Scott Chamberlain

Scott Chamberlain

105 packages on CRAN

2 packages on GitHub

alm

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An R interface to the open source article level metrics platform <https://github.com/articlemetrics/lagotto/> created by the Public Library of Science (PLOS). A number of publishers are using the open source app created by PLOS, so you can drop in a different base URL to the functions in this package to get to not only PLOS data, but data for Crossref, and more as the open source PLOS software is used.

analogsea

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Provides a set of functions for interacting with the 'Digital Ocean' API at <https://developers.digitalocean.com/documentation/v2>, including creating images, destroying them, rebooting, getting details on regions, and available images.

binomen

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Includes functions for working with taxonomic data, including functions for combining, separating, and filtering taxonomic groups by any rank or name. Allows standard ('SE') and non-standard evaluation ('NSE').

bold

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A programmatic interface to the Web Service methods provided by Bold Systems (<http://www.boldsystems.org/>) for genetic 'barcode' data. Functions include methods for searching by sequences by taxonomic names, ids, collectors, and institutions; as well as a function for searching for specimens, and downloading trace files.

brranching

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Includes methods for fetching 'phylogenies' from a variety of sources, including the 'Phylomatic' web service (<http://phylodiversity.net/phylomatic>), and 'Phylocom' (<https://github.com/phylocom/phylocom/>).

charlatan

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Make fake data, supporting addresses, person names, dates, times, colors, coordinates, currencies, digital object identifiers ('DOIs'), jobs, phone numbers, 'DNA' sequences, doubles and integers from distributions and within a range.

citecorp

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Client for the Open Citations Corpus (<http://opencitations.net/>). Includes a set of functions for getting one identifier type from another, as well as getting references and citations for a given identifier.

ckanr

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Client for 'CKAN' API (<https://ckan.org/>). Includes interface to 'CKAN' 'APIs' for search, list, show for packages, organizations, and resources. In addition, provides an interface to the 'datastore' API.

conditionz

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Provides ability to control how many times in function calls conditions are thrown (shown to the user). Includes control of warnings and messages.

cowsay

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Allows printing of character strings as messages/warnings/etc. with ASCII animals, including cats, cows, frogs, chickens, ghosts, and more.

crminer

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Text mining client for 'Crossref' (<https://crossref.org>). Includes functions for getting getting links to full text of articles, fetching full text articles from those links or Digital Object Identifiers ('DOIs'), and text extraction from 'PDFs'.

crul

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A simple HTTP client, with tools for making HTTP requests, and mocking HTTP requests. The package is built on R6, and takes inspiration from Ruby's 'faraday' gem (<https://rubygems.org/gems/faraday>). The package name is a play on curl, the widely used command line tool for HTTP, and this package is built on top of the R package 'curl', an interface to 'libcurl' (<https://curl.haxx.se/libcurl>).

discgolf

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Client for the Discourse API. Discourse is a open source discussion forum platform (<https://www.discourse.org/>). It comes with 'RESTful' API access to an installation. This client requires that you are authorized to access a Discourse installation, either yours or another.

elastic

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Connect to 'Elasticsearch', a 'NoSQL' database built on the 'Java' Virtual Machine. Interacts with the 'Elasticsearch' 'HTTP' API (<https://www.elastic.co/products/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.

enigma

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The company 'Enigma' (<http://enigma.io>) holds many public 'datasets' from governments, companies, universities, and organizations. 'Enigma' provides an 'API' for data, 'metadata', and statistics on each of the 'datasets'. 'enigma' is a client to interact with the 'Enigma' 'API', including getting the data and 'metadata' for 'datasets' in 'Enigma', as well as collecting statistics on 'datasets'. In addition, you can download a 'gzipped' 'csv' file of a 'dataset' if you want the whole 'dataset'. An 'API' key from 'Enigma' is required to use 'enigma'.

etseed

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Client to interact with the 'etcd' 'key-value' data store <https://github.com/coreos/etcd>. Functions included for managing directories, keys, nodes, and getting statistics.

fauxpas

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HTTP error helpers. Methods included for general purpose HTTP error handling, as well as individual methods for every HTTP status code, both via status code numbers as well as their descriptive names. Supports ability to adjust behavior to stop, message or warning. Includes ability to use custom whisker template to have any configuration of status code, short description, and verbose message. Currently supports integration with 'crul', 'curl', and 'httr'.

finch

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Parse and create Darwin Core (<http://rs.tdwg.org/dwc/>) Simple and Archives. Functionality includes reading and parsing all the files in a Darwin Core Archive, including the datasets and metadata; read and parse simple Darwin Core files; and validation of Darwin Core Archives.

fulltext

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Provides a single interface to many sources of full text 'scholarly' data, including 'Biomed Central', Public Library of Science, 'Pubmed Central', 'eLife', 'F1000Research', 'PeerJ', 'Pensoft', 'Hindawi', 'arXiv' 'preprints', and more. Functionality included for searching for articles, downloading full or partial text, downloading supplementary materials, converting to various data formats.

geoaxe

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Split 'geospatial' objects into pieces. Includes support for some spatial object inputs, 'Well-Known Text', and 'GeoJSON'.

geojson

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Classes for 'GeoJSON' to make working with 'GeoJSON' easier. Includes S3 classes for 'GeoJSON' classes with brief summary output, and a few methods such as extracting and adding bounding boxes, properties, and coordinate reference systems; working with newline delimited 'GeoJSON'; linting through the 'geojsonlint' package; and serializing to/from 'Geobuf' binary 'GeoJSON' format.

geojsonio

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Convert data to 'GeoJSON' or 'TopoJSON' from various R classes, including vectors, lists, data frames, shape files, and spatial classes. 'geojsonio' does not aim to replace packages like 'sp', 'rgdal', 'rgeos', but rather aims to be a high level client to simplify conversions of data from and to 'GeoJSON' and 'TopoJSON'.

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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.

geoops

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Tools for doing calculations and manipulations on 'GeoJSON', a 'geospatial' data interchange format (<https://tools.ietf.org/html/rfc7946>). 'GeoJSON' is also valid 'JSON'.

getlandsat

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Get Landsat 8 Data from Amazon Web Services ('AWS') public data sets (<https://registry.opendata.aws/landsat-8/>). Includes functions for listing images and fetching them, and handles caching to prevent unnecessary additional requests.

gistr

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Work with 'GitHub' 'gists' from 'R' (e.g., <http://en.wikipedia.org/wiki/GitHub#Gist>, <https://help.github.com/articles/about-gists/>). A 'gist' is simply one or more files with code/text/images/etc. This package allows the user to create new 'gists', update 'gists' with new files, rename files, delete files, get and delete 'gists', star and 'un-star' 'gists', fork 'gists', open a 'gist' in your default browser, get embed code for a 'gist', list 'gist' 'commits', and get rate limit information when 'authenticated'. Some requests require authentication and some do not. 'Gists' website: <https://gist.github.com/>.

handlr

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

hoardr

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Suite of tools for managing cached files, targeting use in other R packages. Uses 'rappdirs' for cross-platform paths. Provides utilities to manage cache directories, including targeting files by path or by key; cached directories can be compressed and uncompressed easily to save disk space.

httpcode

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Find and explain the meaning of 'HTTP' status codes. Functions included for searching for codes by full or partial number, by message, and get appropriate dog and cat images for many status codes.

httping

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A suite of functions to ping 'URLs' and to time 'HTTP' 'requests'. Designed to work with 'httr'.

isdparser

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Tools for parsing 'NOAA' Integrated Surface Data ('ISD') files, described at <https://www.ncdc.noaa.gov/isd>. Data includes for example, wind speed and direction, temperature, cloud data, sea level pressure, and more. Includes data from approximately 35,000 stations worldwide, though best coverage is in North America/Europe/Australia. Data is stored as variable length ASCII character strings, with most fields optional. Included are tools for parsing entire files, or individual lines of data.

jaod

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Client for the Directory of Open Access Journals ('DOAJ') (<https://doaj.org/>). API documentation at <https://doaj.org/api/v1/docs>. Methods included for working with all 'DOAJ' API routes: fetch article information by identifier, search for articles, fetch journal information by identifier, and search for journals.

jqr

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Client for 'jq', a 'JSON' processor (<https://stedolan.github.io/jq/>), written in C. 'jq' allows the following with 'JSON' data: index into, parse, do calculations, cut up and filter, change key names and values, perform conditionals and comparisons, and more.

lawn

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Client for 'Turfjs' (<http://turfjs.org>) for 'geospatial' analysis. The package revolves around using 'GeoJSON' data. Functions are included for creating 'GeoJSON' data objects, measuring aspects of 'GeoJSON', and combining, transforming, and creating random 'GeoJSON' data objects.

mapr

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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', 'ggmap', 'leaflet' and 'GitHub' 'gists'.

microdemic

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The 'Microsoft Academic Knowledge' API provides programmatic access to scholarly articles in the 'Microsoft Academic Graph' (<https://academic.microsoft.com/>). Includes methods matching all 'Microsoft Academic' API routes, including search, graph search, text similarity, and interpret natural language query string.

mregions

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Tools to get marine regions data from <http://www.marineregions.org/>. Includes tools to get region metadata, as well as data in 'GeoJSON' format, as well as Shape files. Use cases include using data downstream to visualize 'geospatial' data by marine region, mapping variation among different regions, and more.

natserv

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Interface to 'NatureServe' (<http://www.natureserve.org>). Includes methods to get data, image metadata, search taxonomic names, and make maps.

nneo

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'NEON' 'API' (<http://data.neonscience.org/data-api>) client. Includes methods for interacting with all 'API' routes.

nodbi

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Simplified document database manipulation and analysis, including support for many 'NoSQL' databases, including document databases ('Elasticsearch', 'CouchDB', 'MongoDB'), 'key-value' databases ('Redis'), and (with limitations) SQLite/json1.

oai

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A general purpose client to work with any 'OAI-PMH' (Open Archives Initiative Protocol for 'Metadata' Harvesting) service. The 'OAI-PMH' protocol is described at <http://www.openarchives.org/OAI/openarchivesprotocol.html>. Functions are provided to work with the 'OAI-PMH' verbs: 'GetRecord', 'Identify', 'ListIdentifiers', 'ListMetadataFormats', 'ListRecords', and 'ListSets'.

openadds

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'Openaddresses' (<https://openaddresses.io/>) client. Search, fetch data, and combine 'datasets'. Outputs are easy to visualize with base plots, 'ggplot2', or 'leaflet'.

originr

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Get species origin data (whether species is native/invasive) from the following sources on the web: Encyclopedia of Life (<http://eol.org>), Flora 'Europaea' (<http://rbg-web2.rbge.org.uk/FE/fe.html>), Global Invasive Species Database (<http://www.iucngisd.org/gisd>), the Native Species Resolver (<http://bien.nceas.ucsb.edu/bien/tools/nsr/nsr-ws/>), Integrated Taxonomic Information Service (<http://www.itis.gov/>), and Global Register of Introduced and Invasive Species (<http://www.griis.org/>).

pangaear

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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.

phylocomr

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Interface to 'Phylocom' (<http://phylodiversity.net/phylocom/>), a library for analysis of 'phylogenetic' community structure and character evolution. Includes low level methods for interacting with the three executables, as well as higher level interfaces for methods like 'aot', 'ecovolve', 'bladj', 'phylomatic', and more.

pleiades

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Provides a set of functions for interacting with the 'Pleiades' (<https://pleiades.stoa.org/>) 'API', including getting status data, places data, and creating a 'GeoJSON' based map on 'GitHub' 'gists'.

pubchunks

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Get chunks of XML scholarly articles without having to know how to work with XML. Custom mappers for each publisher and for each article section pull out the information you want. Works with outputs from package 'fulltext', 'xml2' package documents, and file paths to XML documents.

randgeo

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Generate random positions (latitude/longitude), Well-known text ('WKT') points or polygons, or 'GeoJSON' points or polygons.

rbhl

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Interface to 'Biodiversity' 'Heritage' Library ('BHL') (<http://www.biodiversitylibrary.org/>) 'API' (<http://www.biodiversitylibrary.org/api2/docs/docs.html>). 'BHL' is a repository of 'digitized' literature on 'biodiversity' studies, including 'floras', research papers, and more.

rbison

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Interface to the 'USGS' 'BISON' (<https://bison.usgs.gov/>) API, a 'database' for species occurrence data. Data comes from species in the United States from participating data providers. You can get data via 'taxonomic' and location based queries. A simple function is provided to help visualize data.

rbraries

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Interface to the 'Libraries.io' API (<https://libraries.io/api>). 'Libraries.io' indexes data from 36 different package managers for programming languages.

rcitoid

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Client for 'Citoid' (<https://www.mediawiki.org/wiki/Citoid>), an API for getting citations for various scholarly work identifiers found on 'Wikipedia'.

rcoreoa

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Client for the CORE API (<https://core.ac.uk/docs/>). CORE (<https://core.ac.uk>) aggregates open access research outputs from repositories and journals worldwide and make them available to the public.

rcrossref

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Client for various 'CrossRef' 'APIs', including 'metadata' search with their old and newer search 'APIs', get 'citations' in various formats (including 'bibtex', 'citeproc-json', 'rdf-xml', etc.), convert 'DOIs' to 'PMIDs', and 'vice versa', get citations for 'DOIs', and get links to full text of articles when available.

rdatacite

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Client for the web service methods provided by 'DataCite' (<https://www.datacite.org/>), including functions to interface with their 'OAI-PMH' 'metadata' service, and a 'RESTful' search API. The API is backed by 'SOLR', allowing expressive queries, including faceting, statistics on variables, and 'more-like-this' queries.

rdpla

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Interact with the Digital Public Library of America <https://dp.la> ('DPLA') 'REST' 'API' <https://dp.la/info/developers/codex/> from R, including search and more.

rdryad

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

rerddap

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General purpose R client for 'ERDDAP' servers. Includes functions to search for 'datasets', get summary information on 'datasets', and fetch 'datasets', in either 'csv' or 'netCDF' format. 'ERDDAP' information: <https://upwell.pfeg.noaa.gov/erddap/information.html>.

rgbif

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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.

rif

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Client for 'Neuroscience' Information Framework ('NIF') 'APIs' (<https://neuinfo.org/>; <https://neuinfo.org/about/webservices>). Package includes functions for each 'API' route, and gives back data in tidy data.frame format.

ritis

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An interface to the Integrated Taxonomic Information System ('ITIS') (<https://www.itis.gov>). Includes functions to work with the 'ITIS' REST API methods (<https://www.itis.gov/ws_description.html>), as well as the 'Solr' web service (<https://www.itis.gov/solr_documentation.html>).

rjsonapi

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Consumer for APIs that Follow the JSON API Specification (<http://jsonapi.org/>). Package mostly consumes data - with experimental support for serving JSON API data.

rnoaa

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Client for many 'NOAA' data sources including the 'NCDC' climate 'API' at <https://www.ncdc.noaa.gov/cdo-web/webservices/v2>, with functions for each of the 'API' 'endpoints': data, data categories, data sets, data types, locations, location categories, and stations. In addition, we have an interface for 'NOAA' sea ice data, the 'NOAA' severe weather inventory, 'NOAA' Historical Observing 'Metadata' Repository ('HOMR') data, 'NOAA' storm data via 'IBTrACS', tornado data via the 'NOAA' storm prediction center, and more.

rnpn

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Programmatic interface to the Web Service methods provided by the National 'Phenology' Network (<https://usanpn.org/>), which includes data on various life history events that occur at specific times.

rorcid

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Client for the 'Orcid.org' API (<https://orcid.org/>). Functions included for searching for people, searching by 'DOI', and searching by 'Orcid' 'ID'.

rphylopic

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Work with 'Phylopic' web service (<http://phylopic.org/api/>) to get 'silhouette' images of 'organisms', search names, and more. Includes functions for adding 'silhouettes' to both base plots and ggplot2 plots.

rplos

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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.

rredlist

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'IUCN' Red List (<http://apiv3.iucnredlist.org/api/v3/docs>) client. The 'IUCN' Red List is a global list of threatened and endangered species. Functions cover all of the Red List 'API' routes. An 'API' key is required.

rsnps

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A programmatic interface to various 'SNP' 'datasets' on the web: 'OpenSNP' (<https://opensnp.org>), and 'NBCIs' 'dbSNP' database (<https://www.ncbi.nlm.nih.gov/projects/SNP>). Functions are included for searching for 'NCBI'. For 'OpenSNP', functions are included for getting 'SNPs', and data for 'genotypes', 'phenotypes', annotations, and bulk downloads of data by user.

rsunlight

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Interface to 'APIs' for US government data previously under the 'Sunlight' Foundation, now under 'ProPublica' (<https://www.propublica.org/datastore/'apis'>), and Open States (<http://docs.openstates.org/en/latest/api/>). Functions are provided to interact with each of the routes in each API.

rtimes

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Interface to Congress, Campaign Finance, Article Search, and Geographic 'APIs' from the New York Times (<http://developer.nytimes.com/>) and 'ProPublica' (<https://www.propublica.org/datastore/apis>). This client covers a subset of the New York Times and 'ProPublica' 'APIs'.

rvertnet

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Retrieve, map and summarize data from the 'VertNet.org' archives (<http://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.

scrubr

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Clean biological occurrence records. Includes functionality for cleaning based on various aspects of spatial coordinates, unlikely values due to political 'centroids', coordinates based on where collections of specimens are held, and more.

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Access Sea Around Us (<http://www.seaaroundus.org/>) fish catch data, including tools for visualizing the data.

sofa

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Provides an interface to the 'NoSQL' database 'CouchDB' (<http://couchdb.apache.org>). Methods are provided for managing databases within 'CouchDB', including creating/deleting/updating/transferring, and managing documents within databases. One can connect with a local 'CouchDB' instance, or a remote 'CouchDB' databases such as 'Cloudant' (<https://docs.cloudant.com>). Documents can be inserted directly from vectors, lists, data.frames, and 'JSON'. Targeted at 'CouchDB' v2 or greater.

solr

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Provides a set of functions for querying and parsing data from Solr endpoints (local and remote), including search, faceting, highlighting, stats, and 'more like this'.

solrium

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Provides a set of functions for querying and parsing data from 'Solr' (<https://lucene.apache.org/solr>) 'endpoints' (local and remote), including search, 'faceting', 'highlighting', 'stats', and 'more like this'. In addition, some functionality is included for creating, deleting, and updating documents in a 'Solr' 'database'.

spocc

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A programmatic interface to many species occurrence data sources, including Global Biodiversity Information Facility ('GBIF'), 'USGSs' Biodiversity Information Serving Our Nation ('BISON'), 'iNaturalist', Berkeley 'Ecoinformatics' Engine, '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.

spoccutils

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Utilities for use with 'spocc'. Includes functions to clean occurrence data, find and remove duplicates, combine data, and make maps with base 'R' plots, 'ggplot2', and various interactive maps.

request

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High level and easy 'HTTP' client for 'R'. Provides functions for building 'HTTP' queries, including query parameters, body requests, headers, authentication, and more.

taxize

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Interacts with a suite of web 'APIs' for taxonomic tasks, such as getting database specific taxonomic identifiers, verifying species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more.

taxizedb

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Tools for working with 'taxonomic' databases, including utilities for downloading databases, loading them into various 'SQL' databases, cleaning up files, and providing a 'SQL' connection that can be used to do 'SQL' queries directly or used in 'dplyr'.

traits

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Species trait data from many different sources, including sequence data from 'NCBI', plant trait data from 'BETYdb', plant data from the USDA plants database, data from 'EOL' 'Traitbank', Coral traits data (<https://coraltraits.org>), 'Birdlife' International, and more.

vcr

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Record test suite 'HTTP' requests and replays them during future runs. A port of the Ruby gem of the same name (<https://github.com/vcr/vcr/>). Works by hooking into the 'webmockr' R package for matching 'HTTP' requests by various rules ('HTTP' method, 'URL', query parameters, headers, body, etc.), and then caching real 'HTTP' responses on disk in 'cassettes'. Subsequent 'HTTP' requests matching any previous requests in the same 'cassette' use a cached 'HTTP' response.

webmockr

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Stubbing and setting expectations on 'HTTP' requests. Includes tools for stubbing 'HTTP' requests, including expected request conditions and response conditions. Match on 'HTTP' method, query parameters, request body, headers and more. Can be used for unit tests or outside of a testing context.

wellknown

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Convert 'WKT' to 'GeoJSON' and 'GeoJSON' to 'WKT'. Functions included for converting between 'GeoJSON' to 'WKT', creating both 'GeoJSON' features, and non-features, creating 'WKT' from R objects (e.g., lists, data.frames, vectors), and linting 'WKT'.

wikitaxa

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'Taxonomic' information from 'Wikipedia', 'Wikicommons', 'Wikispecies', and 'Wikidata'. Functions included for getting taxonomic information from each of the sources just listed, as well performing taxonomic search.

worrms

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Client for World Register of Marine Species (<http://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.

zbank

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Interface to the 'ZooBank' API (<http://zoobank.org/Api>) client. 'ZooBank' (<http://zoobank.org/>) is the official registry of zoological nomenclature. Methods are provided for using each of the API endpoints, including for querying by author, querying for publications, get statistics on 'ZooBank' activity, and more.

dataone

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Provides read and write access to data and metadata from the DataONE network <https://www.dataone.org> of data repositories. Each DataONE repository implements a consistent repository application programming interface. Users call methods in R to access these remote repository functions, such as methods to query the metadata catalog, get access to metadata for particular data packages, and read the data objects from the data repository. Users can also insert and update data objects on repositories that support these methods.

FedData

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Functions to automate downloading geospatial data available from several federated data sources (mainly sources maintained by the US Federal government). Currently, the package enables extraction from seven datasets: The National Elevation Dataset digital elevation models (1 and 1/3 arc-second; USGS); The National Hydrography Dataset (USGS); The Soil Survey Geographic (SSURGO) database from the National Cooperative Soil Survey (NCSS), which is led by the Natural Resources Conservation Service (NRCS) under the USDA; the Global Historical Climatology Network (GHCN), coordinated by National Climatic Data Center at NOAA; the Daymet gridded estimates of daily weather parameters for North America, version 3, available from the Oak Ridge National Laboratory's Distributed Active Archive Center (DAAC); the International Tree Ring Data Bank; and the National Land Cover Database (NLCD).

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Interact with the 'Google Compute Engine' API in R. Lets you create, start and stop instances in the 'Google Cloud'. Support for preconfigured instances, with templates for common R needs.

nasapower

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Client for 'NASA' 'POWER' global meteorology, surface solar energy and climatology data 'API'. 'POWER' (Prediction Of Worldwide Energy Resource) data are freely available global meteorology and surface solar energy climatology data for download with a resolution of 1/2 by 1/2 arc degree longitude and latitude and are funded through the 'NASA' Earth Science Directorate Applied Science Program. For more on the data themselves, a web-based data viewer and web access, please see <https://power.larc.nasa.gov/>.

plotly

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Create interactive web graphics from 'ggplot2' graphs and/or a custom interface to the (MIT-licensed) JavaScript library 'plotly.js' inspired by the grammar of graphics.

rebird

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A programmatic client for the eBird database, including functions for searching for bird observations by geographic location (latitude, longitude), eBird hotspots, location identifiers, by notable sightings, by region, and by taxonomic name.

redland

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Provides methods to parse, query and serialize information stored in the Resource Description Framework (RDF). RDF is described at <http://www.w3.org/TR/rdf-primer>. This package supports RDF by implementing an R interface to the Redland RDF C library, described at <http://librdf.org/docs/api/index.html>. In brief, RDF provides a structured graph consisting of Statements composed of Subject, Predicate, and Object Nodes.

rentrez

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Provides an R interface to the NCBI's 'EUtils' API, allowing users to search databases like 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> and 'PubMed' <https://www.ncbi.nlm.nih.gov/pubmed/>, process the results of those searches and pull data into their R sessions.

rfigshare

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An interface to 'figshare' (http://figshare.com), a scientific repository to archive and assign 'DOIs' to data, software, figures, and more.

rfishbase

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A programmatic interface to <http://www.fishbase.org>, 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 <http://www.sealifebase.org> data, which contains nearly 200,000 species records for all types of aquatic life not covered by 'FishBase.'

ridigbio

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An interface to iDigBio's search API that allows downloading specimen records. Searches are returned as a data.frame. Other functions such as the metadata end points return lists of information. iDigBio is a US project focused on digitizing and serving museum specimen collections on the web. See <https://www.idigbio.org> for information on iDigBio.

RNeXML

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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.

rotl

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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.

Rphylip

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Rphylip provides an R interface for the PHYLIP package. All users of Rphylip will thus first have to install the PHYLIP phylogeny methods program package (Felsenstein 2013). See http://www.phylip.com for more information about installing PHYLIP.

sbtools

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Tools for interacting with U.S. Geological Survey ScienceBase <https://www.sciencebase.gov> interfaces. ScienceBase is a data cataloging and collaborative data management platform. Functions included for querying ScienceBase, and creating and fetching datasets.

suppdata

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Downloads data supplementary materials from manuscripts, using papers' DOIs as references. Facilitates open, reproducible research workflows: scientists re-analyzing published datasets can work with them as easily as if they were stored on their own computer, and others can track their analysis workflow painlessly. The main function suppdata() returns a (temporary) location on the user's computer where the file is stored, making it simple to use suppdata() with standard functions like read.csv().

taxa

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Provides taxonomic classes for groupings of taxonomic names without data, and those with data. Methods provided are "taxonomically aware", in that they know about ordering of ranks, and methods that filter based on taxonomy also filter associated data.

testdat

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A suite for running automated tests to detect common problems with tabular data