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.