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, focus on scalable and reproducibile computing, data visualization, data tools, image processing, taxonomy, HTTP tools, data analysis or geospatial work. Packages with a cran, or bioc 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, and our GitHub organization for bleeding edge projects. All of our software packages are open source. Please see package description files for more information on specific licenses.
Many of our packages are community-contributed. If you are interested in contributing a package, please visit our onboarding repository for details.
Data Publication Packages that not only retrieve data but also allows for data submission.
| Package | Description | Details |
|---|---|---|
| dataone | Search across repositories, and read and write data and metadata from the DataONE federation of data repositories from R. Includes over 30 data repositories such as the KNB and Dryad. | cran github |
| datapack | A flexible container to transport and manipulate data and associated resources | 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 |
| biomartr | Genomic Data Retrieval from NCBI and ENSEMBL databases | cran github |
| bittrex | Client for the Bitrex Exchange | cran github |
| bold | R client for BOLD Systems (Barcode Of Life Database). | cran github |
| brranching | Fetching phylogenies from a variety of sources, currently includes Phylomatic | cran github |
| camsRad | R client for CAMS radiation service - providing time series of global, direct, and diffuse irradiations on horizontal surface, and direct irradiation on normal plane for the actual weather conditions as well as for clear-sky conditions | cran github |
| ccafs | R Client for downscaled CCAFS GCM data | crangithub |
| ckanr | R client for CKAN RESTful API | cran github |
| chromer | Interact with the chromosome counts database (CCDB) at http://ccdb.tau.ac.il | cran github |
| clifro | An R client for New Zealand's National Climate Database | cran github |
| dbhydroR | R interface to the South Florida Water Management District's DBHYDRO Database | cran github |
| ecoengine | Retrieve 3+ MM records, checklists and photos from Berkeley's ecoengine | cran github |
| eechidna | Data from the 2013 Australian Federal Election (House of Representatives) and the 2011 Australian Census | cran github |
| gender | gender is an R package to encode gender based on names and dates of birth | cran github |
| GSODR | NOAA Global Summary Daily Weather Data | cran github |
| gtfsr | Obtain, validate, view, and store GTFS (transit) data. | cran github |
| gutenbergr | Download and process public domain works in the Project Gutenberg collection | cran github |
| hddtools | Hydrological Data Discovery Tools | cran github |
| helminthR | Access parasite occurrences from the London Natural History Museum's Host-Parasite database, which contains over a quarter-million helminth records | 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 | cran github |
| hoasts | Gather data from occurrence databases that have information on hosts/parasites In early development | cran github |
| internetarchive | This API client for the Internet Archive is intended primarily for searching for items, retrieving metadata for items, and downloading the files associated with the items. | cran github |
| isdparser | Parse NOAA Integrated Surface Data files (see also rnoaa) | cran github |
| laselva | Client for working with Forest Inventory and Analysis (FIA) data In early development | cran github |
| mregions | Tools to get marine regions data from Marineregions. | 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 |
| natserv | Interface to NatureServe | cran github |
| neotoma | Search for sites and download data for use in analytical workflows of paleoecological research using the Neotoma Paleoecological Database | cran github |
| nneo | Client for the National Ecological Observatory Network (NEON) API | cran github |
| patentsview | Provides functions to simplify the PatentsView API http://www.patentsview.org/api/doc.html query language | 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. | cran github |
| mapr | Functions for making maps with species occurrence data, taking inputs from spocc, rgbif, and dismo, and more | cran github |
| originr | Get species origin data (whether species is native/invasive) from many sources on the web | cran github |
| pleiades | Search for and retrieve metadata and spatial location data on archeological places and names from Pleiades | cran github |
| rAvis | Download occurrence data for bird species, and associated metadata from ProyectoAvis, a citizen science bird project in Spain. | cran github |
| rbison | R client for USGS's BISON (Biodiversity Information Serving Our Nation). | cran github |
| rdataretriever | R interface to Dataretriever. | cran github |
| rdefra | Interact with the UK AIR pollution database from DEFRA | cran github |
| rdpla | An R client to interact with Digital Public Library of America (DPLA) metadata. | cran github |
| rdryad | Get data from Dryad a repository of data associated with published scholarly papers. | 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. | 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 | cran github |
| riem | Weather data from Automated Surface Observing System (ASOS) stations (airports) globally via the Iowa Environment Mesonet | cran github |
| rif | R client for Neuroscience Information Network | cran github |
| rinat | A programmatic interface to the API provided by iNaturalist. | cran github |
| rnoaa | Access climate data from NOAA, including temperature and precipitation, as well as sea ice cover data, and extreme weather events (see also isdparser) | cran github |
| rnpn | Access phenological data from US National Phenology Network for plants and animals | cran github |
| ropenaq | Access to air quality data from the API of the OpenAQ platform | cran github |
| rotl | Interact with the Open Tree of Life data APIs | cran github |
| rredlist | Interact with the IUCN Red List API | 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 |
| rtimicropem | Supports the Analysis of RTI MicroPEM Output Files | cran github |
| rusda | Interface to some USDA databases | 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 |
| seaaroundus | R bindings for Seaaroundus API | cran github |
| spocc | Collect and map species occurrence data from GBIF, iDigBio, iNaturalist, Ecoengine, AntWeb, eBird, and USGS's BISON. | cran github |
| stplanr | Functionality and data access tools for transport planning, including origin-destination analysis, route allocation and modelling travel patterns | cran github |
| traits | A high level R package to acquire species trait data from many sources, including Polytraits, BETTYdb, NCBI, Phylomatic, and more. | 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 |
| webchem | webchem is a R package to retrieve chemical information from many sources. Currently includes: Chemical Identifier Resolver, ChemSpider, PubChem, and Chemical Translation Service. | cran github |
Literature Packages that interface with journal full-text or metadata
| Package | Description | Details |
|---|---|---|
| antiword | Extract text from Microsoft Word documents using the antiword C library | cran github |
| aRxiv | Access to the aRxiv preprint repository | cran github |
| cld2 | Bindings to Google's Compact Language Detector 2 | cran github |
| cld3 | Bindings to Google's Compact Language Detector 3 | cran github |
| rcoreoa | CORE (core.ac.uk) API R Client In early development | cran github |
| crminer | Client for doing text-mining using Crossref's APIs | cran github |
| europepmc | R Interface to the Europe PubMed Central RESTful Web Service | cran github |
| ezknitr | Avoid the Typical Working Directory Pain When Using knitr | 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. | cran github |
| IEEER | Interface to the IEEE Xplore Gateway. In early development | cran github |
| jaod | R client for the Directory of Open Access Journals API In early development | cran github |
| lingtypology | Linguistic Typology and Mapping | cran github |
| monkeylearn | Access to the Monkeylearn API for text classifiers and extractors | cran github |
| oai | Work with OAI-PMH (Open Archives Initiative Protocol for Metadata Harvesting) services, a protocol developed by the Open Archives Initiative. | cran github |
| pdftools | A fast and portable package to extract text and data from PDF documents using the Poppler C++ library. | cran github |
| rbace | BASE (Bielefeld Academic Search Engine) R client In early development | cran github |
| rbhl | Access full text and metadata on scanned and OCR text for biodiversity literature from Biodiversity Heritage Library | cran github |
| rcrossref | An R interface to Crossref metadata search API. | cran github |
| rdatacite | Wrapper to DataCite metadata. | cran github |
| refimpact | API Wrapper for the UK REF 2014 Impact Case Studies Database http://impact.ref.ac.uk/CaseStudies/ | cran github |
| roadoi | Find Free Versions of Scholarly Publications via the oaDOI Service | cran github |
| rorcid | A programmatic interface the Orcid.org API | 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 |
| scatr | Interact with the Scholastic Commentaries and Texts Archive | cran github |
| scitations | Citations client for R In early development | cran github |
| seasl | Explore CSL styles and locales. In early development | cran github |
| tabulizer | R bindings to the Tabula java library for computationally extracting tables from PDF documents | cran github |
| unrtf | Extract Text from Rich Text Format (RTF) Documents | cran github |
Altmetrics Packages that interface with raw and aggregate altmetrics data.
New to the idea of Altmetrics? Digging into altmetrics and the original manifesto are good primers.
| Package | Description | Details |
|---|---|---|
| rAltmetric | Programmatic interface to article-level metrics data from Altmetric.com | cran github |
Scalable & Reproducible Computing Packages that support scalable and/or reproducibile computing.
| Package | Description | Details |
|---|---|---|
| assertr | Assertive Programming for R Analysis Pipelines | cran github |
| gistr | gistr is a light interface to GitHub's gists for R. |
cran github |
| git2r | Git bindings from R | cran github |
| RefManageR | Straightforward BibTeX and BibLaTeX Bibliography Management | cran github |
| rzmq | Interface to the ZeroMQ lightweight messaging kernel zeromq.org | cran github |
| textreuse | An R package to detect text reuse and document similarity in natural language corpora | cran github |
| tokenizers | Convert natural language text into tokens. The tokenizers have a consistent interface and are compatible with Unicode, thanks to being built on the 'stringi' package. Includes tokenizers for shingled n-grams, skip n-grams, words, word stems, sentences, paragraphs, characters, lines, and regular expressions. | cran github |
Databases Packages for interfacing with databases.
| Package | Description | Details |
|---|---|---|
| elastic | An R client for Elasticsearch | cran github |
| elasticdsl | A DSL for Elasticsearch, built on top of elastic In early development | cran github |
| etseed | R client for etcd, a key-value store from the folks at CoreOS | cran github |
| nodbi | Provides a single UI for interacting with many NoSQL databases (including so far: MongoDB, Redis, CouchDB, Elasticsearch). In early development | cran github |
| rrlite | R bindings to rlite - a self-contained, serverless, zero-configuration, transactional redis-compatible database engine | cran github |
| sofa | Easy interface to CouchDB from R. | cran github |
| solrium | An R client for Apache Solr | cran github |
Data Visualization Packages primarily for data vizualization.
| 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 |
| cartographer | Cartographer provides interactive maps in R Markdown documents or at the R console. These maps are suitable for data exploration. It wraps Elijah Meeks's d3-carto-map. | cran github |
| iheatmapr | Interactive, Complex Heatmaps | cran github |
Image Processing Packages primarily for image processing.
| Package | Description | Details |
|---|---|---|
| tesseract | R bindings to the tesseract engine for optical character recognition (OCR) | cran github |
| magick | Bindings to ImageMagick: the most comprehensive open-source image processing library available. | cran github |
Data Tools Packages for manipulating data.
| Package | Description | Details |
|---|---|---|
| charlatan | Make many kinds of fake data, including entire datasets. | cran github |
| convertr | Conversion functionality between a broad range of scientific, historical, and industrial unit types. | cran github |
| crul | An HTTP client for R | cran github |
| finch | Read Darwin Core Archive files. | cran github |
| genbankr | Parse GenBank files into semantically useful objects. | bioc github |
| graphql | Bindings to libgraphqlparser - A GraphQL query parser in C++ | cran github |
| hoardr | Manage cached files | cran github |
| hunspell | High-Performance Stemmer, Tokenizer, and Spell Checker for R | cran github |
| jqr | R interface to jq, a JSON processor | cran github |
| jsonld | R client for JSON-LD, a light-weight syntax for expressing linked data | cran github |
| jsonvalidate | Uses the node library is-my-json-valid to validate JSON against a JSON schema. | cran github |
| plater | Tools for interacting with data from experiments done in microtiter plates. Easily read in plate-shaped data and convert it to tidy format, combine plate-shaped data with tidy data, and view tidy data in plate shape | cran github |
| robotstxt | A robots.txt parser and webbot/spider/crawler permissions checker | cran github |
| scrubr | Clean biological occurrence records | cran github |
Taxonomy Packages for handling taxonomic names.
| Package | Description | Details |
|---|---|---|
| binomen | Taxonomic classes and functions for working with taxonomic data, combining, separating, and filtering taxonomic groups by rank/name. | cran github |
| ritis | An interface to the Integrated Taxonomic Information System (ITIS). | cran github |
| taxa | Taxonomic classes for R | 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 |
| taxizedb | Tools for Working with Taxonomic SQL Databases | cran github |
| wikitaxa | Taxonomy data from Wikipedia/Wikidata/Wikispecies | cran github |
| worrms | World Register of Marine Species R client | cran github |
HTTP Tools Utilities for working with the web.
Data Analysis Utilities for doing data analysis.
Geospatial Spatial data I/O and mapping.
| Package | Description | Details |
|---|---|---|
| getlandsat | Get Landsat 8 Data from Amazon Public Data Sets. | cran github |
| geoaxe | Chop up polygons into pieces | cran github |
| geofilter | Filter GeoJSON without heavy C libraries - but using jqr | cran github |
| geojson | Classes for GeoJSON to make working with GeoJSON easier. | cran github |
| geojsonio | A package to convert many data formats to geoJSON or Bostock's topoJSON |
cran github |
| geojsonlint | Tools for linting GeoJSON, including for interacting with the online tool geojsonlint.com, the JS library geojsonhint, and validating against a GeoJSON schema via the JS library is-my-json-valid. |
cran github |
| geojsonrewind | Port of the JS library geojson-rewind for changing winding direction of GeoJSON poloygons |
cran github |
| geonames | Grab data from the GeoNames geographical database which covers all countries and contains over eight million placenames | cran github |
| geoops | GeoJSON Manipulation Operations. | cran github |
| geoparser | Interface to the Geoparser.io API for Identifying and Disambiguating Places Mentioned in Text | cran github |
| lawn | An R client for turf.js, a Javascript library for advanced geospatial analysis | cran github |
| opencage | Tool for accessing the OpenCage API, which provides forward and reverse geocoding | cran github |
| osmdata | Import 'OpenStreetMap' Data as Simple Features or Spatial Objects | cran github |
| osmplotr | Customisable images of OpenStreetMap (OSM) data and data visualisation using OSM objects | cran github |
| proj | An R client for proj4js, a Javascript library for transforming coordinates from one coordinate system to another, including datum transformations | cran github |
| randgeo | Generate random positions (latitude/longitude), Well-known text (WKT) points or polygons, or GeoJSON points or polygons. | cran github |
| rnaturalearth | Tools to obtain natural earth map data from naturalearthdata.com. | cran github |
| wellknown | Convert WKT to GeoJSON and vice versa. Inspired by Python's geomet. | cran github |
| wicket | Fast utilities to handle WKT (Well-Known Text) spatial data | 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 or the open data task view for related packages that might suit your needs, or post to our discussion forum.