wcvp_match_names: Match names to the WCVP.

In rWCVP: Generating Summaries, Reports and Plots from the World Checklist of Vascular Plants

Match names to the WCVP.

Description

Match names to WCVP, first using exact matching and then using fuzzy matching on any remaining unmatched names.

Usage

wcvp_match_names(
  names_df,
  wcvp_names = NULL,
  name_col = NULL,
  id_col = NULL,
  author_col = NULL,
  join_cols = NULL,
  fuzzy = TRUE,
  progress_bar = TRUE
)

Arguments

names_df	Data frame of names for matching.
wcvp_names	Data frame of taxonomic names from WCVP version 7 or later. If NULL (the default), names will be loaded from rWCVPdata::wcvp_names.
name_col	Character. The column in names_df that has the taxon name for matching.
id_col	Character. A column in names_df with a unique ID for each name. Will be created from the row number if not provided.
author_col	the column in names_df that has the name authority, to aid matching. Set to NULL to match with no author string.
join_cols	Character. A vector of name parts to make the taxon name, if name_col is not provided.
fuzzy	Logical; whether or not fuzzy matching should be used for names that could not be matched exactly.
progress_bar	Logical. Show progress bar when matching? Defaults to TRUE; should be changed to FALSE if used in a markdown report.

Details

By default, exact matching uses only the taxon name (supplied by name_col) unless a column specifying the author string is provided (as author_col).

Columns setting out name parts can be supplied as join_cols in place of a taxon name, but must be supplied in the order you want them joined (e.g. c("genus", "species", "infra_rank", "infra")).

Fuzzy matching uses a combination of phonetic and edit distance matching, and can optionally be turned off using fuzzy=FALSE.

The WCVP can be loaded for matching from rWCVPdata::wcvp_names.

See here for an example workflow.

Value

Match results from WCVP bound to the original data from names_df.

See Also

Other name matching functions: wcvp_match_exact(), wcvp_match_fuzzy()

Examples

 # these examples require 'rWCVPdata'
if(requireNamespace("rWCVPdata")){
wcvp_names <- rWCVPdata::wcvp_names

# without author
wcvp_match_names(redlist_example, wcvp_names,
  name_col = "scientificName",
  id_col = "assessmentId"
)

# with author
wcvp_match_names(redlist_example, wcvp_names,
  name_col = "scientificName",
  id_col = "assessmentId", author_col = "authority"
)
}

rWCVP documentation built on Feb. 16, 2023, 8:30 p.m.