALSE) for whether we search for hybrid issues.
do_rm_autonym: Flag (TRUE/FALSE) for whether we try removing autonyms.
...: Arguments (i.e., attributes) used in the matching algorithm (passed along to nested functions). Examples include enrich_taxon_authors_column, enrich_display_in_message_column and enrich_plant_identifier_column.
enrich_taxon_name_column: The name of the column in the iucnRedlist corresponding to taxonomic names.Default value is scientific_name.
enrich_taxon_authors_column: The name of the column in enrich_database that corresponds to the authors of taxonomic names. Default value is sanitise_author.
enrich_display_in_message_column: The name of the column in iucnRedlist that contains values to show in the matching messages. Default value is taxonid.
enrich_plant_identifier_column: The name of the column in iucnRedlist that corresponds to record identifier. Default value is taxonid.
matching_criterion: A function used to chose the best method from extracts of the iucnRedlist.
try_hybrid: Flag (TRUE/FALSE) whether we want to look at hybrid fixes across all fixing methods.

Value

A list of length seven containing:

$match the index of the record in iucnRedlist which matches the record in the collection database.
$details_short a simplified message detailing the match.
$match_taxon_name a longer format message detailing the match.
$original_authors The author/s (extracted) from the collection database.
$match_authors The author/s of the matched record in iucnRedlist.
$author_check Either Identical, Partial or Different (No Match if a match to iucnRedlist cannot be found). A message informing the similarity of the collection's taxon authors and the authors found in iucnRedlist. Author similarity is found using the function author_check().

match = taxon_match_full,

Details

This function allows matching of a collection's database to IUCN Red List of Threatened Species database. This function relies of matching functions found that are documented in match_single(), and is broadly similar to the function match_collection_to_wcvp().

Note that by default the matching functions use column names from (WCVP) therefore these will often require changing prior to matching unless you change the column names in iucnRedlist to concure with wcvp column names.

Within the algorithm there exists methods to improve the matching such as trying to change infraspecific levels (e.g var. to subsp.) or adding hybridisation. These methods can be turned on and off using do_add_split, do_fix_hybrid, do_rm_autonym and typo_method.