Prefilter Target Backbone by Input Genera (Exact + Fuzzy)

Reduces the target backbone to genera relevant for the current input names. This is designed as a pre-step before wcvp_matching() to reduce search space.

Strategy:

• Exact genus candidates are always included.

• Optional fuzzy genus candidates are included when include_fuzzy = TRUE.

• Returned object preserves the standard target schema used by the package.

Usage

prefilter_target_by_genus(
  df,
  target_df = NULL,
  genus_index = NULL,
  include_fuzzy = TRUE,
  max_dist = 1,
  method = "osa"
)

Arguments

df

Input tibble/data.frame with either Genus/Species or Orig.Genus/Orig.Species.

target_df

Optional custom target table. If NULL, the optional wcvpdata checklist is used when available; otherwise pass a backbone explicitly.

genus_index

Optional pre-built index from build_genus_index(). If NULL, it is built on the fly.

include_fuzzy

Logical. If TRUE, include fuzzy-matched genera.

max_dist

Maximum fuzzy distance for genus matching (used when include_fuzzy = TRUE).

method

String distance method passed to fozziejoin.

Value

A prefiltered target_df tibble compatible with wcvp_matching(target_df = ...). Attributes:

candidate_genera

Character vector of selected genera.

exact_genera

Character vector of exact matched genera.

fuzzy_genera

Character vector of fuzzy matched genera.

Examples

# \donttest{
library(wcvpmatch)
df <- data.frame(Genus = "Opuntia", Species = "yanganucensis")
prefilter_target_by_genus(df)
#> ℹ Input was converted from <data.frame> to a <tibble>.
#>   See <https://tibble.tidyverse.org/> for more details.
#> # A tibble: 1,509 × 33
#>    plant_name_id ipni_id    taxon_rank taxon_status family    genus_hybrid genus
#>            <dbl> <chr>      <chr>      <chr>        <chr>     <chr>        <chr>
#>  1       2401900 175654-2   Variety    Synonym      Cactaceae NA           Opun…
#>  2       3294155 77302436-1 Subspecies Synonym      Cactaceae NA           Opun…
#>  3       2877217 175097-2   Variety    Accepted     Cactaceae NA           Opun…
#>  4       3294157 77302438-1 Subspecies Synonym      Cactaceae NA           Opun…
#>  5       2877218 175098-2   Variety    Accepted     Cactaceae NA           Opun…
#>  6       3245753 77212806-1 Subspecies Synonym      Cactaceae NA           Opun…
#>  7       2877219 175099-2   Variety    Accepted     Cactaceae NA           Opun…
#>  8       2877222 175102-2   Variety    Accepted     Cactaceae NA           Opun…
#>  9       2877259 175376-2   Variety    Synonym      Cactaceae NA           Opun…
#> 10       2400776 175023-2   Variety    Synonym      Cactaceae NA           Opun…
#> # ℹ 1,499 more rows
#> # ℹ 26 more variables: species_hybrid <chr>, species <chr>,
#> #   infraspecific_rank <chr>, infraspecies <chr>, parenthetical_author <chr>,
#> #   primary_author <chr>, publication_author <chr>, place_of_publication <chr>,
#> #   volume_and_page <chr>, first_published <chr>, nomenclatural_remarks <chr>,
#> #   geographic_area <chr>, lifeform_description <chr>,
#> #   climate_description <chr>, taxon_name <chr>, taxon_authors <chr>, …
# }