Title: Reptile Database Data
Version: 0.0.0.1
Description: Provides easy access to 'The Reptile Database', a comprehensive catalogue of all living reptile species and their classification. This package includes taxonomic data for over 10,000 reptile species, approximately 2,800 of which are subspecies, covering all extant reptiles. The dataset features taxonomic names, synonyms, distribution data, type specimens, and literature references, making it ready for research and analysis. Data is sourced from 'The Reptile Database' http://www.reptile-database.org/.
License: MIT + file LICENSE
Depends: R (≥ 4.1.0)
Suggests: testthat (≥ 3.0.0), knitr, rmarkdown
Config/testthat/edition: 3
Encoding: UTF-8
RoxygenNote: 7.3.2
LazyData: true
URL: https://github.com/PaulESantos/reptiledb.data
BugReports: https://github.com/PaulESantos/reptiledb.data/issues
Imports: httr, rvest, stringr, tibble
Maintainer: Paul Efren Santos Andrade <paulefrens@gmail.com>
NeedsCompilation: no
Packaged: 2025-07-01 01:55:08 UTC; PC
Author: Paul Efren Santos Andrade ORCID iD [aut, cre]
Repository: CRAN
Date/Publication: 2025-07-05 15:40:02 UTC

Check if reptile database data needs updating based on date comparison

Description

This function checks if the local reptile database data is up-to-date by comparing the date extracted from the local dataset name with the date from the latest available file on The Reptile Database website.

Usage

check_data_update(silent = FALSE, check_connection = TRUE)

Arguments

silent

Logical. If TRUE, suppresses messages and only returns results. Default is FALSE.

check_connection

Logical. If TRUE, checks internet connection before attempting to access online data. Default is TRUE.

Value

A list containing the following elements:

update_needed

Logical. TRUE if an update is needed, FALSE otherwise

local_info

List. Information about the local dataset

remote_info

List. Information about the remote dataset

message

Character. Status message describing the comparison result

recommendation

Character. Recommendation for user action

local_date

Character. Date of local data in YYYY-MM-DD format

remote_date

Character. Date of remote data in YYYY-MM-DD format (if available)

remote_filename

Character. Filename of the remote file (if available)

days_difference

Numeric. Number of days difference between local and remote data (if both dates available)

If an error occurs or internet connection is not available, only the message element will contain relevant error information.

Examples


# Silent check (no messages) - requires internet connection
update_status <- check_data_update(silent = TRUE)

# Verbose check with connection verification
update_status <- check_data_update(silent = FALSE, check_connection = TRUE)

# Check without internet connection verification
update_status <- check_data_update(check_connection = FALSE)

Check Internet Connection

Description

Helper function to check if internet connection is available

Usage

check_internet_connection()

Value

Logical. TRUE if internet is available, FALSE otherwise.

Extract date from dataset name or filename

Description

Extract date from dataset name or filename

Usage

extract_date_from_name(name, type = "local")

Arguments

name

Dataset name or filename

type

Type of name ("local" or "remote")

Value

A Date object representing the extracted date, or NULL if extraction fails. For local datasets, expects pattern "reptiledb_MMYYYY" (e.g., reptiledb_012025). For remote files, expects pattern "reptile_checklist_YYYY_MM.xlsx".

Get Latest Reptile Database Download Link

Description

This function retrieves the most recent download link for reptile database files from the Reptile Database website. It searches for files from the current year first, and if none are found, searches for files from the previous year.

Usage

get_latest_reptile_download(
  base_url = "http://www.reptile-database.org/data/",
  current_year = as.numeric(format(Sys.Date(), "%Y")),
  file_types = c("xls", "xlsx", "zip"),
  return_info = FALSE
)

Arguments

base_url

Character string. The base URL of the reptile database data page. Default is "http://www.reptile-database.org/data/".

current_year

Numeric. The current year to search for files. Default is the current system year.

file_types

Character vector. File extensions to search for. Default is c("xls", "xlsx", "zip").

return_info

Logical. If TRUE, returns a list with detailed information about the found file. If FALSE, returns only the URL. Default is FALSE.

Details

The function performs web scraping on the specified URL to find download links. It prioritizes files from the current year, but will fall back to the previous year if no current year files are available.

The function requires the following packages: rvest, dplyr, and stringr. These packages must be installed before using this function.

Value

If return_info = FALSE, returns a character string with the URL of the most recent file, or NULL if no suitable file is found. If return_info = TRUE, returns a list containing:

url

Character. The complete URL of the file

filename

Character. The name of the file

file_type

Character. The file extension

extraction_date

Date. The date when the link was extracted

source_page

Character. The source webpage URL

Returns NULL if no suitable file is found or if an error occurs during web scraping.

See Also

http://www.reptile-database.org/ for more information about the Reptile Database.

Examples


# Get just the URL - requires internet connection
url <- get_latest_reptile_download()

# Get detailed information
info <- get_latest_reptile_download(return_info = TRUE)

# Search for specific file types
zip_url <- get_latest_reptile_download(file_types = "zip")

# Search for files from a specific year
url_2024 <- get_latest_reptile_download(current_year = 2024)

Reptile Checklist with Subspecies Information

Description

A comprehensive dataset extracted from The Reptile Database containing taxonomic and nomenclatural information for reptile species and their subspecies. This tibble includes detailed columns related to authorship, type species, and taxonomic changes.

Usage

reptiledb_012025

Format

A tibble with 14,474 rows and 16 columns:

order

Taxonomic order of the reptile (e.g., "Sauria").

family

Taxonomic family (e.g., "Scincidae").

genus

Genus name.

epithet

Species epithet (second part of the species name).

species

Full species name (genus + epithet).

species_author

Primary author(s) of the species name.

species_name_year

Year the species was described.

subspecies_name

Epithet of the subspecies (if any).

subspecie_author_info

Full author citation of the subspecies.

subspecies_name_author

Author(s) of the subspecies name.

subspecies_year

Year the subspecies was described.

type_species

Name of the type species, if available.

change

Text description of any taxonomic or nomenclatural change.

rdb_sp_id

Unique identifier assigned by The Reptile Database.

nomenclature_change

Logical flag indicating if a nomenclatural change has occurred (TRUE / FALSE).

nomenclature_change_species

Logical flag indicating if the nomenclatural change affects the species level (TRUE / FALSE).

Details

This dataset is part of the reptiledb.data package and provides structured access to reptile taxonomy data, enabling users to filter, analyze, or visualize species and subspecies information across multiple reptile families and genera.

Source

http://www.reptile-database.org/