This package was developed to facilitate the processes of reptile nomenclature update based on a search for species synonyms according to The Reptile Databse website (Uetz et al., 2025).
Currently, the package access many species information from The Reptile Database using R interface.
I hope it to be useful, to people trying to match databases from different sources (IUCN, species traits database, etc), or trying to get summaries from a given higher taxa or region (e.g.: Snakes from Brazil). But it can also just print single species information directly in R.
Any feedback, suggestion or request are welcome!
To install the stable version of this package user must run:
# install.packages("devtools")
devtools::install_github("joao-svalencar/letsHerp", ref="main")
library(letsHerp)
Function herpSearch:
Prints species information sampled from the respective species page in RD:
#single species:
herpSearch(binomial = "Apostolepis adhara")
Function herpAdvancedSearch:
Creates a link for a page as derived from an Advanced Search in RD (multiple species in a page):
#create multiple species link:
link <- herpAdvancedSearch(genus = "Apostolepis") #returns a link to access a list of all Apostolepis species
link <- herpAdvancedSearch(higher = "snakes", location = "Brazil") #returns a link to access a list of all snake species in Brazil
Function herpSpecies:
Sample species data from the species link created by herpAdvancedSearch. It includes higher taxa information, authors, year of description, and the species url.
- Returns higher taxa information and species url:
#sample multiple species data:
apo <- herpSpecies(link, taxonomicInfo = TRUE, getLink = TRUE)
- Returns only species url - Faster and recommended for large datasets:
apo <- herpSpecies(link, taxonomicInfo = FALSE, getLink = TRUE)
Function herpSynonyms:
Samples species synonyms using a data frame with species names and the species link (e.g.: the result of herpSpecies(link, getLink=TRUE)).
The complex regex pattern used to sample synonyms from The Reptile Database is quite efficient but still sample 0.2% of them in bad format. Most cases represent unusual nomenclature so users might not face any problems trying to match current valid names. In any case, I fixed (pottentially) all unusual synonym formats the internal dataset allSynonyms (last update: 23rd May, 2025)
#sample species synonyms
apo_syn <- herpSynonyms(apo)
Function herpSync:
Inspired in function aswSync from package AmphiNom (Liedtke, 2018), this function compares a given list of species (e.g.: IUCN, or a regional list) with the list of species synonyms and returns a tyde comparison allowing faster nomenclature check.
#comparing synonyms:
apo_list <- c("Vieira-Alencar authorisensis",
"Apostolepis ambiniger",
"Apostolepis cerradoensis",
"Elapomorphus assimilis",
"Apostolepis tertulianobeui",
"Apostolepis goiasensis")
herpSync(apo_list, apo_syn)
-
The package counts with a full list of current valid species (
allReptiles- 12,440 species) with their respective higher taxa information (updated to 23th of May, 2025); -
A dataset with all unique synonyms for each current valid species (
allSynonyms- 53,159 entries - updated to 23th of May, 2025); -
Another synonyms dataset with all entries considering their respective references (
allSynonymsRef110,413 entries - updated to 23rd of May, 2025).
- Implement
herpAdvancedSearchlink testing and result summary - Implement
herpSynonymbatch sampling and tryCatch() mechanism -
herpSpecies()with parallel sampling -
herpSynonyms()with parallel sampling - CRAN submission (June 14th, 2025)
- CRAN release
- Paper submission
- Implement adapted version of
AmphiNom::asw_stats()(Liedtke, 2018) - Implement adapted version of
AmphiNom::synonym_report()(Liedtke, 2018) - Implement IUCN match
To cite this package in publications, run:
citation("letsHerp")Liedtke, H. C. (2018). AmphiNom: an amphibian systematic tool. Systematics and Biodiversity, 17(1) 1-6. https://doi.org/10.1080/14772000.2018.1518935
Uetz, P., Freed, P, Aguilar, R., Reyes, F., Kudera, J. & Hošek, J. (eds.) (2025) The Reptile Database. http://www.reptile-database.org
Vieira-Alencar, João Paulo dos Santos (joaopaulo.valencar@gmail.com)
Ph.D in Ecology at USP
Post-Doc at: Laboratório de Evolução e Diversidade I - "LED 1" - Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, SP – Brazil