Package: dataone 2.2.2

Matthew B. Jones

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.

Authors:Matthew B. Jones [aut, cre], Peter Slaughter [aut], Rob Nahf [aut], Carl Boettiger [aut], Chris Jones [aut], Bryce Mecum [aut], Jeanette Clark [aut], Jordan Read [ctb], Lauren Walker [aut], Edmund Hart [ctb], Scott Chamberlain [ctb], Regents of the University of California [cph]

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dataone.pdf |dataone.html
dataone/json (API)
NEWS

# Install 'dataone' in R:
install.packages('dataone', repos = c('https://dataoneorg.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/dataoneorg/rdataone/issues

On CRAN:

9.93 score 36 stars 3 packages 468 scripts 453 downloads 86 exports 46 dependencies

Last updated 2 years agofrom:97ef173bce. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 27 2024
R-4.5-winNOTEOct 27 2024
R-4.5-linuxNOTEOct 27 2024
R-4.4-winNOTEOct 27 2024
R-4.4-macNOTEOct 27 2024
R-4.3-winOKOct 27 2024
R-4.3-macOKOct 27 2024

Exports:addDataarchiveasDataFrameAuthenticationManagercanReadCertificateManagerCNodeconvert.csvcreateD1ObjectcreateDataPackagecreateObjectD1Clientd1IdentifierSearchD1NodeD1Objectd1SolrQuerydata.characterEncodingdata.formatFamilydata.tableAttributeNamesdata.tableAttributeOrientationdata.tableAttributeStorageTypesdata.tableAttributeTypesdata.tableFieldDelimiterdata.tableMissingValueCodesdata.tableQuoteCharacterdata.tableSkipLinesHeaderdescribeObjectdocumented.d1Identifiersdocumented.entityNamesdocumented.sizesdownloadCertdownloadObjectechoCredentialsEMLParserencodeSolrencodeUrlPathencodeUrlQuerygenerateIdentifiergetCapabilitiesgetCertExpiresgetCertInfogetCertLocationgetChecksumgetCNgetD1ObjectgetDatagetDataObjectgetDataPackagegetEndpointgetFormatgetFormatIdgetIdentifiergetMetadataMembergetMNgetMNodegetMNodeIdgetObjectgetPackagegetQueryEngineDescriptiongetSystemMetadatagetTokenInfohasReservationinitializeisAuthorizedisCertExpiredlistFormatslistMemberNodeslistNodeslistObjectslistQueryEnginesMNodeobscureCertparseSolrResultpingqueryreserveIdentifierresolverestoreCertsetMNodeIdsetObsoletedBysetPublicAccessshowClientSubjectupdateObjectupdateSystemMetadatauploadDataObjectuploadDataPackage

Dependencies:askpassbase64encbrewcallrclicommonmarkcpp11curldatapackdescdigestevaluatefsgluehighrhttrjsonliteknitrlifecyclemagrittrmimeopensslparsedatepkgbuildpkgloadplyrprocessxpspurrrR6Rcppredlandrlangroxygen2rprojrootstringistringrsysuuidvctrswithrxfunXMLxml2yamlzip

DataONE Federation

Rendered fromv02-dataone-federation.Rmdusingknitr::rmarkdownon Oct 27 2024.

Last update: 2020-11-18
Started: 2020-06-24

dataone Package Overview

Rendered fromv01-dataone-overview.Rmdusingknitr::rmarkdownon Oct 27 2024.

Last update: 2020-11-18
Started: 2020-06-24

Downloading Data From DataONE

Rendered fromv04-download-data.Rmdusingknitr::rmarkdownon Oct 27 2024.

Last update: 2020-11-24
Started: 2020-06-24

Known Issues

Rendered fromv07-known-issues.Rmdusingknitr::rmarkdownon Oct 27 2024.

Last update: 2020-11-24
Started: 2020-06-24

Searching DataONE Data Holdings

Rendered fromv03-searching-dataone.Rmdusingknitr::rmarkdownon Oct 27 2024.

Last update: 2022-06-08
Started: 2020-06-24

Updating Datasets on DataONE

Rendered fromv06-update-package.Rmdusingknitr::rmarkdownon Oct 27 2024.

Last update: 2020-11-18
Started: 2020-06-24

Uploading Datasets to DataONE

Rendered fromv05-upload-data.Rmdusingknitr::rmarkdownon Oct 27 2024.

Last update: 2021-02-24
Started: 2020-06-24

Readme and manuals

Help Manual

Help pageTopics
Base Class for Specific Metadata ParsersAbstractTableDescriber-class
Add a D1Object containing a data object to a DataPackageaddData,DataPackage,D1Object-method
Archive an object on a Member Node or Coordinating Node, which hides it from casual searches.archive archive,D1Node-method
return the D1Object data as a data.frame.asDataFrame asDataFrame,D1Object,AbstractTableDescriber-method asDataFrame,D1Object,D1Object-method
DELETE a resource with authenticated credentials.auth_delete
GET a resource with authenticated credentials if available.auth_get
Send a http HEAD request for a resource with authenticated credentials if available.auth_head
POST a resource with authenticated credentials.auth_post
PUT a resource with authenticated credentials.auth_put
POST, PUT, or DELETE a resource with authenticated credentials.auth_put_post_delete
Create an AuthenticationManager objectAuthenticationManager AuthenticationManager,ANY-method
Manage DataONE authentication.AuthenticationManager-class
Test whether the provided subject can read an object.canRead,D1Object-method
Create a CertificateManager objectCertificateManager CertificateManager,ANY-method
CertficateManager provides mechanisms to obtain, load, verify, and display X509 certificates.CertificateManager-class
Create a CNode object.CNode CNode,ANY-method CNode,character-method
Provides R API to DataONE Coordinating Node services.CNode-class
Convert a DataFrame to Standard CSV.convert.csv convert.csv,D1Client-method
Create the Object in the DataONE SystemcreateD1Object createD1Object,D1Client,D1Object-method
Create a DataPackage on a DataONE Member NodecreateDataPackage createDataPackage,D1Client,DataPackage-method
Create an object on a Member Node.createObject createObject,MNode-method
This function parses a DataONE service response message for errors, and extracts and prints error information.d1_errors
The DataONE client class used to download, update and search for data in the DataONE network.D1Client D1Client,ANY,ANY-method D1Client,character,ANY-method D1Client,character,character-method D1Client,character,MNode-method D1Client,CNode,MNode-method
The D1Client class contains methods that perform high level DataONE tasksD1Client-class
Query the DataONE Solr endpoint of the Coordinating Node.d1IdentifierSearch d1IdentifierSearch,D1Client-method
Create a D1Node object.D1Node D1Node,XMLInternalElementNode-method
A base class for CNode and MNode.D1Node-class
Create a D1Object instance.D1Object
D1Object (Defunct) is a representation of a DataObject.D1Object-class
A method to query the DataONE solr endpoint of the Coordinating Node.d1SolrQuery d1SolrQuery,D1Client,character-method d1SolrQuery,D1Client,list-method
CharacterEncodingdata.characterEncoding data.characterEncoding,EMLParser,numeric-method
Data Formatdata.formatFamily data.formatFamily,EMLParser,numeric-method
returns the attribute namesdata.tableAttributeNames data.tableAttributeNames,EMLParser,numeric-method
The Attribute (Header) Orientationdata.tableAttributeOrientation data.tableAttributeOrientation,EMLParser,numeric-method
returns the attributes' data storage typesdata.tableAttributeStorageTypes data.tableAttributeStorageTypes,EMLParser,numeric-method
returns the attributes' data typesdata.tableAttributeTypes data.tableAttributeTypes,EMLParser,numeric-method
Field Delimiterdata.tableFieldDelimiter data.tableFieldDelimiter,EMLParser,numeric-method
returns missing value codesdata.tableMissingValueCodes data.tableMissingValueCodes,EMLParser,numeric-method
Quote Characterdata.tableQuoteCharacter data.tableQuoteCharacter,EMLParser,numeric-method
Number of lines to skip before reading datadata.tableSkipLinesHeader data.tableSkipLinesHeader,EMLParser,numeric-method
Search, download and upload data to the DataONE network.dataone
Efficiently get systemmetadata for an object.describeObject describeObject,D1Node-method
Get DataONE identifiersdocumented.d1Identifiers documented.d1Identifiers,EMLParser-method
Get the entity names associated with each tabledocumented.entityNames documented.entityNames,EMLParser-method
Get the sizes of the described data tables.documented.sizes documented.sizes,EMLParser-method
Open the CILogon Certificate download page in the default browser.downloadCert downloadCert,CertificateManager-method
Download an object from the DataONE Federation to Disk.downloadObject downloadObject,D1Client-method
Echo the credentials used to make the call.echoCredentials echoCredentials,CNode-method
Construct an EML parser object.EMLParser EMLParser,D1Object-method
Handler for Parsing Table Format Details from MetadataEMLParser-class
Encode the input for Solr QueriesencodeSolr encodeSolr,character-method
Encode the Input for a URL Path Segment.encodeUrlPath encodeUrlPath,D1Client-method
Encode the Input for a URL Query Segment.encodeUrlQuery encodeUrlQuery,D1Client-method
Evaluate DataONE authentication.evaluateAuth evaluateAuth,AuthenticationManager-method
Get a unique identifier that is generated by the Member Node repository and guaranteed to be unique.enerateIdentifier generateIdentifier generateIdentifier,MNode-method
User agent stringget_user_agent
Get the expiration date of the current authentication method.getAuthExpires getAuthExpires,AuthenticationManager-method
Get the current valid authentication mechanism.getAuthMethod getAuthMethod,AuthenticationManager-method
Get the authentication subject.getAuthSubject getAuthSubject,AuthenticationManager-method
Get the node capabilities description, and store the information in the MNode.getCapabilities getCapabilities,MNode-method
Get the DataONE X.509 Certificate location.getCert getCert,AuthenticationManager-method
Show the date and time when an X.509 certificate expires.getCertExpires getCertExpires,CertificateManager-method
Get X.509 Certificate informationgetCertInfo getCertInfo,AuthenticationManager-method
Get the file path on disk of the client certificate file.getCertLocation getCertLocation,CertificateManager-method
Get the checksum for the data object associated with the specified pid.getChecksum getChecksum,CNode-method getChecksum,MNode-method
Get the coordinating node associated with this D1Client object.getCN getCN,D1Client-method
Download a data object from the DataONE Federation.getD1Object getD1Object,D1Client-method
Get the data content of a D1Object.getData,D1Object-method
Download a file (and it's associated system metadata) from the DataONE Federation as a DataObject.getDataObject getDataObject,D1Client-method
Download data from the DataONE Federation as a DataPackage.getDataPackage getDataPackage,D1Client-method
Return the URL endpoint for the DataONE Coordinating Node.getEndpoint getEndpoint,D1Client-method
Extract an error message from an http response.getErrorDescription
Get information for a single DataONE object formatgetFormat getFormat,CNode-method
Get the FormatId of the D1ObjectgetFormatId,D1Object-method
Get the Identifier of the D1ObjectgetIdentifier,D1Object-method
Get the DataObject containing package metadatagetMetadataMember getMetadataMember,D1Client,DataPackage-method
Get a member node client based on its node identifier.getMN getMN,D1Client,ANY-method getMN,D1Client,character-method
Get a reference to a node based on its identifiergetMNode getMNode,CNode-method
Get the member node identifier associated with this D1Client object..getMNodeId getMNodeId,D1Client-method
Get the bytes associated with an object on this Node.getObject getObject,CNode-method getObject,MNode-method
Download a data package from a member node.getPackage getPackage,MNode-method
Query a node for the list of query engines available on the nodegetQueryEngineDescription getQueryEngineDescription,D1Node-method
Get the metadata describing system properties associated with an object on this Node.getSystemMetadata getSystemMetadata,CNode-method getSystemMetadata,MNode-method
Get the value of the DataONE Authentication Token, if one exists.getToken getToken,AuthenticationManager-method
Get authentication token informationgetTokenInfo getTokenInfo,AuthenticationManager-method
Checks to determine if the supplied subject is the owner of the reservation of id.hasReservation hasReservation,CNode-method
Initialize a D1Client objectD1Client-initialize initialize,D1Client-method
Initialize a D1NodeD1Node-initialize initialize,D1Node-method
Initialize a D1ObjectD1Object-initialize initialize,D1Object-method
Check if the currently valid authentication method has reached the expiration time.isAuthExpired isAuthExpired,AuthenticationManager-method
Check if an action is authorized for the specified identifierisAuthorized isAuthorized,D1Node-method
Verify authentication for a member node.isAuthValid isAuthValid,AuthenticationManager-method
Determine if an X.509 certificate has expired.isCertExpired isCertExpired,CertificateManager-method
List all object formats registered in DataONE.listFormats listFormats,CNode-method
List DataONE Member Nodes.listMemberNodes listMemberNodes,D1Client-method
Get the list of nodes associated with a CNlistNodes listNodes,CNode-method
Retrieve the list of objects that match the search parameterslistObjects listObjects,D1Node-method
Query a node for the list of query engines available on the nodelistQueryEngines listQueryEngines,D1Node-method
Create a MNode object representing a DataONE Member Node repository.MNode MNode,character-method MNode,D1Node-method
Provides R API to DataONE Member Node services.MNode-class
Temporarily disable DataONE authentication.obscureAuth obscureAuth,AuthenticationManager-method
Obscure the CILogon Client CertificateobscureCert obscureCert,CertificateManager-method
Construct a Node, using a passed in capabilities XMLparseCapabilities parseCapabilities,D1Node-method
Parse Solr output into an R listparseSolrResult parseSolrResult,XMLInternalDocument-method
Test if a node is online and accepting DataONE requestsping ping,D1Node-method
Search DataONE for data and metadata objectsquery query,D1Node-method
Reserve a identifier that is unique in the DataONE network.reserveIdentifier reserveIdentifier,CNode-method reserveIdentifier,D1Client-method
Get a list of coordinating nodes holding a given pid.resolve resolve,CNode-method
Restore authentication (after being disabled with 'obscureAuth').restoreAuth restoreAuth,AuthenticationManager-method
Restore the CILogon client certificate by renaming it to its original locationrestoreCert restoreCert,CertificateManager-method
Set the member node identifier to be associated with the D1Client object.setMNodeId setMNodeId,D1Client,character-method
Set a pid as being obsoleted by another pidsetObsoletedBy setObsoletedBy,CNode,character-method
Make the object publicly readable.setPublicAccess,D1Object-method
Display all authentication informationshowAuth showAuth,AuthenticationManager-method
Get DataONE Identity as Stored in the CILogon Certificate.showClientSubject showClientSubject,CertificateManager-method
Update an object on a Member Node, by creating a new object that replaces an original.updateObject updateObject,MNode-method
Update the system metadata associated with an object.updateSystemMetadata updateSystemMetadata,MNode-method
Upload a DataObject to a DataONE member node.uploadDataObject uploadDataObject,D1Client-method
Upload a DataPackage to a DataONE member node.uploadDataPackage uploadDataPackage,D1Client-method