wcvp_match_names {rWCVP} | R Documentation |
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 |
name_col |
Character. The column in |
id_col |
Character. A column in |
author_col |
the column in |
join_cols |
Character. A vector of name parts to make the taxon name,
if |
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
|
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"
)
}