Package index • ukbAid

All functions

admin_create_project(): Setup the project structure for working within the RAP.
admin_download_proposals(): Download project proposals from Google Form.
admin_read_projects(): Read all approved projects.
admin_start_approved_project(): Start and setup the approved project onto GitHub.
builder_table_exporter(): Build, but not run, the dx table exporter command.
create_csv_from_database(): Extract variables you want from the UKB database and create a CSV file to later upload to your own project.
download_data() deprecated: Downloads your UKB data file to the data/data.csv folder.
gh_add_repo_to_team(): Add a GitHub repo to the UK Biobank Steno team.
gh_add_user_to_repo(): Add a user to a repo.
gh_add_user_to_team(): Add the user to the UK Biobank GitHub team.
gh_create_repo(): Create a GitHub repository based on the existing local project.
gh_create_tag(): Create a Git tag and push it to GitHub as a release.
gh_get_org(): Get the Steno GitHub organization.
gh_get_repos(): Get all repo names in the UK Biobank GitHub team.
gh_get_team(): Get the name of the Steno GitHub team for the UK Biobank project.
gh_get_users(): Get all users who are part of the UK Biobank Steno team on GitHub.
proj_create_dataset(): Extract the variables you want from the UKB database and create a CSV dataset.
proj_create_path_dataset(): Create a file name unique for a project and user, along with timestamp.
get_proj_dependencies() proj_get_dependencies(): Get package dependencies from the DESCRIPTION file.
proj_get_git_config(): Search Git's global config settings and list the user's name and email.
get_rap_project_id() proj_get_name(): Get the RAP project ID, will be the project main folder.
proj_setup_git_config(): Add your name and email to Git's config settings.
setup_ukb_rap() proj_setup_rap(): Run standard setup tasks in the UKB RAP after opening it up.
rap_copy_to() rap_copy_from(): Copying files between the RAP server and the RStudio RAP environment.
rap_get_path_database(): Get the path to the RAP UK Biobank dataset.
rap_get_path_dirs(): Get full paths of folders within the RAP project server.
rap_get_path_files(): Get paths of files within a folder based on a given path in the RAP project server.
rap_get_path_schema(): Get the path to the RAP UK Biobank schema.
rap_get_path_user_files(): Get the paths of files in a single users folder within the RAP project server.
rap_get_path_users(): Get the paths of all the users within the RAP project server.
get_username() rap_get_user(): Get the username of the user who is working within the RAP RStudio session.
rap_move_file(): Move a file from one location to another within the RAP project server.
rap_variables: Variable names that are specific to the RAP
statements: Textual statements required by UK Biobank.
subset_rap_variables() deprecated: Take the selected UKB variables from the protocol stage and subset the RAP specific variables list.
upload_data() deprecated: Upload a data file to the RAP.
zen_copy_json_template(): Copy the Zenodo metadata JSON template to the current working directory.
zen_create_file_record(): Create a record for files on Zenodo.
zen_create_protocol_metadata(): Create the metadata for Zenodo based on the Rmd or qmd protocol file.
zen_create_protocol_pdf(): Create a PDF of the protocol Rmd or qmd file.
zen_get_token(): Store the token for Zenodo.