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Match Species Names to Threatened Plant List of Peru

Source: R/threated_match.R
matching_threatenedperu.Rd

This function matches given species names against the internal database of threatened plant species in Peru. It uses a hierarchical matching strategy that includes direct matching, genus-level matching, fuzzy matching, and suffix matching to maximize successful matches while maintaining accuracy.

Usage

matching_threatenedperu(
  splist,
  source = c("original", "updated"),
  quiet = TRUE
)

Arguments

splist

A character vector containing the species names to be matched. Can include duplicate names - results will be expanded to match the input.

source

Character string specifying which database version to use. Options are:

  • "original" (default): Uses the original threatened species database with support for Rank 4 (quaternomial names)

  • "updated": Uses the updated database with current nomenclature, supporting up to Rank 3 (trinomial names)

quiet

Logical, default TRUE. If FALSE, prints informative messages.

Value

A tibble with detailed matching results including:

sorter

Integer. Original position in input vector

Orig.Name

Character. Original input name (standardized)

Matched.Name

Character. Matched name from database or "—"

Threat.Status

Character. IUCN threat category or "Not threatened"

Rank

Integer. Input taxonomic rank (1-4)

Matched.Rank

Integer. Matched taxonomic rank

Comp.Rank

Logical. Whether ranks match exactly

Match.Level

Character. Description of match quality

matched

Logical. Whether a match was found

Details

**Duplicate Handling:** When the input contains duplicate names, the function automatically:

  • Detects duplicates and creates a tracking column (sorters)

  • Processes only unique names (efficient matching)

  • Expands results to restore all original positions

  • Preserves original input order via sorter column

The duplicate handling uses a `sorters` column that concatenates all original sorter values for duplicate names (e.g., "1 - 3" for a name appearing at positions 1 and 3), enabling accurate result expansion.

**Matching Strategy:** 1. Direct exact matching 2. Genus-level matching (exact and fuzzy) 3. Species-level matching within genus 4. Infraspecies-level matching (up to 2 levels for original database)

**Rank Validation:** The algorithm implements strict rank validation to prevent false positives.

See also

is_threatened_peru for a simplified interface get_ambiguous_matches to retrieve ambiguous match details get_threatened_database to access the raw databases

Examples

if (FALSE) { # \dontrun{
# Basic usage
species_list <- c("Cattleya maxima", "Polylepis incana")
results <- matching_threatenedperu(species_list, source = "original")

# With duplicates
species_dup <- c("Cattleya maxima", "Polylepis incana", "Cattleya maxima")
results_dup <- matching_threatenedperu(species_dup)
nrow(results_dup) == 3  # TRUE - preserves duplicates

# Access metadata
attr(results, "match_rate")

# Check for ambiguous matches
get_ambiguous_matches(results, type = "infraspecies")
} # }