Introduction
The reptiledbr package allows users to access taxonomic
information of reptiles directly from R without the constant need to
make web queries to The
Reptile Database server. This provides several advantages:
- Faster processing when working offline
- Ability to efficiently verify large taxonomic datasets
- Reduction of requests to The Reptile Database server
- Consistency in results, even without a stable internet connection
This vignette demonstrates how to perform local searches using the package’s main functions.
Main Functions for Local Searches
The reptiledbr package offers three key functions for
performing local taxonomic searches:
-
reptiledbr_exact(): For exact searches of scientific names -
reptiledbr_partial(): For searches that allow partial matches (fuzzy matching) -
search_reptiledbr(): Flexible function that combines exact and partial search capabilities -
list_subspecies_reptiledbr(): To obtain information about subspecies
Practical Examples
Exact Search for Species Names
The reptiledbr_exact() function verifies if the provided
species names exist exactly as written in the database. This function is
useful when you need to verify the validity of specific taxonomic
names.
library(reptiledbr)
#> Welcome to reptiledbr (0.0.1)
#> This package provides tools to access and query data from the Reptile Database:
#> https://reptile-database.reptarium.cz/
#> Type ?reptiledbr to get started or visit the documentation for examples and guidance.
# Define a vector of species names to search
species_names <- c(
"Lachesis muta",
"Python bivittatus",
"Crotalus atrox",
"Bothrops atrox insularis", # Trinomial (with subspecies) - will generate an error
"Lachesis sp",
"Crotalus atroxx", # Intentional typo
"Anolis liogaster",
"Lachesis mutta", # Intentional typo
"Python bivitatus" # Intentional typo
)
# Perform exact search
reptiledbr_exact(species_names)
#> # A tibble: 9 × 10
#> id input_name found species_match order family genus epithet author message
#> <int> <chr> <lgl> <chr> <fct> <fct> <fct> <fct> <chr> <chr>
#> 1 1 Lachesis … TRUE Lachesis muta Serp… Viper… Lach… muta Linna… No sub…
#> 2 2 Python bi… TRUE Python bivit… Serp… Pytho… Pyth… bivitt… Kuhl … Specie…
#> 3 3 Crotalus … TRUE Crotalus atr… Serp… Viper… Crot… atrox Baird… No sub…
#> 4 4 Bothrops … FALSE NA NA NA NA NA NA Specie…
#> 5 5 Lachesis … FALSE NA NA NA NA NA NA Specie…
#> 6 6 Crotalus … FALSE NA NA NA NA NA NA Specie…
#> 7 7 Anolis li… TRUE Anolis lioga… Saur… Anoli… Anol… liogas… Boule… No sub…
#> 8 8 Lachesis … FALSE NA NA NA NA NA NA Specie…
#> 9 9 Python bi… FALSE NA NA NA NA NA NA Specie…As can be observed, the exact search only returns matches for names that are correctly written. Names with typos or incorrect formats (such as trinomials) are not recognized.
Partial Match Search
The reptiledbr_partial() function is more flexible and
uses fuzzy matching techniques to identify species even when there are
minor typos or variations in spelling.
# Perform search with partial matching
reptiledbr_partial(species_names)
#> # A tibble: 9 × 11
#> id input_name found species_match order family genus epithet author
#> <int> <chr> <lgl> <chr> <fct> <fct> <fct> <fct> <chr>
#> 1 1 Lachesis muta TRUE Lachesis muta Serp… Viper… Lach… muta Linna…
#> 2 2 Python bivittatus TRUE Python bivit… Serp… Pytho… Pyth… bivitt… Kuhl …
#> 3 3 Crotalus atrox TRUE Crotalus atr… Serp… Viper… Crot… atrox Baird…
#> 4 4 Bothrops atrox in… FALSE NA NA NA NA NA NA
#> 5 5 Lachesis sp FALSE NA NA NA NA NA NA
#> 6 6 Crotalus atroxx TRUE Crotalus atr… Serp… Viper… Crot… atrox Baird…
#> 7 7 Anolis liogaster TRUE Anolis lioga… Saur… Anoli… Anol… liogas… Boule…
#> 8 8 Lachesis mutta TRUE Lachesis muta Serp… Viper… Lach… muta Linna…
#> 9 9 Python bivitatus TRUE Python bivit… Serp… Pytho… Pyth… bivitt… Kuhl …
#> # ℹ 2 more variables: fuzzy_match <lgl>, message <chr>Notice how reptiledbr_partial() was able to find matches
for “Crotalus atroxx”, “Lachesis mutta”, and “Python bivitatus” despite
the typos, but still does not recognize incorrect formats such as
trinomials or incomplete names (e.g., “Lachesis sp”).
Flexible Search with Additional Options
The search_reptiledbr() function offers greater
flexibility, allowing you to specify whether to use partial matching or
not:
# Define a list of valid species
subspecies_names <- c("Lachesis muta",
"Anilius scytale",
"Anolis bahorucoensis",
"Anolis baleatus",
"Crotalus atrox",
"Anolis barahonae",
"Anolis bremeri")
# Exact search (without fuzzy matching)
search_reptiledbr(subspecies_names, use_fuzzy = FALSE)
#> # A tibble: 7 × 12
#> id input_name found species_match order family genus epithet author message
#> <int> <chr> <lgl> <chr> <fct> <fct> <fct> <fct> <chr> <chr>
#> 1 1 Lachesis … TRUE Lachesis muta Serp… Viper… Lach… muta Linna… No sub…
#> 2 2 Anilius s… TRUE Anilius scyt… Serp… Anili… Anil… scytale Linna… Specie…
#> 3 3 Anolis ba… TRUE Anolis bahor… Saur… Anoli… Anol… bahoru… Noble… Specie…
#> 4 4 Anolis ba… TRUE Anolis balea… Saur… Anoli… Anol… baleat… Cope … Specie…
#> 5 5 Crotalus … TRUE Crotalus atr… Serp… Viper… Crot… atrox Baird… No sub…
#> 6 6 Anolis ba… TRUE Anolis barah… Saur… Anoli… Anol… baraho… Willi… Specie…
#> 7 7 Anolis br… TRUE Anolis breme… Saur… Anoli… Anol… bremeri Barbo… Specie…
#> # ℹ 2 more variables: match_type <chr>, fuzzy_match <lgl>Obtaining Subspecies Information
A particularly useful feature is the ability to list all recognized
subspecies for a given species using
list_subspecies_reptiledbr():
# List all subspecies for the found species
search_reptiledbr(subspecies_names, use_fuzzy = FALSE) |>
list_subspecies_reptiledbr()
#> # A tibble: 20 × 3
#> species subspecies_name author
#> <chr> <chr> <chr>
#> 1 Anilius scytale Anilius scytale phelpsorum Roze 1958
#> 2 Anilius scytale Anilius scytale scytale Linnaeus 1758
#> 3 Anolis bahorucoensis Anolis bahorucoensis bahorucoensis Noble & Hassler 1933
#> 4 Anolis bahorucoensis Anolis bahorucoensis southerlandi Schwartz 1978
#> 5 Anolis baleatus Anolis baleatus baleatus Cope 1864
#> 6 Anolis baleatus Anolis baleatus altager Schwartz 1975
#> 7 Anolis baleatus Anolis baleatus caeruleolatus Schwartz 1974
#> 8 Anolis baleatus Anolis baleatus fraudator Schwartz 1974
#> 9 Anolis baleatus Anolis baleatus lineatacervix Schwartz 1978
#> 10 Anolis baleatus Anolis baleatus litorisilva Schwartz 1974
#> 11 Anolis baleatus Anolis baleatus multistruppus Schwartz 1974
#> 12 Anolis baleatus Anolis baleatus samanae Schwartz 1974
#> 13 Anolis baleatus Anolis baleatus scelestus Schwartz 1974
#> 14 Anolis baleatus Anolis baleatus sublimis Schwartz 1974
#> 15 Anolis barahonae Anolis barahonae barahonae Williams 1962
#> 16 Anolis barahonae Anolis barahonae albocellatus Schwartz 1974
#> 17 Anolis barahonae Anolis barahonae ininquinatus Cullom & Schwartz 19…
#> 18 Anolis barahonae Anolis barahonae mulitus Cullom & Schwartz 19…
#> 19 Anolis bremeri Anolis bremeri bremeri Barbour 1914
#> 20 Anolis bremeri Anolis bremeri insulaepinorum Garrido 1972We can also combine partial matching search and subspecies retrieval:
# Partial matching search followed by subspecies listing
reptiledbr_partial(c("Lachesis mutta",
"Python bivitatus",
"Anolis barahonae")) |>
list_subspecies_reptiledbr()
#> # A tibble: 6 × 3
#> species subspecies_name author
#> <chr> <chr> <chr>
#> 1 Anolis barahonae Anolis barahonae barahonae Williams 1962
#> 2 Anolis barahonae Anolis barahonae albocellatus Schwartz 1974
#> 3 Anolis barahonae Anolis barahonae ininquinatus Cullom & Schwartz 1980
#> 4 Anolis barahonae Anolis barahonae mulitus Cullom & Schwartz 1980
#> 5 Python bivittatus Python bivittatus progschai Jacobs, Aulyia & Böhme 2009
#> 6 Python bivittatus Python bivittatus bivittatus Kuhl 1820Recommended Workflow
For working with large taxonomic datasets, we recommend the following workflow:
- Perform an initial search with
reptiledbr_exact()to identify names that match exactly - For names not found, use
reptiledbr_partial()to capture possible typos - Finally, use
list_subspecies_reptiledbr()to obtain detailed information about subspecies when needed
Conclusions
The reptiledbr package provides efficient tools for
verifying and obtaining taxonomic information about reptiles without the
need to make constant queries to The Reptile Database
serverusing reptiledbr::search_reptiledbr(). This greatly
facilitates working with large datasets and allows for consistent
taxonomic verification even without an internet connection.
The local search functions are particularly useful for researchers and professionals working with herpetological data, enabling efficient cleaning and validation of species lists, identification of common typos, and access to up-to-date taxonomic information about reptiles.