World Register of Marine Species (WoRMS) Client

Client for World Register of Marine Species (< https://www.marinespecies.org/>). Includes functions for each of the API methods, including searching for names by name, date and common names, searching using external identifiers, fetching synonyms, as well as fetching taxonomic children and taxonomic classification.

Bibtex Parser

Utility to parse a bibtex file.

Generate Citation File Format ('cff') Metadata for R Packages

The Citation File Format version 1.2.0 is a human and machine readable file format which provides citation metadata for software. This package provides core utilities to generate and validate this metadata.

General Purpose Interface to 'Elasticsearch'

Connect to 'Elasticsearch', a 'NoSQL' database built on the 'Java' Virtual Machine. Interacts with the 'Elasticsearch' 'HTTP' API (< https://www.elastic.co/elasticsearch/>), including functions for setting connection details to 'Elasticsearch' instances, loading bulk data, searching for documents with both 'HTTP' query variables and 'JSON' based body requests. In addition, 'elastic' provides functions for interacting with API's for 'indices', documents, nodes, clusters, an interface to the cat API, and more.

R Interface to 'FishBase'

A programmatic interface to 'FishBase', re-written based on an accompanying 'RESTful' API. Access tables describing over 30,000 species of fish, their biology, ecology, morphology, and more. This package also supports experimental access to 'SeaLifeBase' data, which contains nearly 200,000 species records for all types of aquatic life not covered by 'FishBase.'

Interface to Species Occurrence Data Sources

A programmatic interface to many species occurrence data sources, including Global Biodiversity Information Facility ('GBIF'), 'iNaturalist', 'eBird', Integrated Digitized 'Biocollections' ('iDigBio'), 'VertNet', Ocean 'Biogeographic' Information System ('OBIS'), and Atlas of Living Australia ('ALA'). Includes functionality for retrieving species occurrence data, and combining those data.

Client for the 'Pangaea' Database

Tools to interact with the 'Pangaea' Database (< https://www.pangaea.de>), including functions for searching for data, fetching 'datasets' by 'dataset' 'ID', and working with the 'Pangaea' 'OAI-PMH' service.

A Grammar of Data Manipulation

A fast, consistent tool for working with data frame like objects, both in memory and out of memory.

Parse Scientific Names

Parse scientific names using 'gnparser' (< https://github.com/gnames/gnparser>), written in Go. 'gnparser' parses scientific names into their component parts; it utilizes a Parsing Expression Grammar specifically for scientific names.

Visualize Species Occurrence Data

Utilities for visualizing species occurrence data. Includes functions to visualize occurrence data from 'spocc', 'rgbif', and other packages. Mapping options included for base R plots, 'ggplot2', 'leaflet' and 'GitHub' 'gists'.