Semantically Rich I/O for the 'NeXML' Format

Provides access to phyloinformatic data in 'NeXML' format. The package should add new functionality to R such as the possibility to manipulate 'NeXML' objects in more various and refined way and compatibility with 'ape' objects.

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.

Humane Interface to Amazon Web Services

An opinionated interface to Amazon Web Services < https://aws.amazon.com>, with functions for interacting with 'IAM' (Identity and Access Management), 'S3' (Simple Storage Service), 'RDS' (Relational Data Service), Redshift, and Billing. Lower level functions ('aws_' prefix) are for do it yourself workflows, while higher level functions ('six_' prefix) automate common tasks.

Search 'Vertnet', a 'Database' of Vertebrate Specimen Records

Retrieve, map and summarize data from the 'VertNet.org' archives (< https://vertnet.org/>). Functions allow searching by many parameters, including 'taxonomic' names, places, and dates. In addition, there is an interface for conducting spatially delimited searches, and another for requesting large 'datasets' via email.

Classes for Storing and Manipulating Taxonomic Data

Provides classes for storing and manipulating taxonomic data. Most of the classes can be treated like base R vectors (e.g. can be used in tables as columns and can be named). Vectorized classes can store taxon names and authorities, taxon IDs from databases, taxon ranks, and other types of information. More complex classes are provided to store taxonomic trees and user-defined data associated with them.

Interface to the Search API for 'PLoS' Journals

A programmatic interface to the 'SOLR' based search API (< http://api.plos.org/>) provided by the Public Library of Science journals to search their articles. Functions are included for searching for articles, retrieving articles, making plots, doing 'faceted' searches, 'highlight' searches, and viewing results of 'highlighted' searches in a browser.

Interface to the Global Biodiversity Information Facility API

A programmatic interface to the Web Service methods provided by the Global Biodiversity Information Facility (GBIF; < https://www.gbif.org/developer/summary>). GBIF is a database of species occurrence records from sources all over the globe. rgbif includes functions for searching for taxonomic names, retrieving information on data providers, getting species occurrence records, getting counts of occurrence records, and using the GBIF tile map service to make rasters summarizing huge amounts of data.

Tools for Validating 'GeoJSON'

Tools for linting 'GeoJSON'. Includes tools for interacting with the online tool < http://geojsonlint.com>, the 'Javascript' library 'geojsonhint' (< https://www.npmjs.com/package/geojsonhint>), and validating against a 'GeoJSON' schema via the 'Javascript' library (< https://www.npmjs.com/package/is-my-json-valid>). Some tools work locally while others require an internet connection.

Access for Dryad Web Services

Interface to the Dryad "Solr" API, their "OAI-PMH" service, and fetch datasets. Dryad (< https://datadryad.org/>) is a curated host of data underlying scientific publications.

Convert Among Citation Formats

Converts among many citation formats, including 'BibTeX', 'Citeproc', 'Codemeta', 'RDF XML', 'RIS', 'Schema.org', and 'Citation File Format'. A low level 'R6' class is provided, as well as stand-alone functions for each citation format for both read and write.