Reptile Data Formatting Tutorial

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

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

This tutorial explains how to use our reptile taxonomy functions to format and access structured information about reptile species in your research or applications.

Overview of Functions

Our package provides two main functions for working with reptile taxonomic data:

1. format_all_attributes()
2. format_selected_attributes()

These functions help researchers efficiently organize and access taxonomic information about reptile species from various sources into standardized formats.

Using format_all_attributes()

The format_all_attributes() function processes a complete reptile dataset and formats all available taxonomic attributes into structured tibbles (data frames).

Syntax

format_all_attributes(reptile_data)

Parameters

• reptile_data: A dataframe or list containing raw reptile taxonomic information

Return Value

The function returns a list of tibbles, with each tibble containing a specific category of taxonomic information:

• distribution: Geographic distribution information
• synonyms: Scientific name synonyms throughout taxonomic history
• higher_taxa: Taxonomic classification hierarchy
• subspecies: Information about recognized subspecies
• common_names: Common names in different languages
• reproduction: Reproductive biology information
• types: Type specimen information
• diagnosis: Diagnostic morphological features
• comments: Additional taxonomic notes
• etymology: Origin and meaning of scientific names
• references: Scientific literature references

Example

library(reptiledbr)
species_list <- c(
  "Lachesis muta",
  "Python bivittatus",
  "Crotalus atrox",
  "Bothrops atrox insularis", # Trinomial (con subespecie) - debería dar error
  "Lachesis sp"
)

# 
reptile_data <- get_reptiledb_data(species_list)

# 
reptile_data

# Format all attributes
all_attributes <- format_all_attributes(reptile_data)

# Access specific attribute categories
all_attributes$distribution
all_attributes$common_names

Using format_selected_attributes()

If you only need specific taxonomic attributes, the format_selected_attributes() function allows you to extract only the categories you're interested in.

Syntax

format_selected_attributes(reptile_data, attributes, quiet = FALSE)

Parameters

• reptile_data: A dataframe or list containing raw reptile taxonomic information
• attributes: A character vector listing the specific attributes to extract
• quiet: Logical value. If TRUE, suppresses processing messages

Return Value

Returns a list containing only the requested attribute tibbles.

Example

# Extract only synonyms, higher taxa, and common names
selected_info <- format_selected_attributes(
  reptile_data = reptile_data,
  attributes = c("Synonym", "Higher Taxa", "Common Names"),
  quiet = TRUE
)

# Access the selected information
selected_info$Synonym
selected_info$`Higher Taxa`
selected_info$`Common Names`

Working with the Formatted Data

Once you have formatted your reptile data, you can use standard R data manipulation techniques to analyze the information:

# Find all venomous species
all_attributes$comments |> 
  dplyr::filter(stringr::str_detect(comment_detail, "Venomous"))


# Extract distribution information for a specific species
all_attributes$distribution |>
  dplyr::filter(input_name == "Crotalus atrox")

Data Structure

Each formatted attribute tibble includes at least these standard columns:

• input_name: The original species name provided
• genus: The genus name
• species: The species epithet
• Attribute-specific column (e.g., distribution, common_name, synonym, etc.)

This consistent structure allows for easy filtering, joining, and analysis across different attribute categories.

Tips for Effective Use

• When working with large datasets, use format_selected_attributes() to improve performance
• Consider that some species may have multiple entries in certain categories (e.g., multiple common names or distribution records)
• The input_name column provides a reliable key for joining information across different attribute tibbles

By effectively using these formatting functions, you can streamline your reptile taxonomic research and data analysis workflows.

reptiledbr documentation built on Aug. 8, 2025, 7:15 p.m.