herpSynonyms {letsHerp} | R Documentation |
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))
Arguments
x |
A data frame with columns |
getRef |
Logical. If |
showProgress |
Logical. If |
checkpoint |
Optional. Integer specifying the number of species to process before saving a temporary backup. Backup is only saved if |
backup_file |
Optional. Character string specifying the path to an |
resume |
Logical. If |
cores |
Integer. Number of CPU cores to use for parallel processing. Default is one less than the total available cores. |
Value
A data frame with columns:
-
species
: The valid species name according to RDB. -
synonym
: A recognized synonym for the species. -
reference
(optional): IfgetRef = TRUE
, the citation where the synonym was reported.
Note
To enable safe resuming or backup progress saving, set cores = 1
. Parallel processing does not support backups.
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. doi:10.1080/14772000.2018.1518935
See Also
herpSpecies
, herpAdvancedSearch
Examples
# Filter species belonging to genus Boa
boa <- letsHerp::allReptiles[grep("^Boa\\s", letsHerp::allReptiles$species), ]
# Retrieve synonyms (without references)
boa_syn <- herpSynonyms(boa, getRef = FALSE, cores = 2)