Title:	Interface to the Reptile Database for Querying and Retrieving Taxonomic Data
Version:	0.0.1
Description:	Provides tools to search, access, and format taxonomic information from the Reptile Database (http://reptile-database.org) directly within R. Users can retrieve species-level data, distribution, etymology, synonyms, common names, and other relevant information for reptiles. Designed for taxonomists, ecologists, and biodiversity researchers.
License:	MIT + file LICENSE
Encoding:	UTF-8
RoxygenNote:	7.3.2
Imports:	xml2, stringr, purrr, tibble, tidyr, dplyr, utils, lifecycle, fuzzyjoin
Suggests:	covr, knitr, mockery, reptiledb.data, rmarkdown, testthat (≥ 3.0.0)
Config/testthat/edition:	3
Depends:	R (≥ 4.1.0)
URL:	https://github.com/PaulESantos/reptiledbr, https://paulesantos.github.io/reptiledbr/
BugReports:	https://github.com/PaulESantos/reptiledbr/issues
VignetteBuilder:	knitr
Maintainer:	Paul Efren Santos Andrade <paulefrens@gmail.com>
NeedsCompilation:	no
Packaged:	2025-07-05 16:20:49 UTC; PC
Author:	Paul Efren Santos Andrade [aut, cre]
Repository:	CRAN
Date/Publication:	2025-07-09 10:40:02 UTC

reptiledbr: Interface to the Reptile Database for Querying and Retrieving Taxonomic Data

Description

Provides tools to search, access, and format taxonomic information from the Reptile Database (http://reptile-database.org) directly within R. Users can retrieve species-level data, distribution, etymology, synonyms, common names, and other relevant information for reptiles. Designed for taxonomists, ecologists, and biodiversity researchers.

Author(s)

Maintainer: Paul Efren Santos Andrade paulefrens@gmail.com (ORCID)

See Also

Useful links:

• https://github.com/PaulESantos/reptiledbr

• https://paulesantos.github.io/reptiledbr/

• Report bugs at https://github.com/PaulESantos/reptiledbr/issues

Check if data package is required and available

Description

Check if data package is required and available

Usage

check_data_required()

Clean and standardize column names in a data.frame

Description

This function standardizes column names in a data.frame to make them syntactically valid and consistent. It converts uppercase to lowercase, removes spaces and special characters, replaces accents, and ensures names are unique and valid for R. It is an alternative to the janitor::clean_names() function implemented in base R.

Usage

clean_names_rdbr(
  df,
  case = c("snake", "lower_camel", "upper_camel", "screaming_snake"),
  replace_special_chars = TRUE,
  unique_names = TRUE
)

Arguments

Details

The cleaning process includes:

• Converting everything to lowercase (except in camel or screaming_snake formats)

• Replacing accents and common special characters with their ASCII equivalents

• Removing parentheses and their content

• Replacing non-alphanumeric characters with underscores

• Removing redundant underscores (leading, trailing, or duplicated)

• Ensuring names don't start with numbers (adding "x" at the beginning)

• Applying the selected case format

• Ensuring names are unique by adding numeric suffixes

Value

A data.frame with the same data as the input but with clean and standardized column names according to the specified parameters.

Extract and optionally format a specific attribute

Description

Usage

extract_attribute(reptile_data, attribute_name, format_function = NULL)

Arguments

Details

Extracts and optionally formats structured information for a given attribute.

Value

A tibble with formatted information for the specified attribute.

Format all available reptile attributes

Description

Usage

format_all_attributes(reptile_data, quiet = FALSE)

Arguments

Details

Applies formatting functions to all known attributes in the reptile dataset.

Value

A list containing all formatted attributes.

Format reptile comment data Extracts and formats general comments associated with reptile species.

Description

Format reptile comment data Extracts and formats general comments associated with reptile species.

Usage

format_comments(reptile_data)

Arguments

Value

A tibble containing formatted comments for each species.

Format common names for reptiles

Description

Format common names for reptiles

Usage

format_common_names(reptile_data)

Arguments

Value

A tibble with formatted common names by species.

Format diagnostic information for reptiles

Description

Format diagnostic information for reptiles

Usage

format_diagnosis(reptile_data)

Arguments

Value

A tibble with formatted diagnostic descriptions by species.

Format distribution data into a long table format

Description

Usage

format_distribution(reptile_data)

Arguments

Value

A tibble with distribution data in long format.

Format etymological data of reptiles Extracts and formats the etymological information associated with reptile species.

Description

Format etymological data of reptiles Extracts and formats the etymological information associated with reptile species.

Usage

format_etymology(reptile_data)

Arguments

Value

A tibble containing the formatted etymological details for each species.

Format higher-level taxonomic data for reptiles

Description

Format higher-level taxonomic data for reptiles

Usage

format_higher_taxa(reptile_data)

Arguments

Value

A tibble with formatted higher taxonomic classification by species.

Format bibliographic reference data of reptiles Extracts and formats bibliographic references associated with reptile species.

Description

Format bibliographic reference data of reptiles Extracts and formats bibliographic references associated with reptile species.

Usage

format_references(reptile_data)

Arguments

Value

A tibble containing formatted references for each species.

Format reproductive data for reptiles

Description

Format reproductive data for reptiles

Usage

format_reproduction(reptile_data)

Arguments

Value

A tibble with formatted reproductive information by species.

Format selected reptile attributes

Description

Usage

format_selected_attributes(reptile_data, attributes, quiet = FALSE)

Arguments

Details

Extracts and formats only the specified attributes from the reptile dataset.

Value

A list containing the selected formatted attributes.

Format subspecies data for reptiles

Description

Format subspecies data for reptiles

Usage

format_subspecies(reptile_data)

Arguments

Value

A tibble with formatted subspecies by species.

Format synonym data for reptiles

Description

Usage

format_synonyms(reptile_data)

Arguments

Value

A tibble with formatted synonym names by species.

Format nomenclatural type data for reptiles

Description

Format nomenclatural type data for reptiles

Usage

format_types(reptile_data)

Arguments

Value

A tibble with formatted type information by species.

Extract a specific attribute from reptile species data

Description

Usage

get_attribute(reptile_data, attribute_name)

Arguments

Value

A tibble with columns input_name, genus, species, and attribute_value containing the extracted values.

Access Reptile Database Taxonomic Information

Description

Retrieves taxonomic information on living reptile species from The Reptile Database. This function allows users to explore scientific names, synonyms, distributions, and taxonomic references for all known species of snakes, lizards, turtles, amphisbaenians, tuataras, and crocodiles.

Usage

get_reptiledb_data(species_names, timeout = 10, quiet = FALSE)

Arguments

Details

The Reptile Database currently includes more than 10,000 species and around 2,800 subspecies. It focuses on taxonomic and nomenclatural data, including valid names, synonyms, type localities, distribution, and original references. However, ecological and behavioral data are largely absent.

Data are compiled from peer-reviewed literature, expert contributions, and curated by an editorial team. Updates and corrections from users are welcome and help improve the resource.

The classification follows recent phylogenetic studies (e.g., Zheng & Wiens, 2016), although the database takes a conservative approach to rapidly changing taxonomic hypotheses. New genera or species proposals may first appear in the "synonyms" field pending wider scientific acceptance.

Note: The database does not support species identification by traits, but users can search by geographical distribution and higher taxonomic groups.

Value

A list or data frame containing available taxonomic information (e.g., accepted name, synonyms, family, distribution, literature references).

Author(s)

Data curated by P. Uetz and collaborators. Function implementation by Paul E. Santos Andrade.

Source

Uetz, P., Freed, P., & Hosek, J. (eds.) (2021). The Reptile Database. Available at: https://reptile-database.reptarium.cz

For more on phylogenetic background see: Zheng, Y., & Wiens, J. J. (2016). Combining phylogenomics and fossils in higher-level squamate reptile phylogeny. BMC Evolutionary Biology, 16, 1-20.

See Also

https://reptile-database.reptarium.cz

Examples

get_reptiledb_data("Anolis carolinensis",
                           quiet = TRUE)

List Subspecies from ReptileDB

Description

This function processes results from a ReptileDB database search to extract subspecies information. It identifies species that have subspecies and returns a tibble with the species name, subspecies name, and author information.

Usage

list_subspecies_reptiledbr(df)

Arguments

Value

A tibble with three columns:

Examples

## Not run: 
# These examples require the 'reptiledb.data' package to be installed.
subspecies_names <- c("Lachesis muta",
  "Anilius scytale",
  "Anolis bahorucoensis")

search_reptiledbr(subspecies_names, use_fuzzy = FALSE) |>
  list_subspecies_reptiledbr()

## End(Not run)

Search Reptile Species by Exact Match and Subspecies Presence

Description

This function searches for exact matches of scientific species names and indicates whether each matched species has associated subspecies in the dataset.

Usage

reptiledbr_exact(species_names)

Arguments

Value

A tibble with taxonomic information and a message indicating subspecies presence.

The response variable may return different messages depending on the outcome of the query. Possible values include:

• "Species not found" – The specified species could not be matched in the database.

• "Species has subspecies" – The specified species exists and has one or more subspecies registered.

• "No subspecies found" – The species was found, but there are no subspecies associated with it in the database.

Examples

## Not run: 
# These examples require the 'reptiledb.data' package to be installed.
# You can install it from its source if not on CRAN.
reptiledbr_exact(c("Ablepharus alaicus", "Anolis limon"))

## End(Not run)

Fuzzy Search for Species Names Using Approximate Matching

Description

This function performs approximate (fuzzy) matching of species names from a given list of input terms against the species names in the reptile database, and indicates whether each matched species has subspecies.

Usage

reptiledbr_partial(species_names, max_dist = 2)

Arguments

Value

A tibble with matched species, taxonomic info, fuzzy match flag, and subspecies presence. The response variable may return different messages depending on the outcome of the query. Possible values include:

• "Species not found" – The specified species could not be matched in the database.

• "Species has subspecies" – The specified species exists and has one or more subspecies registered.

• "No subspecies found" – The species was found, but there are no subspecies associated with it in the database.

Examples

## Not run: 
# These examples require the 'reptiledb.data' package to be installed.
reptiledbr_partial(c("Ablepharus alaicuss", "Anolis limom"))

## End(Not run)

Comprehensive Search for Reptile Species with Exact and Fuzzy Matching

Description

This function combines both exact and fuzzy matching approaches to search for reptile species names in the database. It first attempts exact matches and then uses fuzzy matching for any species names that weren't found exactly.

Usage

search_reptiledbr(species_names, max_dist = 2, use_fuzzy = TRUE)

Arguments

Value

A combined tibble with results from both exact and fuzzy matching approaches, with a flag indicating the match type. Results maintain the original order of species_names. The response variable may return different messages depending on the outcome of the query. Possible values include:

• "Species not found" – The specified species could not be matched in the database.

• "Species has subspecies" – The specified species exists and has one or more subspecies registered.

• "No subspecies found" – The species was found, but there are no subspecies associated with it in the database.

Examples

## Not run: 
# These examples require the 'reptiledb.data' package to be installed.
search_reptiledbr(c("Ablepharus alaicus", "Anolis limom"))

## End(Not run)