Match Species Names to Endemic Plant List of Peru

This function matches given species names against the internal database of endemic plant species in Peru.

Usage

matching_ppendemic(
  splist,
  max_dist = 2,
  save_ambiguous = FALSE,
  ambiguous_path = "ambiguous_genera.csv"
)

Arguments

splist

A non-empty character vector containing taxon names. Missing and empty values are not accepted. Indeterminate sp. and spp. names are treated as genus-level records and are not classified as endemic taxa.

max_dist

Maximum edit distance used in fuzzy matching steps. Defaults to 2 (the default in fuzzyjoin::stringdist_left_join()).

save_ambiguous

Logical flag. If TRUE, ambiguous fuzzy genus matches are exported to disk.

ambiguous_path

File path used when save_ambiguous = TRUE. Defaults to "ambiguous_genera.csv".

Value

Returns a tibble with the matched names in Matched.Genus, Matched.Species for binomial names, and Matched.Infraspecies for valid infra species names.

Details

The function first attempts to directly match species names with exact matches in the database (genus and specific epithet, or genus, specific epithet, and infra species). If no exact match is found, the function performs a fuzzy match using the fuzzyjoin package with optimal string alignment distance as implemented in stringdist.

The maximum edit distance can be controlled through max_dist.

The function matching_ppendemic returns a tibble with new columns Matched.Genus, Matched.Species, and Matched.Infraspecies, containing the matched names or NA if no match was found.

Additionally, a logical column is added for each function called, allowing users to see which functions were applied to each name during the matching process. If a process column shows NA, the corresponding function was not called for that name because it was already matched by a preceding function.

Examples

# \donttest{
matching_ppendemic(c("Aa aurantiaca", "Aa aurantiaaia", "Werneria nubigena"))
#>   sorter         Orig.Name  Matched.Name Endemic.Tag Orig.Genus Orig.Species
#> 1      1     Aa aurantiaca Aa aurantiaca     Endemic         AA   AURANTIACA
#> 2      2    Aa aurantiaaia Aa aurantiaca     Endemic         AA  AURANTIAAIA
#> 3      3 Werneria nubigena      Werneria Not endemic   WERNERIA     NUBIGENA
#>   Orig.Infraspecies Rank Infra.Rank Comp.Rank Matched.Genus Matched.Species
#> 1              <NA>    2       <NA>      TRUE            AA      AURANTIACA
#> 2              <NA>    2       <NA>      TRUE            AA      AURANTIACA
#> 3              <NA>    2       <NA>     FALSE      WERNERIA            <NA>
#>   Matched.Infraspecies Matched.Rank matched direct_match genus_match
#> 1                 <NA>            2    TRUE         TRUE          NA
#> 2                 <NA>            2    TRUE        FALSE        TRUE
#> 3                 <NA>            1   FALSE        FALSE        TRUE
#>   fuzzy_match_genus direct_match_species_within_genus
#> 1                NA                                NA
#> 2                NA                             FALSE
#> 3                NA                             FALSE
#>   suffix_match_species_within_genus fuzzy_match_species_within_genus
#> 1                                NA                               NA
#> 2                             FALSE                             TRUE
#> 3                             FALSE                            FALSE
#>   fuzzy_genus_dist fuzzy_species_dist Author
#> 1               NA                 NA       
#> 2               NA                  2       
#> 3               NA                 NA       
# }