R: R Interface to the 'DataONE' REST API

# R Interface to the 'DataONE' REST API

## Documentation for package ‘dataone’ version 2.3.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A C D E G H I L M O P Q R S U

## -- A --

AbstractTableDescriber-class | Base Class for Specific Metadata Parsers
addData-method | Add a D1Object containing a data object to a DataPackage
archive | Archive an object on a Member Node or Coordinating Node, which hides it from casual searches.
archive-method | Archive an object on a Member Node or Coordinating Node, which hides it from casual searches.
asDataFrame | return the D1Object data as a data.frame.
asDataFrame-method | return the D1Object data as a data.frame.
AuthenticationManager | Create an AuthenticationManager object
AuthenticationManager-class | Manage DataONE authentication.
AuthenticationManager-method | Create an AuthenticationManager object
auth_delete | DELETE a resource with authenticated credentials.
auth_get | GET a resource with authenticated credentials if available.
auth_head | Send a http HEAD request for a resource with authenticated credentials if available.
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 credentials.

## -- C --

canRead-method | Test whether the provided subject can read an object.
CertificateManager | Create a CertificateManager object
CertificateManager-class | CertficateManager provides mechanisms to obtain, load, verify, and display X509 certificates.
CertificateManager-method | Create a CertificateManager object
CNode | Create a CNode object.
CNode-class | Provides R API to DataONE Coordinating Node services.
CNode-method | Create a CNode object.
convert.csv | Convert a DataFrame to Standard CSV.
convert.csv-method | Convert a DataFrame to Standard CSV.
createD1Object | Create the Object in the DataONE System
createD1Object-method | Create the Object in the DataONE System
createDataPackage | Create a DataPackage on a DataONE Member Node
createDataPackage-method | Create a DataPackage on a DataONE Member Node
createObject | Create an object on a Member Node.
createObject-method | Create an object on a Member Node.

## -- D --

D1Client | The DataONE client class used to download, update and search for data in the DataONE network.
D1Client-class | The D1Client class contains methods that perform high level DataONE tasks
D1Client-initialize | Initialize a D1Client object
D1Client-method | The DataONE client class used to download, update and search for data in the DataONE network.
d1IdentifierSearch | Query the DataONE Solr endpoint of the Coordinating Node.
d1IdentifierSearch-method | 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
D1Node-method | Create a D1Node object.
D1Object | Create a D1Object instance.
D1Object-class | D1Object (Defunct) is a representation of a DataObject.
D1Object-initialize | Initialize a D1Object
d1SolrQuery | A method to query the DataONE solr endpoint of the Coordinating Node.
d1SolrQuery-method | A method to query the DataONE solr endpoint of the Coordinating Node.
d1_errors | This function parses a DataONE service response message for errors, and extracts and prints error information.
data.characterEncoding | CharacterEncoding
data.characterEncoding-method | CharacterEncoding
data.formatFamily | Data Format
data.formatFamily-method | Data Format
data.tableAttributeNames | returns the attribute names
data.tableAttributeNames-method | returns the attribute names
data.tableAttributeOrientation | The Attribute (Header) Orientation
data.tableAttributeOrientation-method | The Attribute (Header) Orientation
data.tableAttributeStorageTypes | returns the attributes' data storage types
data.tableAttributeStorageTypes-method | returns the attributes' data storage types
data.tableAttributeTypes | returns the attributes' data types
data.tableAttributeTypes-method | returns the attributes' data types
data.tableFieldDelimiter | Field Delimiter
data.tableFieldDelimiter-method | Field Delimiter
data.tableMissingValueCodes | returns missing value codes
data.tableMissingValueCodes-method | returns missing value codes
data.tableQuoteCharacter | Quote Character
data.tableQuoteCharacter-method | Quote Character
data.tableSkipLinesHeader | Number of lines to skip before reading data
data.tableSkipLinesHeader-method | Number of lines to skip before reading data
describeObject | Efficiently get systemmetadata for an object.
describeObject-method | Efficiently get systemmetadata for an object.
documented.d1Identifiers | Get DataONE identifiers
documented.d1Identifiers-method | Get DataONE identifiers
documented.entityNames | Get the entity names associated with each table
documented.entityNames-method | Get the entity names associated with each table
documented.sizes | Get the sizes of the described data tables.
documented.sizes-method | Get the sizes of the described data tables.
downloadCert | Open the CILogon Certificate download page in the default browser.
downloadCert-method | Open the CILogon Certificate download page in the default browser.
downloadObject | Download an object from the DataONE Federation to Disk.
downloadObject-method | Download an object from the DataONE Federation to Disk.

## -- E --

echoCredentials | Echo the credentials used to make the call.
echoCredentials-method | Echo the credentials used to make the call.
EMLParser | Construct an EML parser object.
EMLParser-class | Handler for Parsing Table Format Details from Metadata
EMLParser-method | Construct an EML parser object.
encodeSolr | Encode the input for Solr Queries
encodeSolr-method | Encode the input for Solr Queries
encodeUrlPath | Encode the Input for a URL Path Segment.
encodeUrlPath-method | Encode the Input for a URL Path Segment.
encodeUrlQuery | Encode the Input for a URL Query Segment.
encodeUrlQuery-method | Encode the Input for a URL Query Segment.
enerateIdentifier | Get a unique identifier that is generated by the Member Node repository and guaranteed to be unique.
evaluateAuth | Evaluate DataONE authentication.
evaluateAuth-method | Evaluate DataONE authentication.

## -- G --

generateIdentifier | Get a unique identifier that is generated by the Member Node repository and guaranteed to be unique.
generateIdentifier-method | Get a unique identifier that is generated by the Member Node repository and guaranteed to be unique.
getAuthExpires | Get the expiration date of the current authentication method.
getAuthExpires-method | Get the expiration date of the current authentication method.
getAuthMethod | Get the current valid authentication mechanism.
getAuthMethod-method | Get the current valid authentication mechanism.
getAuthSubject | Get the authentication subject.
getAuthSubject-method | Get the authentication subject.
getCapabilities | Get the node capabilities description, and store the information in the MNode.
getCapabilities-method | Get the node capabilities description, and store the information in the MNode.
getCert | Get the DataONE X.509 Certificate location.
getCert-method | Get the DataONE X.509 Certificate location.
getCertExpires | Show the date and time when an X.509 certificate expires.
getCertExpires-method | Show the date and time when an X.509 certificate expires.
getCertInfo | Get X.509 Certificate information
getCertInfo-method | Get X.509 Certificate information
getCertLocation | Get the file path on disk of the client certificate file.
getCertLocation-method | Get the file path on disk of the client certificate file.
getChecksum | Get the checksum for the data object associated with the specified pid.
getChecksum-method | Get the checksum for the data object associated with the specified pid.
getCN | Get the coordinating node associated with this D1Client object.
getCN-method | Get the coordinating node associated with this D1Client object.
getD1Object | Download a data object from the DataONE Federation.
getD1Object-method | Download a data object from the DataONE Federation.
getData-method | Get the data content of a D1Object.
getDataObject | Download a file (and it's associated system metadata) from the DataONE Federation as a DataObject.
getDataObject-method | Download a file (and it's associated system metadata) from the DataONE Federation as a DataObject.
getDataPackage | Download data from the DataONE Federation as a DataPackage.
getDataPackage-method | Download data from the DataONE Federation as a DataPackage.
getEndpoint | Return the URL endpoint for the DataONE Coordinating Node.
getEndpoint-method | 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
getFormat-method | Get information for a single DataONE object format
getFormatId-method | Get the FormatId of the D1Object
getIdentifier-method | Get the Identifier of the D1Object
getMetadataMember | Get the DataObject containing package metadata
getMetadataMember-method | Get the DataObject containing package metadata
getMN | Get a member node client based on its node identifier.
getMN-method | Get a member node client based on its node identifier.
getMNode | Get a reference to a node based on its identifier
getMNode-method | Get a reference to a node based on its identifier
getMNodeId | Get the member node identifier associated with this D1Client object..
getMNodeId-method | Get the member node identifier associated with this D1Client object..
getObject | Get the bytes associated with an object on this Node.
getObject-method | Get the bytes associated with an object on this Node.
getPackage | Download a data package from a member node.
getPackage-method | Download a data package from a member node.
getQueryEngineDescription | Query a node for the list of query engines available on the node
getQueryEngineDescription-method | Query a node for the list of query engines available on the node
getSystemMetadata | Get the metadata describing system properties associated with an object on this Node.
getSystemMetadata-method | Get the metadata describing system properties associated with an object on this Node.
getToken | Get the value of the DataONE Authentication Token, if one exists.
getToken-method | Get the value of the DataONE Authentication Token, if one exists.
getTokenInfo | Get authentication token information
getTokenInfo-method | Get authentication token information
get_user_agent | User agent string

## -- H --

hasReservation | Checks to determine if the supplied subject is the owner of the reservation of id.
hasReservation-method | Checks to determine if the supplied subject is the owner of the reservation of id.

## -- I --

initialize-method | Initialize a D1Client object
initialize-method | Initialize a D1Node
initialize-method | Initialize a D1Object
isAuthExpired | Check if the currently valid authentication method has reached the expiration time.
isAuthExpired-method | Check if the currently valid authentication method has reached the expiration time.
isAuthorized | Check if an action is authorized for the specified identifier
isAuthorized-method | Check if an action is authorized for the specified identifier
isAuthValid | Verify authentication for a member node.
isAuthValid-method | Verify authentication for a member node.
isCertExpired | Determine if an X.509 certificate has expired.
isCertExpired-method | Determine if an X.509 certificate has expired.
is_windows | Is the OS Windows?

## -- L --

listFormats | List all object formats registered in DataONE.
listFormats-method | List all object formats registered in DataONE.
listMemberNodes | List DataONE Member Nodes.
listMemberNodes-method | List DataONE Member Nodes.
listNodes | Get the list of nodes associated with a CN
listNodes-method | Get the list of nodes associated with a CN
listObjects | Retrieve the list of objects that match the search parameters
listObjects-method | Retrieve the list of objects that match the search parameters
listQueryEngines | Query a node for the list of query engines available on the node
listQueryEngines-method | Query a node for the list of query engines available on the node

## -- M --

MNode | Create a MNode object representing a DataONE Member Node repository.
MNode-class | Provides R API to DataONE Member Node services.
MNode-method | Create a MNode object representing a DataONE Member Node repository.

## -- O --

obscureAuth | Temporarily disable DataONE authentication.
obscureAuth-method | Temporarily disable DataONE authentication.
obscureCert | Obscure the CILogon Client Certificate
obscureCert-method | Obscure the CILogon Client Certificate

## -- P --

parseCapabilities | Construct a Node, using a passed in capabilities XML
parseCapabilities-method | Construct a Node, using a passed in capabilities XML
parseSolrResult | Parse Solr output into an R list
parseSolrResult-method | Parse Solr output into an R list
ping | Test if a node is online and accepting DataONE requests
ping-method | Test if a node is online and accepting DataONE requests

## -- Q --

query | Search DataONE for data and metadata objects
query-method | Search DataONE for data and metadata objects

## -- R --

reserveIdentifier | Reserve a identifier that is unique in the DataONE network.
reserveIdentifier-method | Reserve a identifier that is unique in the DataONE network.
resolve | Get a list of coordinating nodes holding a given pid.
resolve-method | Get a list of coordinating nodes holding a given pid.
restoreAuth | Restore authentication (after being disabled with 'obscureAuth').
restoreAuth-method | Restore authentication (after being disabled with 'obscureAuth').
restoreCert | Restore the CILogon client certificate by renaming it to its original location
restoreCert-method | Restore the CILogon client certificate by renaming it to its original location

## -- S --

setMNodeId | Set the member node identifier to be associated with the D1Client object.
setMNodeId-method | Set the member node identifier to be associated with the D1Client object.
setObsoletedBy | Set a pid as being obsoleted by another pid
setObsoletedBy-method | Set a pid as being obsoleted by another pid
setPublicAccess-method | Make the object publicly readable.
showAuth | Display all authentication information
showAuth-method | Display all authentication information
showClientSubject | Get DataONE Identity as Stored in the CILogon Certificate.
showClientSubject-method | Get DataONE Identity as Stored in the CILogon Certificate.

## -- U --

updateObject | Update an object on a Member Node, by creating a new object that replaces an original.
updateObject-method | Update an object on a Member Node, by creating a new object that replaces an original.
updateSystemMetadata | Update the system metadata associated with an object.
updateSystemMetadata-method | Update the system metadata associated with an object.
uploadDataObject | Upload a DataObject to a DataONE member node.
uploadDataObject-method | Upload a DataObject to a DataONE member node.
uploadDataPackage | Upload a DataPackage to a DataONE member node.
uploadDataPackage-method | Upload a DataPackage to a DataONE member node.