dataone: R Interface to the DataONE REST API

Provides read and write access to data and metadata from the DataONE network <https://www.dataone.org> of data repositories. Each DataONE repository implements a consistent repository application programming interface. Users call methods in R to access these remote repository functions, such as methods to query the metadata catalog, get access to metadata for particular data packages, and read the data objects from the data repository. Users can also insert and update data objects on repositories that support these methods.

AuthorMatthew B. Jones [aut, cre], Peter Slaughter [aut], Rob Nahf [aut], Carl Boettiger [aut], Chris Jones [aut], Jordan Read [aut], Lauren Walker [aut], Edmund Hart [aut], Scott Chamberlain [aut], Regents of the University of California [cph]
Date of publication2016-08-30 01:33:34
MaintainerMatthew B. Jones <jones@nceas.ucsb.edu>
LicenseApache License 2.0
Version2.0.1
https://github.com/DataONEorg/rdataone

View on CRAN

Man pages

AbstractTableDescriber-class: Base Class for Specific Metadata Parsers

addData: Add a D1Object containing a data object to a DataPackage

archive: Archive an object on a Member Node or Coordinating Node,...

asDataFrame: return the D1Object data as a data.frame.

auth_delete: DELETE a resource with authenticated credentials.

AuthenticationManager: Create an AuthenticationManager object

AuthenticationManager-class: Manage DataONE authentication.

auth_get: GET a resource with authenticated credentials if available.

auth_head: Send a http HEAD request for a resource with authenticated...

auth_post: POST a resource with authenticated credentials.

auth_put: PUT a resource with authenticated credentials.

auth_put_post_delete: POST, PUT, or DELETE a resource with authenticated...

canRead: Test whether the provided subject can read an object.

CertificateManager: Create a CertificateManager object

CertificateManager-class: CertficateManager provides mechanisms to obtain, load,...

CNode: Create a CNode object.

CNode-class: Provides R API to DataONE Coordinating Node services.

convert.csv: Convert a DataFrame to Standard CSV.

createD1Object: Create the Object in the DataONE System

createDataPackage: Create a DataPackage on a DataONE Member Node

createObject: Create an object on a Member Node.

D1Client: The DataONE client class used to downlaod, update and search...

D1Client-class: The D1Client class contains methods that perform high level...

D1Client-initialize: Initialize a D1Client object

d1_errors: This function parses a DataONE service response message for...

d1IdentifierSearch: Query the DataONE Solr endpoint of the Coordinating Node.

D1Node: Create a D1Node object.

D1Node-class: A base class for CNode and MNode.

D1Node-initialize: Initialize a D1Node

D1Object: Create a D1Object instance.

D1Object-class: D1Object (Deprecated) is a representation of a DataObject.

D1Object-initialize: Initialize a D1Object

d1SolrQuery: A method to query the DataONE solr endpoint of the...

data.characterEncoding: CharacterEncoding

data.formatFamily: Data Format

dataone: Search, download and upload data to the DataONE network.

dataone-defunct: Defunct

dataone-deprecated: Deprecated Classes, Methods

data.tableAttributeNames: returns the attribute names

data.tableAttributeOrientation: The Attribute (Header) Orientation

data.tableAttributeStorageTypes: returns the attributes' data storage types

data.tableAttributeTypes: returns the attributes' data types

data.tableFieldDelimiter: Field Delimiter

data.tableMissingValueCodes: returns missing value codes

data.tableQuoteCharacter: Quote Character

data.tableSkipLinesHeader: Number of lines to skip before reading data

describeObject: Efficiently get systemmetadat for an object.

documented.d1Identifiers: Get DataONE identifiers

documented.entityNames: Get the entity names associated with each table

documented.sizes: Get the sizes of the described data tables.

downloadCert: Open the CILogon Certificate download page in the default...

echoCredentials: Echo the credentials used to make the call.

EMLParser: Construct an EML parser object.

EMLParser-class: Handler for Parsing Table Format Details from Metadata

encodeSolr: Encode the input for Solr Queries

encodeUrlPath: Encode the Input for a URL Path Segment.

encodeUrlQuery: Encode the Input for a URL Query Segment.

evaluateAuth: Evaluate DataONE authentication.

generateIdentifier: Get a unique identifier that is generated by the Member Node...

getAuthExpires: Get the expiration date of the current authentication method.

getAuthMethod: Get the current valid authentication mechanism.

getAuthSubject: Get the authentication subject.

getCapabilities: Get the node capabilities description, and store the...

getCert: Get the DataONE X.509 Certificate location.

getCertExpires: Show the date and time when an X.509 certificate expires.

getCertInfo: Get X.509 Certificate information

getCertLocation: Get the file path on disk of the client certificate file.

getChecksum: Get the checksum for the data object associated with the...

getCN: Get the coordinating node associated with this D1Client...

getD1Object: Download a data object from the DataONE Federation.

getData: Get the data content of a D1Object.

getDataObject: Download a data object from the DataONE Federation as a...

getEndpoint: Return the URL endpoint for the DataONE Coordinating Node.

getErrorDescription: Extract an error message from an http response.

getFormat: Get information for a single DataONE object format

getFormatId: Get the FormatId of the D1Object

getIdentifier: Get the Identifier of the D1Object

getMN: Get a member node client based on its node identifier.

getMNode: Get a reference to a node based on its identifier

getMNodeId: Get the member node identifier associated with this D1Client...

getObject: Get the bytes associated with an object on this Node.

getPackage: Download a data package from a member node.

getQueryEngineDescription: Query a node for the list of query engines available on the...

getSystemMetadata: Get the metadata describing system properties associated with...

getToken: Get the value of the DataONE Authentication Token, if one...

getTokenInfo: Get authentication token information

get_user_agent: User agent string

hasReservation: Checks to determine if the supplied subject is the owner of...

isAuthExpired: Check if the currently valid authentication method has...

isAuthorized: Check if an action is authorized for the specified identifier

isAuthValid: Verify authentication for a member node.

isCertExpired: Determine if an X.509 certificate has expired.

listFormats: List all object formats registered in DataONE.

listMemberNodes: List DataONE Member Nodes.

listNodes: Get the list of nodes associated with a CN

listObjects: Retrieve the list of objects that match the search parameters

listQueryEngines: Query a node for the list of query engines available on the...

MNode: Create a MNode object representing a DataONE Member Node...

MNode-class: Provides R API to DataONE Member Node services.

obscureAuth: Temporarity disable DataONE authentication.

obscureCert: Obscure the CILogon Client Certificate

parseCapabilities: Construct a Node, using a passed in capabilities XML

parseSolrResult: Parse Solr output into an R list

ping: Test if a node is online and accepting DataONE requests

query: Search DataONE for data and metadata objects

reserveIdentifier: Reserve a identifier that is unique in the DataONE network.

resolve: Get a list of coordinating nodes holding a given pid.

restoreAuth: Restore authentication (after being disabled with...

restoreCert: Restore the CILogon client certificate by renaming it to its...

setMNodeId: Set the member node identifier to be associated with the...

setObsoletedBy: Set a pid as being obsoleted by another pid

setPublicAccess: Make the object publicly readable.

showAuth: Display all authentication information

showClientSubject: Get DataONE Identity as Stored in the CILogon Certificate.

updateObject: Update an object on a Member Node, by creating a new object...

updateSystemMetadata: Update the system metadata associated with an object.

uploadDataObject: Upload a DataObject to a DataONE member node.

uploadDataPackage: Upload a DataPackage to a DataONE member node.

Files in this package

dataone
dataone/inst
dataone/inst/testfiles
dataone/inst/testfiles/testDataTableParamsDoc-eml-2.1.0.xml
dataone/inst/testfiles/testdoc-eml-2.1.0.xml
dataone/inst/testfiles/sysmeta.xml
dataone/inst/CITATION
dataone/inst/COPYRIGHTS
dataone/inst/extdata
dataone/inst/extdata/sample.csv
dataone/inst/extdata/sample2-eml.xml
dataone/inst/extdata/sample-eml.xml
dataone/inst/doc
dataone/inst/doc/upload-data.R
dataone/inst/doc/download-data.html
dataone/inst/doc/dataone-overview.R
dataone/inst/doc/download-data.Rmd
dataone/inst/doc/dataone-overview.Rmd
dataone/inst/doc/upload-data.Rmd
dataone/inst/doc/upload-data.html
dataone/inst/doc/searching-dataone.Rmd
dataone/inst/doc/searching-dataone.R
dataone/inst/doc/dataone-overview.html
dataone/inst/doc/download-data.R
dataone/inst/doc/searching-dataone.html
dataone/tests
dataone/tests/testthat.R
dataone/tests/testthat
dataone/tests/testthat/test.EMLParser.R
dataone/tests/testthat/test.CertificateManager.R
dataone/tests/testthat/test.CNode.R
dataone/tests/testthat/test.SystemMetadata.R
dataone/tests/testthat/test.MNode.R
dataone/tests/testthat/test.D1Node.R
dataone/tests/testthat/test.AuthenticationManager.R
dataone/tests/testthat/test.auth_request.R
dataone/tests/testthat/test.D1Client.R
dataone/NAMESPACE
dataone/NEWS
dataone/R
dataone/R/CertificateManager.R dataone/R/AuthenticationManager.R dataone/R/auth_request.R dataone/R/MNode.R dataone/R/D1Node.R dataone/R/D1Client.R dataone/R/yyy.R dataone/R/dataone-package.R dataone/R/AbstractTableDescriber.R dataone/R/CNode.R dataone/R/zzz.R dataone/R/EMLParser.R dataone/R/D1Object.R
dataone/vignettes
dataone/vignettes/download-data.Rmd
dataone/vignettes/dataone-overview.Rmd
dataone/vignettes/upload-data.Rmd
dataone/vignettes/download-data_cache
dataone/vignettes/download-data_cache/html
dataone/vignettes/download-data_cache/html/unnamed-chunk-1_66a44dbe59f3fccda904f2c815fa2b24.rdb
dataone/vignettes/download-data_cache/html/unnamed-chunk-4_6439e2b9d4d7521f258abc450d547191.rdx
dataone/vignettes/download-data_cache/html/unnamed-chunk-5_c8b332f84be48fca34735139557c38ce.rdx
dataone/vignettes/download-data_cache/html/unnamed-chunk-1_66a44dbe59f3fccda904f2c815fa2b24.RData
dataone/vignettes/download-data_cache/html/__objects
dataone/vignettes/download-data_cache/html/__globals
dataone/vignettes/download-data_cache/html/unnamed-chunk-5_c8b332f84be48fca34735139557c38ce.rdb
dataone/vignettes/download-data_cache/html/unnamed-chunk-8_dc0766765f366a50fc944b2895757c23.RData
dataone/vignettes/download-data_cache/html/unnamed-chunk-10_2a43bb4137744c85d8bcb71e1ec23e32.RData
dataone/vignettes/download-data_cache/html/unnamed-chunk-2_b38fcbdcd904f039400b66c434f6f425.rdx
dataone/vignettes/download-data_cache/html/unnamed-chunk-10_2a43bb4137744c85d8bcb71e1ec23e32.rdb
dataone/vignettes/download-data_cache/html/__packages
dataone/vignettes/download-data_cache/html/unnamed-chunk-9_b0f9807bcb598084fc89bf192813fd0e.rdx
dataone/vignettes/download-data_cache/html/unnamed-chunk-7_ffe7157c1fb3492156e7a88f0ec42d58.RData
dataone/vignettes/download-data_cache/html/unnamed-chunk-5_c8b332f84be48fca34735139557c38ce.RData
dataone/vignettes/download-data_cache/html/unnamed-chunk-6_d9b012bf8434434f29da4582a8cfdb24.RData
dataone/vignettes/download-data_cache/html/unnamed-chunk-4_6439e2b9d4d7521f258abc450d547191.rdb
dataone/vignettes/download-data_cache/html/unnamed-chunk-10_2a43bb4137744c85d8bcb71e1ec23e32.rdx
dataone/vignettes/download-data_cache/html/unnamed-chunk-6_d9b012bf8434434f29da4582a8cfdb24.rdb
dataone/vignettes/download-data_cache/html/unnamed-chunk-3_9c74fc00ea9a0aee169317f5541c6572.rdb
dataone/vignettes/download-data_cache/html/unnamed-chunk-7_ffe7157c1fb3492156e7a88f0ec42d58.rdb
dataone/vignettes/download-data_cache/html/unnamed-chunk-3_9c74fc00ea9a0aee169317f5541c6572.RData
dataone/vignettes/download-data_cache/html/unnamed-chunk-2_b38fcbdcd904f039400b66c434f6f425.RData
dataone/vignettes/download-data_cache/html/unnamed-chunk-3_9c74fc00ea9a0aee169317f5541c6572.rdx
dataone/vignettes/download-data_cache/html/unnamed-chunk-8_dc0766765f366a50fc944b2895757c23.rdx
dataone/vignettes/download-data_cache/html/unnamed-chunk-4_6439e2b9d4d7521f258abc450d547191.RData
dataone/vignettes/download-data_cache/html/unnamed-chunk-6_d9b012bf8434434f29da4582a8cfdb24.rdx
dataone/vignettes/download-data_cache/html/unnamed-chunk-2_b38fcbdcd904f039400b66c434f6f425.rdb
dataone/vignettes/download-data_cache/html/unnamed-chunk-9_b0f9807bcb598084fc89bf192813fd0e.rdb
dataone/vignettes/download-data_cache/html/unnamed-chunk-7_ffe7157c1fb3492156e7a88f0ec42d58.rdx
dataone/vignettes/download-data_cache/html/unnamed-chunk-8_dc0766765f366a50fc944b2895757c23.rdb
dataone/vignettes/download-data_cache/html/unnamed-chunk-1_66a44dbe59f3fccda904f2c815fa2b24.rdx
dataone/vignettes/download-data_cache/html/unnamed-chunk-9_b0f9807bcb598084fc89bf192813fd0e.RData
dataone/vignettes/searching-dataone.Rmd
dataone/README.md
dataone/MD5
dataone/build
dataone/build/vignette.rds
dataone/DESCRIPTION
dataone/man
dataone/man/CNode-class.Rd dataone/man/createD1Object.Rd dataone/man/dataone.Rd dataone/man/listMemberNodes.Rd dataone/man/data.tableMissingValueCodes.Rd dataone/man/data.tableQuoteCharacter.Rd dataone/man/encodeUrlQuery.Rd dataone/man/convert.csv.Rd dataone/man/listObjects.Rd dataone/man/listFormats.Rd dataone/man/getFormatId.Rd dataone/man/getMNode.Rd dataone/man/get_user_agent.Rd dataone/man/MNode-class.Rd dataone/man/getDataObject.Rd dataone/man/getToken.Rd dataone/man/getCN.Rd dataone/man/asDataFrame.Rd dataone/man/data.tableAttributeNames.Rd dataone/man/data.characterEncoding.Rd dataone/man/data.tableAttributeOrientation.Rd dataone/man/listQueryEngines.Rd dataone/man/data.formatFamily.Rd dataone/man/auth_post.Rd dataone/man/updateSystemMetadata.Rd dataone/man/encodeUrlPath.Rd dataone/man/getCapabilities.Rd dataone/man/evaluateAuth.Rd dataone/man/createDataPackage.Rd dataone/man/describeObject.Rd dataone/man/obscureCert.Rd dataone/man/CNode.Rd dataone/man/isCertExpired.Rd dataone/man/showAuth.Rd dataone/man/CertificateManager.Rd dataone/man/auth_get.Rd dataone/man/createObject.Rd dataone/man/downloadCert.Rd dataone/man/getIdentifier.Rd dataone/man/getCertInfo.Rd dataone/man/setObsoletedBy.Rd dataone/man/isAuthExpired.Rd dataone/man/CertificateManager-class.Rd dataone/man/parseSolrResult.Rd dataone/man/getEndpoint.Rd dataone/man/reserveIdentifier.Rd dataone/man/getChecksum.Rd dataone/man/D1Client-class.Rd dataone/man/auth_put_post_delete.Rd dataone/man/D1Object.Rd dataone/man/data.tableFieldDelimiter.Rd dataone/man/getQueryEngineDescription.Rd dataone/man/D1Client.Rd dataone/man/encodeSolr.Rd dataone/man/getCertLocation.Rd dataone/man/D1Client-initialize.Rd dataone/man/data.tableSkipLinesHeader.Rd dataone/man/showClientSubject.Rd dataone/man/setMNodeId.Rd dataone/man/documented.sizes.Rd dataone/man/getSystemMetadata.Rd dataone/man/D1Node-initialize.Rd dataone/man/uploadDataPackage.Rd dataone/man/data.tableAttributeTypes.Rd dataone/man/isAuthValid.Rd dataone/man/getTokenInfo.Rd dataone/man/parseCapabilities.Rd dataone/man/auth_head.Rd dataone/man/setPublicAccess.Rd dataone/man/restoreAuth.Rd dataone/man/isAuthorized.Rd dataone/man/MNode.Rd dataone/man/D1Node-class.Rd dataone/man/listNodes.Rd dataone/man/auth_put.Rd dataone/man/documented.d1Identifiers.Rd dataone/man/d1SolrQuery.Rd dataone/man/EMLParser-class.Rd dataone/man/archive.Rd dataone/man/resolve.Rd dataone/man/generateIdentifier.Rd dataone/man/getErrorDescription.Rd dataone/man/D1Node.Rd dataone/man/getCertExpires.Rd dataone/man/query.Rd dataone/man/AuthenticationManager.Rd dataone/man/updateObject.Rd dataone/man/getAuthExpires.Rd dataone/man/echoCredentials.Rd dataone/man/d1IdentifierSearch.Rd dataone/man/dataone-deprecated.Rd dataone/man/getAuthSubject.Rd dataone/man/getCert.Rd dataone/man/getMN.Rd dataone/man/uploadDataObject.Rd dataone/man/canRead.Rd dataone/man/hasReservation.Rd dataone/man/EMLParser.Rd dataone/man/getD1Object.Rd dataone/man/d1_errors.Rd dataone/man/addData.Rd dataone/man/AuthenticationManager-class.Rd dataone/man/D1Object-class.Rd dataone/man/data.tableAttributeStorageTypes.Rd dataone/man/documented.entityNames.Rd dataone/man/getPackage.Rd dataone/man/dataone-defunct.Rd dataone/man/getData.Rd dataone/man/auth_delete.Rd dataone/man/getMNodeId.Rd dataone/man/getFormat.Rd dataone/man/D1Object-initialize.Rd dataone/man/getAuthMethod.Rd dataone/man/ping.Rd dataone/man/restoreCert.Rd dataone/man/obscureAuth.Rd dataone/man/AbstractTableDescriber-class.Rd dataone/man/getObject.Rd

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