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 | Data Access | Literature | Altmetrics | Scalable & Reproducible Computing | Databases | Data Vizualization | Image Processing | Data Tools | Taxonomy | HTTP tools | Geospatial | Data Analysis
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
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 CCAFS GCM Data R Client cran github
ckanr R client for CKAN RESTful API cran github
chromer Interact with the chromosome counts database (CCDB) at 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
ecoretriever R client wrapping the Python Ecoretriever software. 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
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
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
helminthR Access parasite occurrences from the London Natural History Museum's Host-Parasite database, which contains over a quarter-million helminth records 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. 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
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 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, including occurrence records, habitat data, and more cran github
rfisheries Search and retrieve data from the, 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 In early development 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
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
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
RStars Access to the Digital Universe Data set at 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
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
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
crminer Client for doing text-mining using Crossref's APIs In early development cran github
seasl Explore CSL styles and locales. In early development 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
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
rorcid A programmatic interface the 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
tabulizer R bindings to the Tabula java library for computationally extracting tables from PDF documents 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
rAltmetric Programmatic interface to article-level metrics data from cran github
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
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
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
sofa Easy interface to CouchDB from R. cran github
solrium An R client for Apache Solr cran github
Package Description Details
plotly Programmatic interface to the API - construct plots with ggplot2 and push to 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
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
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
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
vcr Record HTTP calls and replay them cran github
webmockr webmock Ruby port for R cran github
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
Package Description Details
fauxpas Flexible HTTP error classes for R cran github
crul An HTTP client for R cran github
rjsonapi Consumer for APIs that Follow the JSON API Specification cran github
vcr Record HTTP calls and replay them cran github
webmockr webmock Ruby port for R cran github
Package Description Details
phylocomr Self-contained interface to Phylocom for analysis of phylogenetic community structure and character evolution cran github
Package Description Details
getlandsat Get Landsat 8 Data from Amazon Pulic 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, 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 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
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
rgeospatialquality Provides native wrappers for the functions available via the spatial quality REST API. cran github
rnaturalearth Tools to obtain natural earth map data from 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

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