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.

Generate Citation File Format ('CFF') Metadata

Citation File Format ('CFF') version 1.2.0 is a human- and machine-readable file format for software citation metadata. Core utilities generate, read, write and validate Citation File Format metadata for 'R' packages.

General Purpose 'GraphQL' Client

A 'GraphQL' client, with an R6 interface for initializing a connection to a 'GraphQL' instance, and methods for constructing queries, including fragments and parameterized queries. Queries are checked with the 'libgraphqlparser' C++ parser via the 'graphql' package.

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 the 'Open Tree of Life' API

An interface to the 'Open Tree of Life' API to retrieve phylogenetic trees, information about studies used to assemble the synthetic tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The 'Open Tree of Life' aims at assembling a comprehensive phylogenetic tree for all named species.

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.

Bibtex Parser

Utility to parse a bibtex file.

Database Interface to 'Elasticsearch' and 'OpenSearch'

Connect to 'Elasticsearch' and 'OpenSearch', 'NoSQL' databases built on the 'Java' Virtual Machine and using the 'Apache' 'Lucene' library. Interacts with the 'Elasticsearch' 'HTTP' API' (< https://www.elastic.co/elasticsearch/>) and the 'OpenSearch' 'HTTP' 'API' (< https://opensearch.org/>). Includes functions for setting connection details to 'Elasticsearch' and 'OpenSearch' 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 APIs for 'indices', documents, nodes, clusters, an interface to the cat API, and more.

A Grammar of Data Manipulation

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

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.