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0.9.3","direct":true,"kind":"suggests","optional":false},{"id":2787677248,"package_name":"xml2","ecosystem":"cran","requirements":"*","direct":true,"kind":"suggests","optional":false}]}],"score":20.21268788250784,"created_at":"2023-10-04T00:09:07.803Z","updated_at":"2026-04-19T08:30:42.317Z","avatar_url":"https://github.com/DataONEorg.png","language":"R","category":"Sustainable Development","sub_category":"Data Catalogs and Interfaces","monthly_downloads":1787,"total_dependent_repos":31,"total_dependent_packages":2,"readme":"# dataone: R interface to the DataONE network of data repositories\n[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/dataone)](https://cran.r-project.org/package=dataone)\n  [![R-CMD-check](https://github.com/DataONEorg/rdataone/workflows/R-CMD-check/badge.svg)](https://github.com/DataONEorg/rdataone/actions)\n\n- **Authors**: Matthew B. Jones ([NCEAS](https://www.nceas.ucsb.edu)), Peter Slaughter, Rob Nahf, Carl Boettiger, Chris Jones, Jordan Read, Lauren Walker, Edmund Hart, Scott Chamberlain\n- [doi:10.5063/F1M61H5X](https://doi.org/10.5063/F1M61H5X)\n- **License**: [Apache 2](https://opensource.org/licenses/Apache-2.0)\n- [Package source code on Github](https://github.com/DataONEorg/rdataone)\n- [**Submit Bugs and feature requests**](https://github.com/DataONEorg/rdataone/issues)\n\nProvides read and write access to data and metadata from the [DataONE network \n    of data repositories](https://www.dataone.org/current-member-nodes), including the\n    [KNB Data Repository](https://knb.ecoinformatics.org), [Dryad](https://datadryad.org/stash),\n    and the NSF [Arctic Data Center](https://arcticdata.io).\n    Each DataONE repository implements a consistent repository application \n    programming interface. Users call methods in R to access these remote \n    repository functions, such as methods to query the metadata catalog, get \n    access to metadata for particular data packages, and read the data objects \n    from the data repository using the global identifier for each data object. \n    Users can also insert and update data objects on repositories that support \n    these methods. For more details, see the vignettes.\n\n## Installation Notes \n\nVersion 2.0 of the *dataone* R package removes the dependency on rJava and significantly changes the base \nAPI to correspond to the published [DataONE API](https://purl.dataone.org/architecture/apis/index.html).  Previous methods for accessing DataONE will be maintained, but new methods have been added. \n\nThe *dataone* R package requires the R package *redland*. If you are installing on Ubuntu then the Redland C libraries\nmust be installed first. If you are installing on Mac OS X or Windows then installing these libraries is not required.\n\n### Installing on Mac OS X\n\nOn Mac OS X dataone can be installed with the following commands:\n\n```\ninstall.packages(\"dataone\")\nlibrary(dataone)\n```\n\nThe *dataone* R package should be available for use at this point.\n\n### Installing on Ubuntu\n\nFor ubuntu, install the required Redland C libraries by entering the following commands \nin a terminal window:\n\n```\nsudo apt-get update\nsudo apt-get install librdf0 librdf0-dev\n```\n\nThen install the R packages from the R console:\n\n```\ninstall.packages(\"dataone\")\nlibrary(dataone)\n```\n\nThe *dataone* R package should be available for use at this point\n\n### Installing on Windows\n\nFor windows, the required *redland* R package is distributed as a binary release, so it is not\nnecessary to install any additional system libraries.\n\nTo install the *dataone* R packages from the R console:\n\n```\ninstall.packages(\"dataone\")\nlibrary(dataone)\n```\n\nThe *dataone* R package should be available for use at this point.\n\n## Quick Start\n\nSee the full manual (`help(dataone)`) for documentation.\n\nTo search the DataONE Federation Member Node *Knowledge Network for Biocomplexity (KNB)* for a dataset:\n\n```\nlibrary(dataone)\ncn \u003c- CNode(\"PROD\")\nmn \u003c- getMNode(cn, \"urn:node:KNB\")\nmySearchTerms \u003c- list(q=\"abstract:salmon+AND+keywords:spawn+AND+keywords:chinook\",\n                      fl=\"id,title,dateUploaded,abstract,size\",\n                      fq=\"dateUploaded:[2017-06-01T00:00:00.000Z TO 2017-07-01T00:00:00.000Z]\",\n                      sort=\"dateUploaded+desc\")\nresult \u003c- query(mn, solrQuery=mySearchTerms, as=\"data.frame\")\nresult[1,c(\"id\", \"title\")]\nid \u003c- result[1,'id']\n```\n\nThe metadata file that describes the located research can be downloaded and viewed in an XML viewer, text \neditor after being written to disk, or in R via the commands below:\n```\nlibrary(XML)\nmetadata \u003c- rawToChar(getObject(mn, id))\ndoc \u003c- xmlRoot(xmlTreeParse(metadata, asText=TRUE, trim = TRUE, ignoreBlanks = TRUE))\ntf \u003c- tempfile()\nsaveXML(doc, tf)\nfile.show(tf)\n```\n\nThis metadata file describes a data file (CSV) in this data collection (package) that can be obtained using \nthe listed identifier, using the commands:\n\n```\ndataRaw \u003c- getObject(mn, \"urn:uuid:49d7a4bc-e4c9-4609-b9a7-9033faf575e0\")\ndataChar \u003c- rawToChar(dataRaw)\ntheData \u003c- textConnection(dataChar)\ndf \u003c- read.csv(theData, stringsAsFactors=FALSE)\ndf[1,]\n```\n\nUploading a CSV file to a DataONE Member Node requires user authentication. DataONE user\nauthentication is described in the vignette `dataone-federation`.\n\nOnce the authentication steps have been followed, uploading is done with:\n```\nlibrary(datapack)\nlibrary(uuid)\nd1c \u003c- D1Client(\"STAGING\", \"urn:node:mnStageUCSB2\")\nid \u003c- paste(\"urn:uuid:\", UUIDgenerate(), sep=\"\")\ntestdf \u003c- data.frame(x=1:10,y=11:20)\ncsvfile \u003c- paste(tempfile(), \".csv\", sep=\"\")\nwrite.csv(testdf, csvfile, row.names=FALSE)\n# Build a DataObject containing the csv, and upload it to the Member Node\nd1Object \u003c- new(\"DataObject\", id, format=\"text/csv\", filename=csvfile)\nuploadDataObject(d1c, d1Object, public=TRUE)\n```\n\nIn addition, a collection of science metadata and data can be downloaded with one\ncommand, for example:\n\n```\nd1c \u003c- D1Client(\"PROD\", \"urn:node:KNB\")\npkg \u003c- getDataPackage(d1c, id=\"urn:uuid:04cd34fd-25d4-447f-ab6e-73a572c5d383\", quiet=FALSE)\n```\nSee the R vignette [dataone R Package ](https://github.com/DataONEorg/rdataone/blob/master/vignettes/v01-dataone-overview.Rmd) for\nmore information.\n\n## Acknowledgments\nWork on this package was supported by:\n\n- NSF-ABI grant #[1262458](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1262458) to C. Gries, M. B. Jones, and S. Collins.\n- NSF-DATANET grants #[0830944](https://www.nsf.gov/awardsearch/showAward?AWD_ID=0830944) and #[1430508](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1430508) to W. Michener, M. B. Jones, D. Vieglais, S. Allard and P. Cruse\n- NSF DIBBS grant #[1443062](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1443062) to T. Habermann and M. B. Jones\n- NSF-PLR grant #[1546024](https://www.nsf.gov/awardsearch/showAward?AWD_ID=1546024) to M. B. Jones, S. Baker-Yeboah, J. Dozier, M. Schildhauer, and A. Budden\n- NSF-PLR grant #[2042102](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2042102) to M. B. Jones, A. Budden, J. Dozier, and M. Schildhauer\n\nAdditional support was provided for working group collaboration by the National Center for Ecological Analysis and Synthesis, a Center funded by the University of California, Santa Barbara, and the State of California.\n\n[![nceas_footer](https://live-ncea-ucsb-edu-v01.pantheonsite.io/sites/default/files/2020-03/NCEAS-full%20logo-4C.png)](https://www.nceas.ucsb.edu)\n\n[![dataone_footer](https://www.dataone.org/sites/all/images/DataONE_LOGO.jpg)](https://www.dataone.org)\n\n\n[![ropensci_footer](https://ropensci.org/public_images/github_footer.png)](https://ropensci.org)\n","funding_links":[],"readme_doi_urls":["https://doi.org/10.5063/F1M61H5X"],"works":{"https://doi.org/10.5063/F1M61H5X":null},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["ecology","eml","semantic-annotations","science-metadata","metadata-editor","metacat","knb","ecoinformatics","doi","dataone"],"project_url":"https://ost.ecosyste.ms/api/v1/projects/109661","html_url":"https://ost.ecosyste.ms/projects/109661"}