R: 'Opal' Data Repository Client and 'DataSHIELD' Utils

# 'Opal' Data Repository Client and 'DataSHIELD' Utils

## Documentation for package ‘opalr’ version 3.6.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

D O

## -- D --

dictionary.annotate | Set variable annotation with a taxonomy term
dictionary.annotate.harmo_status | Set variable annotation with Harmonization Status term
dictionary.annotations | List the annotations
dictionary.apply | Apply the dictionary to a tibble
dictionary.inspect | Inspect the dictionary of a tibble
dsadmin.activity | Get DataSHIELD activity
dsadmin.activity_summary | Get DataSHIELD activity summary
dsadmin.get_method | Get a DataSHIELD method
dsadmin.get_methods | Get DataSHIELD methods
dsadmin.get_options | Get the DataSHIELD options
dsadmin.installed_package | Check DataSHIELD package
dsadmin.install_github_package | Install a DataSHIELD package from GitHub
dsadmin.install_local_package | Install a DataSHIELD package from a local archive file
dsadmin.install_package | Install a DataSHIELD package
dsadmin.log | Get DataSHIELD logs
dsadmin.package_description | Get DataSHIELD package description
dsadmin.package_descriptions | Get DataSHIELD package descriptions
dsadmin.perm | Get the DataSHIELD permissions
dsadmin.perm_add | Add or update a DataSHIELD permission
dsadmin.perm_delete | Delete a DataSHIELD permission
dsadmin.profile | Get a DataSHIELD profile
dsadmin.profiles | Get DataSHIELD profiles
dsadmin.profile_access | Restrict or open access to a DataSHIELD profile
dsadmin.profile_create | Create a DataSHIELD profile
dsadmin.profile_delete | Delete a DataSHIELD profile
dsadmin.profile_enable | Enable or disable a DataSHIELD profile
dsadmin.profile_exists | Check a DataSHIELD profile exists
dsadmin.profile_init | Initialize a DataSHIELD profile
dsadmin.profile_perm | Get the permissions of a DataSHIELD profile
dsadmin.profile_perm_add | Add or update a permission on a DataSHIELD profile
dsadmin.profile_perm_delete | Delete a permission from a DataSHIELD profile
dsadmin.profile_rparser | Set or remove the R parser version of a DataSHIELD profile
dsadmin.publish_package | Publish DataSHIELD package settings
dsadmin.remove_package | Remove DataSHIELD package
dsadmin.rm_method | Remove DataSHIELD method
dsadmin.rm_methods | Remove DataSHIELD methods.
dsadmin.rm_option | Remove a DataSHIELD option
dsadmin.rm_options | Remove all DataSHIELD options
dsadmin.rm_package_methods | Remove DataSHIELD package methods
dsadmin.set_method | Set DataSHIELD method
dsadmin.set_option | Set DataSHIELD option
dsadmin.set_package_methods | Set DataSHIELD package methods
dsadmin.unpublish_package | Unpublish DataSHIELD package settings

## -- O --

oadmin.activity | Get R activity
oadmin.activity_summary | Get R activity summary
oadmin.installed_devtools | Check devtools package
oadmin.installed_package | Check package is installed
oadmin.installed_packages | List installed packages
oadmin.install_bioconductor_package | Install a package from Bioconductor
oadmin.install_cran_package | Install a package from CRAN
oadmin.install_devtools | Install devtools package
oadmin.install_github_package | Install a package from GitHub
oadmin.install_local_package | Install a package from a local archive file
oadmin.install_package | Install CRAN package
oadmin.log | Get Opal main logs
oadmin.log_rest | Get Opal REST API logs
oadmin.log_sql | Get Opal SQL API logs
oadmin.package_description | Get package description
oadmin.perm | Get the R permissions (deprecated)
oadmin.perm_add | Add or update a R permission (deprecated)
oadmin.perm_delete | Delete a R permission (deprecated)
oadmin.remove_package | Remove package
oadmin.r_perm | Get the R permissions
oadmin.r_perm_add | Add or update a R permission
oadmin.r_perm_delete | Delete a R permission
oadmin.system_metrics | Get system metrics
oadmin.system_perm | Get the System permissions
oadmin.system_perm_add | Add or update a System permission
oadmin.system_perm_delete | Delete a System permission
oadmin.users | Get the users
oadmin.user_add | Add a user
oadmin.user_delete | Delete a user
oadmin.user_enable | Enable a user
oadmin.user_exists | Check user exists
oadmin.user_profiles | Get user profiles
oadmin.user_profile_delete | Delete a user profile
oadmin.user_reset_password | Reset user password
opal.annotate | Apply the annotations to a Opal table
opal.annotations | Get the annotations of a Opal table
opal.assign | Data or expression assignment
opal.assign.data | Data assignment
opal.assign.resource | Resource assignment
opal.assign.script | R script assignment
opal.assign.table | Data assignment to a data.frame
opal.assign.table.tibble | Data assignment to a tibble
opal.as_md_table | Array to Markdown
opal.attribute_values | Get a vector of attribute values
opal.command | Get an asynchronous command
opal.commands | List the asynchronous commands
opal.commands_rm | Remove all asynchronous commands
opal.command_result | Get result of an asynchronous command
opal.command_rm | Remove an asynchronous command
opal.datasource | Get a datasource
opal.datasources | Get datasources
opal.delete | Generic REST resource deletion.
opal.execute | Execute a R script
opal.execute.source | Execute a R file script
opal.file | Get file content
opal.file_cp | Copy a file
opal.file_download | Download a file
opal.file_info | Get file information
opal.file_ls | List content of a folder
opal.file_mkdir | Make a folder
opal.file_mkdir_tmp | Make a temporary folder
opal.file_mv | Move and/or rename a file
opal.file_read | Read a file
opal.file_rm | Remove a file
opal.file_unzip | Unzip a zip archive file
opal.file_upload | Upload a file or a folder
opal.file_write | Write a file
opal.get | Generic REST resource getter.
opal.load_package | Load package
opal.login | Opal login
opal.logout | Logout from Opal(s)
opal.perms | Get the permissions of a subject
opal.post | Generic REST resource creation.
opal.profiles | List R profiles
opal.project | Get a project
opal.projects | Get projects
opal.projects_databases | Get projects databases
opal.project_backup | Backup a project
opal.project_command | Get project task
opal.project_create | Create a project
opal.project_delete | Delete a project
opal.project_exists | Check a project exists
opal.project_perm | Get the permissions on a project
opal.project_perm_add | Add or update a permission on a project
opal.project_perm_delete | Delete a permission from a project
opal.project_restore | Restore a project
opal.put | Generic REST resource update.
opal.report | Opal report
opal.resource | Get a resource reference of a project
opal.resources | Get the resource references of a project
opal.resources_perm | Get the permissions on any resource
opal.resources_perm_add | Add or update a permission on any resource
opal.resources_perm_delete | Delete a permission from any resource
opal.resource_create | Create a resource reference in a project
opal.resource_delete | Delete a resource reference
opal.resource_exists | Check a resource reference exists
opal.resource_extension_create | Create an extended resource reference in a project
opal.resource_get | Get the resource object of a project
opal.resource_perm | Get the permissions on a resource
opal.resource_perm_add | Add or update a permission on a resource
opal.resource_perm_delete | Delete a permission from a resource
opal.resource_view_create | Create an Opal view over a resource reference
opal.resource_view_reconnect | Reconnect an Opal view to its underlying resource
opal.rm | Remove a R symbol (deprecated)
opal.session | Create the R session
opal.session_delete | Delete the R session
opal.session_events | Get the events associated to the R session
opal.session_exists | Check if the R session exists
opal.session_get | Get the R session
opal.session_running | Check if the R session is running
opal.sql | Execute a SQL query on tables
opal.sql_history | SQL query execution history
opal.symbols | List R symbols
opal.symbol_import | Import a tibble
opal.symbol_rm | Remove a R symbol
opal.symbol_save | Save a tibble
opal.table | Get a table of a datasource
opal.tables | Get tables of a datasource
opal.tables_perm | Get the permissions on any table of a project
opal.tables_perm_add | Add or update a permission on any table of a project
opal.tables_perm_delete | Delete a permission from any table of a project
opal.table_create | Create an Opal table or view
opal.table_delete | Delete a Opal table
opal.table_dictionary_get | Get the dictionary of a Opal table
opal.table_dictionary_update | Update the dictionary of a Opal table
opal.table_exists | Check a Opal table exists
opal.table_export | Export a table as a file
opal.table_get | Get a Opal table as a tibble
opal.table_import | Import a file as table
opal.table_perm | Get the permissions on a table
opal.table_perm_add | Add or update a permission on a table
opal.table_perm_delete | Delete a permission from a table
opal.table_save | Save a local tibble as a Opal table
opal.table_truncate | Truncate a Opal table
opal.table_view_create | Create an Opal view over tables
opal.table_view_update | Update the table references and the entity filter of an Opal view
opal.task | Get a task
opal.tasks | Get the tasks
opal.task_cancel | Cancel a task
opal.task_delete | Delete a task
opal.task_wait | Wait for a task to complete or anticipate its cancellation.
opal.taxonomies | Get taxonomies
opal.taxonomy | Get a taxonomy
opal.taxonomy_delete | Delete a taxonomy
opal.taxonomy_download | Download a taxonomy file
opal.taxonomy_upload | Upload a taxonomy file
opal.terms | Get the terms of a vocabulary
opal.token | Get a personal access token
opal.tokens | Get the personal access tokens
opal.token_datashield_create | Create a personal access token for Datashield usage
opal.token_delete | Delete a personal access token
opal.token_renew | Renew an inactive personal access token
opal.token_r_create | Create a personal access token for R usage
opal.token_sql_create | Create a personal access token for SQL usage
opal.unload_package | Unload package
opal.valueset | Get the values of an entity
opal.variable | Get a variable of a table
opal.variables | Get variables of a table
opal.variable_summary | Get summary statistics of a variable of a table
opal.version_compare | Compare
opal.vocabularies | Get the vocabularies of a taxonomy
opal.vocabulary | Get a taxonomy vocabulary
opal.workspaces | Get the R workspaces from a opal.
opal.workspace_restore | Restore a R workspace from a opal.
opal.workspace_rm | Remove a R workspace from a opal.
opal.workspace_save | Save the current session in a opal R workspace.