herpSynonyms: Retrieve Synonyms for Reptile Species from RDB

Description

Retrieves a data frame containing the current valid names of reptile species along with all their recognized synonyms, as listed in The Reptile Database (RDB). Optionally, the references citing each synonym can also be included.

Usage

herpSynonyms(x,
                    getRef = FALSE,
                    showProgress = TRUE,
                    checkpoint = NULL,
                    backup_file = NULL,
                    resume = FALSE,
                    cores = max(1, parallel::detectCores() - 1))

Value

A data frame with columns:

species: The valid species name according to RDB.
synonym: A recognized synonym for the species.
reference (optional): If getRef = TRUE, the citation where the synonym was reported.

Arguments

x: A data frame with columns species and url, typically the output of herpSpecies with getLink = TRUE.
getRef: Logical. If TRUE, includes the reference(s) in which each synonym was mentioned. Default is FALSE.
showProgress: Logical. If TRUE, prints data sampling progress. Default is TRUE.
checkpoint: Optional. Integer specifying the number of species to process before saving a temporary backup. Backup is only saved if cores = 1. If set to 1, saves progress after each species (safest but slowest).
backup_file: Optional. Character string specifying the path to an .rds file used to save or resume intermediate results. Required if using checkpoint or resume.
resume: Logical. If TRUE, resumes sampling from a previous run using the file provided in backup_file. Only works when cores = 1.
cores: Integer. Number of CPU cores to use for parallel processing. Default is one less than the total available cores.

References

Uetz, P., Freed, P., Aguilar, R., Reyes, F., Kudera, J., & Hošek, J. (eds.) (2025). The Reptile Database. Retrieved from http://www.reptile-database.org Liedtke, H. C. (2018). AmphiNom: an amphibian systematics tool. Systematics and Biodiversity, 17(1), 1–6. tools:::Rd_expr_doi("10.1080/14772000.2018.1518935")

Examples

Run this code

# Filter species belonging to genus Boa
boa <- letsHerp::allReptiles[grep("^Boa\\s", letsHerp::allReptiles$species), ]

# \donttest{
# Retrieve synonyms (without references)
boa_syn <- herpSynonyms(boa, getRef = FALSE, cores = 2)
# }