letsRept (version 1.1.0)

reptSync: Synchronize Species Names Using The Reptile Database

Description

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

Usage

reptSync(
  x,
  solveAmbiguity = TRUE,
  cores = 1,
  showProgress = TRUE,
  getLink = 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.

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.

getLink

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

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)
# }