Synchronize Species Names Using The Reptile Database

Source: R/reptSync.R

Queries a list of species names through reptSearch() and returns a data frame with the currently valid names and taxonomic status for each input.

reptSync(
  x,
  solveAmbiguity = TRUE,
  cores = 1,
  showProgress = TRUE,
  getLink = FALSE
)

Arguments

x

A character vector of taxon names to be matched (e.g., species lists, phylogenetic tip labels, or trait table entries).

solveAmbiguity

Logical. If TRUE, attempts to resolve ambiguous names by retrieving all possible valid species to which the query may refer. Default is TRUE.

cores

Integer. Number of CPU cores to use for parallel processing. Default is cores = 1.

showProgress

Logical. If TRUE, displays progress updates during processing. Default is TRUE.

Logical. If TRUE, retrieves searched species URLs. Defaults if FALSE.

Value

A data frame with the following columns:

  • query: the original input names.

  • RDB: the best-matching valid names according to The Reptile Database.

  • status: a status label indicating the result of the match ("up_to_date", "updated", "updated_typo", "ambiguous", "merge", or "not_found").

  • url: Optional, if getLink = TRUE returns the URL of the species page retrieved for each match, or a list of possible matches if ambiguous.

Note

reptSync() does not make authoritative taxonomic decisions. It matches input names against currently accepted names in The Reptile Database (RDB). A name marked as "up_to_date" may still refer to a taxon that has been split, and thus may not reflect the most recent population-level taxonomy.

For ambiguous names, the url field may contain multiple links corresponding to all valid species to which the queried name is considered a synonym.

See package vignettes for more details.

References

Liedtke, H. C. (2018). AmphiNom: an amphibian systematics tool. Systematics and Biodiversity, 17(1), 1–6. https://doi.org/10.1080/14772000.2018.1518935

Examples

query <- c("Vieira-Alencar authoristicus", "Boa atlantica", "Boa diviniloqua", "Boa imperator")

# \donttest{
reptSync(x = query, cores = 2)
#> Sampling synonyms to approach ambiguity for 1 species
#>                          query                           RDB     status
#> 1 Vieira-Alencar authoristicus                     not_found  not_found
#> 2                Boa atlantica               Boa constrictor    updated
#> 3              Boa diviniloqua Boa constrictor; Boa orophias  ambiguous
#> 4                Boa imperator                 Boa imperator up_to_date
# }