rOpenSci packages

This is a complete list of all available rOpenSci packages. Packages are grouped by ones that acquire data, full-text of journal articles, altmetrics, data-publication, reproducibility and data visualization. Packages with a cran sign are stable versions that you can quickly install from your nearest mirror using install.packages("PACKAGE_NAME"). Others are in various stages of development (bleeding edge packages are not listed here) and you can learn more by following our GitHub organization page. All of our software packages are open source. Please see package description files for more license details.

Data Packages that interface with data repositories

Package Description Details
spocc Collect and map species occurrence data from GBIF, iNaturalist, Ecoengine, AntWeb, eBird, and USGS's BISON. cran github
AntWeb Access data from the world's largest ant database. Maintained and developed by the California Academy of Science cran github
ecoengine Retrieve 3+ MM records, checklists and photos from Berkeley's ecoengine cran github
rebird Search and acquire occurrence records of bird sightings collated in the eBird database cran github
rAvis Download occurrence data for bird species, and associated metadata from ProyectoAvis, a citizen science bird project in Spain. cran github
BEFdata Connects to instances of BEFdata portals for collaborative data management (e.g BEF-China and FUNdiv) cran github
rfisheries Search and retrieve data from the OpenFisheries.org, currently providing access to global capture fishing landings from the Food and Agriculture Organization (FAO) of the United Nations cran github
RMendeley This package is now deprecated. Programmatic interface to the Mendeley network - push up data to Mendeley as well as search and retrieve data from your private data and public Mendeley records. Updates pending upcoming API changes. cran github
rWBClimate Programmatic interface to the World Bank climate data used in the World Bank climate knowledge portal. cran github
treebase Programmatic interface to Treebase - a database of phylogenetic trees cran github
rfishbase Access any fish data from Fishbase.org, including occurrence records, habitat data, and more cran github
rnpn Access phenological data from US National Phenology Network for plants and animals cran github
rbhl Access full text and metadata on scanned and OCR text for biodiversity literature from Biodiversity Heritage Library cran github
rgbif Access more than 400 million species occurrence records from across the globe in one place, from the Global Biodiversity Information Facility cran github
taxize Get taxonomic identifiers from many different databases; taxonomic synonyms; taxonomic hierarchies; retrieve common names, and more. Access to a dozen different sources cran github
rsnps Search and retrieve Single Nucleotide Polymorphism data from openSNP, a repository of direct-to-customer genetic test results cran github
rvertnet Access to specimen records for vertebrates across many museums though VertNet cran github
rentrez rentrez provides functions that work with the NCBI eutils to search or download data from various NCBI databases cran github
neotoma Search for sites and download data for use in analytical workflows of paleoecological research using the Neotoma Paleoecological Database cran github
paleobioDB Access data from the Paleobiology Database, a warehouse of paleobiology database cran github
rnoaa Access climate data from NOAA, including temperature and precipitation, as well as sea ice cover data, and extreme weather events cran github
rdryad Push data to and get data from Dryad a repository of data associated with published scholarly papers. Development pending upcoming API changes. cran github
gender gender is an R package to encode gender based on names and dates of birth cran github
geonames Grab data from the GeoNames geographical database which covers all countries and contains over eight million placenames cran github
RSelenium An R client for Selenium Remote WebDriver cran github
clifro An R client for New Zealand's National Climate Database cran github
reol R client to the Encyclopedia of Life a website and database of data/images/descriptions of species. cran github
rinat A programmatic interface to the API provided by iNaturalist. cran github
rbison R client for USGS's BISON (Biodiversity Information Serving Our Nation). cran github
bold R client for BOLD Systems (Barcode Of Life Database). cran github
ecoretriever R client wrapping the Python Ecoretriever software. cran github
traits A high level R package to acquire species trait data from many sources, including Polytraits, BETTYdb, NCBI, Phylomatic, and more. In early devlopment cran github
Package Description Details
rplos Connects to the full-text API of the Public Library of Science (PLOS). They provide a powerful search engine by exposing Solr search endpoints cran github
aRxiv Access to the aRxiv preprint repository cran github
rebi Access to the European PubMed Central database of papers and metadata cran github
rspringer Full-text access to Springer journals. Development pending upcoming API changes. cran github
rpensoft Access to Pensoft journals full text and metadata. Not in active development. cran github
rhindawi R interface to the Hindawi Journals metadata and corpus. Not in active development. cran github
rorcid A programmatic interface the Orcid.org API In early development cran github
elife R interface to the eLife API In early devlopment cran github
rdatacite Wrapper to DataCite metadata. In early devlopment cran github
bmc An R interface to Biomed Central (BMC) search API and full text XML. In early devlopment cran github
rcrossref An R interface to Crossref metadata search API. In early devlopment cran github
rmetadata A high level R interface to many different scholarly metadata sources, which will include Crossref, any OAI-PMH provider, Digital Public Library of America, Hathi Trust, Europeana, and more. In early devlopment cran github
fulltext An high level R interface to many different sources for full text (or nearly) scholarly texts, including PLOS, PMC, PeerJ, eLife, arXiv, and many more. In early devlopment cran github
Package Description Details
rImpactStory Programmatic interface to ImpactStory Package no longer works. cran github
rAltmetric Programmatic interface to article-level metrics data from Altmetric.com cran github
Citeulike R interface to CiteULike. Not in active development. cran github
alm R wrapper to the almetrics API platform developed by PLoS API - other publishers have built on this and work out of the box: CrossRef, Copernicus Publishers, and the Public Knowledge Project (PKP) cran github
Package Description Details
rfigshare Push data, figures, and text to, and search and retrieve data from, Figshare from R cran github
dvn Programmatic interface to the DataVerse Network. cran github
EML An R package for reading, writing, integrating and publishing data using the Ecological Metadata Language (EML) format. cran github
RNeXML Semantically rich NeXML I/O in R - next generation XML for Phylogenetic data. cran github
Package Description Details
git2r Git bindings from R cran github
testdat A test suite to ensure that tabular data are correctly formatted. cran github
gistr gistr is a light interface to GitHub's gists for R. In early development cran github
Package Description Details
elastic An R client for Elasticsearch In early development cran github
solr An R client for Apache Solr cran github
Package Description Details
plotly Programmatic interface to the Plot.ly API - construct plots with ggplot2 and push to Plot.ly for an interactive plot with a few lines of code cran github
rMaps Generate interactive Javascript maps from R, using Mapbox, Leaflet, CrossLet, DataMaps, and more - and share maps on the interwebs cran github
togeojson A package to convert many data formats to geoJSON or Bostock's topoJSON cran github

Didn't find what you're looking for? We're working on several new packages and updates so check back later (or browse our Github org account). You can also browse the web technologies task view on CRAN (maintained by our very own Scott) for related packages that might suit your needs, or post to our discuss list.