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 information on specific licenses. We also have a package status dashboard.


Data Publication | Data Access | Literature | Altmetrics | Reproducibility | Databases | Data Vizualization
Package Description Details
dataone Search across repositories, and read and write data and metadata from the DataONE federation of data repositories from R. Includes repositories such as the KNB and Dryad. 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
rfigshare Push data, figures, and text to, and search and retrieve data from, Figshare from R cran github
RNeXML Semantically rich NeXML I/O in R - next generation XML for Phylogenetic data. cran github

Data Access Packages that interface with data repositories

Package Description Details
AntWeb Access data from the world's largest ant database. Maintained and developed by the California Academy of Science cran github
BEFdata Connects to instances of BEFdata portals for collaborative data management (e.g BEF-China and FUNdiv) cran github
bold R client for BOLD Systems (Barcode Of Life Database). cran github
ckanr R client for CKAN RESTful API. In early development cran github
chromer Interact with the chromosome counts database (CCDB) at http://ccdb.tau.ac.il In early development cran github
clifro An R client for New Zealand's National Climate Database cran github
ecoengine Retrieve 3+ MM records, checklists and photos from Berkeley's ecoengine cran github
ecoretriever R client wrapping the Python Ecoretriever software. 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
historydata An R package with datasets of interest to historians. It is primarily intended for pedagogic purposes in teaching historians how to use R.. In early development cran github
musemeta R Client for Scraping Museum Metadata, including The Metropolitan Museum of Art, the Canadian Science & Technology Museum Corporation, the National Gallery of Art, and the Getty Museum, and more to come. In early development 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
pangaear An R client to interact with the Pangaea database. In early development cran github
pleiades Search for and retrieve metadata and spatial location data on archeological places and names from Pleiades. In early development cran github
rAvis Download occurrence data for bird species, and associated metadata from ProyectoAvis, a citizen science bird project in Spain. cran github
rbhl Access full text and metadata on scanned and OCR text for biodiversity literature from Biodiversity Heritage Library cran github
rbison R client for USGS's BISON (Biodiversity Information Serving Our Nation). cran github
RCryptsy Allows data to be pulled from the Cryptsy exchange into R via the Cryptsy Public API. For more infomation about Cryptsy see https://www.cryptsy.com In early development cran github
rdpla An R client to interact with Digital Public Library of America (DPLA) metadata. In early development cran github
rdryad Get data from Dryad a repository of data associated with published scholarly papers. Development pending upcoming API changes. cran github
rebird Search and acquire occurrence records of bird sightings collated in the eBird database cran github
rentrez rentrez provides functions that work with the NCBI eutils to search or download data from various NCBI databases cran github
reol R client to the Encyclopedia of Life a website and database of data/images/descriptions of species. cran github
rerddap General purpose R client for working with ERDDAP servers. More infomation on ERDDAP. ERDDAP is a specific case of OPeNDAP. In early development cran github
reuropeana An R client to interact with Europeana metadata. In early development cran github
rfishbase Access any fish data from Fishbase.org, including occurrence records, habitat data, and more 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
rgbif Access more than 400 million species occurrence records from across the globe in one place, from the Global Biodiversity Information Facility cran github
rglobi R interface to the aggregated biotic interaction data of GloBI In early development cran github
rinat A programmatic interface to the API provided by iNaturalist. 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
rnoaa Access climate data from NOAA, including temperature and precipitation, as well as sea ice cover data, and extreme weather events cran github
rnbn Acess to the United Kingdom's National Biodiversity Network data. cran github
rnpn Access phenological data from US National Phenology Network for plants and animals cran github
RSelenium An R client for Selenium Remote WebDriver cran github
rsnps Search and retrieve Single Nucleotide Polymorphism data from openSNP, a repository of direct-to-customer genetic test results cran github
RStars Access to the Digital Universe Data set at http://star-api.herokuapp.com/ In early development cran github
rvertnet Access to specimen records for vertebrates across many museums though VertNet cran github
rWBClimate Programmatic interface to the World Bank climate data used in the World Bank climate knowledge portal. cran github
spocc Collect and map species occurrence data from GBIF, iNaturalist, Ecoengine, AntWeb, eBird, and USGS's BISON. 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
traits A high level R package to acquire species trait data from many sources, including Polytraits, BETTYdb, NCBI, Phylomatic, and more. In early development cran github
treebase Programmatic interface to Treebase - a database of phylogenetic trees cran github
USAboundaries Historical boundaries of the United States. Map the United States (or the colonies that became the United States) on any date from 1629 to 2000. Contains both county and state/territory level polygons. cran github
Package Description Details
aRxiv Access to the aRxiv preprint repository cran github
bmc An R interface to Biomed Central (BMC) search API and full text XML. In early development cran github
elife R interface to the eLife API Deprecated - eLife is shutting their API down soon. See the package fulltext for eLife access 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 development cran github
IEEER Interface to the IEEE Xplore Gateway. In early development cran github
rcrossref An R interface to Crossref metadata search API. cran github
rdatacite Wrapper to DataCite metadata. In early development cran github
rebi Access to the European PubMed Central database of papers and metadata cran github
rhindawi R interface to the Hindawi Journals metadata and corpus. No further development - See package fulltext for full text data access. 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 development cran github
rorcid A programmatic interface the Orcid.org API In early development cran github
rpensoft Access to Pensoft journals full text and metadata. No further development - See package fulltext for full text data access. cran github
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
rspringer Full-text access to Springer journals. Development pending upcoming API changes. cran github
Package Description Details
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
Citeulike R interface to CiteULike. Not in active development. cran github
rAltmetric Programmatic interface to article-level metrics data from Altmetric.com cran github
rImpactStory Programmatic interface to ImpactStory Package deprecated. cran github
Package Description Details
gistr gistr is a light interface to GitHub's gists for R. cran github
git2r Git bindings from R cran github
testdat A test suite to ensure that tabular data are correctly formatted. 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.