Enrich a collection's database — enrich

This function enriches plant records in a collection using information from POWO (WCVP), IUCN redlist and BGCI.

Usage

enrich_collection(
  collection,
  wcvp = NA,
  iucnRedlist = NA,
  BGCI = NA,
  taxon_name_column = "TaxonName",
  taxon_name_full_column = NA,
  taxon_author_column = NA,
  do_is_autonym = FALSE,
  do_status_year = FALSE,
  do_taxon_types = FALSE,
  ...,
  wcvp_wanted_info = c("plant_name_id", "taxon_name", "taxon_authors", "taxon_rank",
    "taxon_status", "powo_id", "family", "genus", "species", "lifeform_description",
    "climate_description", "geographic_area", "Dist_000_area_code_l3", "Dist_000_labels",
    "Dist_100_area_code_l3", "Dist_010_area_code_l3", "Dist_001_area_code_l3",
    "Dist_101_area_code_l3", "Dist_110_area_code_l3", "Dist_011_area_code_l3",
    "main_common_name", "assessment_date", "category", "criteria", "population_trend"),
  redlist_wanted_info = c("plant_name_id", "main_common_name", "assessment_date",
    "category", "criteria", "population_trend")
)

Arguments

collection: A data frame containing a collection.
wcvp: World Checklist of Vascular Plants (WCVP) database, obtained using the function import_wcvp_names(). If NA WCVP enrichment is not performed.
iucnRedlist: IUCN Red List of Threatened Species database, obtained using the function XXXX. If NA IUCN red list enrichment is not performed.
BGCI: Requires a cleaned BGCI plant search database to obtain how many collections globally a taxon is contained (Not freely available). If NA BGCI plant search enrichment is not performed.
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.
do_is_autonym: Flag (TRUE/FALSE) for whether to add the column is_autonym, see add_is_autonym() for details.
do_status_year: Flag (TRUE/FALSE) for whether to add the column status_year, see add_status_year() for details.
do_taxon_types: Flag (TRUE/FALSE) for whether to add the column taxon_type, see add_taxon_type() for details.
...: Arguments (i.e., attributes) used in the matching algorithm (passed along to match_collection_to_wcvp()). Examples include typo_method, do_convert_accepted and try_fix_hybrid.
wcvp_wanted_info: A character vector containing the information we want to extract from WCVP. These are matched to column names in wcvp$wcvp_names, wcvp$geography and wcvp$redlist (if the later two exist).
redlist_wanted_info: A character vector containing the information we want to extract from IUCN red list, corresponding to column names in iucnRedlist.

Value

The collection data frame enriched with information dependent on function inputs (new columns).