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Reconcile mammal names against MDD

Source: R/mdd-reconcile.R
mdd_matching.Rd

[Experimental]

This function is experimental and may change in future releases.

Run a staged species-level reconciliation pipeline against an MDD backbone. The workflow prioritizes exact evidence first, then progressively relaxes criteria through exact genus, fuzzy genus, exact species-within-genus, and fuzzy species-within-genus matching.

Usage

mdd_matching(
  x,
  target_df = NULL,
  prefilter_genus = TRUE,
  allow_duplicates = FALSE,
  max_dist = 1,
  method = "osa"
)

Arguments

x

Character vector of names or a data frame with parsed name columns.

target_df

Optional backbone produced by build_mdd_match_backbone().

prefilter_genus

Logical. If TRUE, restrict the backbone to exact and fuzzy candidate genera before the full pipeline.

allow_duplicates

Logical. If TRUE, deduplicate internally and expand results back to the original rows.

max_dist

Maximum string distance used in fuzzy stages.

method

Distance method passed to fuzzyjoin::stringdist_*_join().

Value

A tibble with row-level traceability, pathway flags, matched name context, accepted-name context, and fuzzy distance columns.

Examples

checklist <- tibble::tibble(
  id = c("1", "2"),
  sci_name = c("Puma_concolor", "Vicugna_vicugna"),
  genus = c("Puma", "Vicugna"),
  specific_epithet = c("concolor", "vicugna"),
  authority_species_author = c("Linnaeus", "Molina")
)
synonyms <- tibble::tibble(
  mdd_syn_id = c("1001", "1002"),
  mdd_species_id = c("1", "2"),
  mdd_author = c("Linnaeus", "Molina"),
  mdd_original_combination = c("Felis concolor", "Auchenia vicugna")
)
backbone <- build_mdd_match_backbone(checklist, synonyms)
mdd_matching(
  c("Puma concolor", "Felis concolor", "Pumma concolor"),
  target_df = backbone
)
#> # A tibble: 3 × 51
#>   input_index input_name     orig_name     orig_genus orig_subgenus orig_species
#>         <int> <chr>          <chr>         <chr>      <chr>         <chr>       
#> 1           1 Puma concolor  Puma concolor Puma       NA            concolor    
#> 2           2 Felis concolor Felis concol… Felis      NA            concolor    
#> 3           3 Pumma concolor Pumma concol… Pumma      NA            concolor    
#> # ℹ 45 more variables: orig_subspecies <chr>, author <chr>,
#> #   matched_name_id <chr>, matched_name <chr>, matched_author <chr>,
#> #   taxon_status <chr>, accepted_id <chr>, accepted_name <chr>,
#> #   accepted_author <chr>, is_accepted_name <lgl>, matched <lgl>,
#> #   match_stage <chr>, direct_match <lgl>, genus_match <lgl>,
#> #   fuzzy_match_genus <lgl>, direct_match_species_within_genus <lgl>,
#> #   fuzzy_match_species_within_genus <lgl>, fuzzy_genus_dist <dbl>, …