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Opal R

Opal R Client for the Opal data warehouse. Most of the web services of Opal can be reached by an opalr function: import/export, data dictionaries, projects, tables, resources, permissions, users, DataSHIELD profiles etc.

See opalr documentation.

Installation:

# install from CRAN
install.packages("opalr")

# or install latest development version
remotes::install_github("obiba/opalr")

Basic usage:

library(opalr)
o <- opal.login('administrator', 'password', url = 'https://opal-demo.obiba.org')

# assign a table (as a data.frame) to a R symbol
opal.assign(o, 'D', 'CNSIM.CNSIM1')

# perform R operations on the server side
opal.execute(o, 'summary(D$GENDER)')
opal.execute(o, 'summary(D$LAB_GLUC)')

opal.logout(o)

Options

Some helper options can be defined to control default values and behavior:

• opal.username, the login user name (default is NULL).
• opal.password, the login user password (default is NULL).
• opal.token, the login personal access token (default is NULL).
• opal.url, the login Opal URL (default is NULL).
• opal.opts, the curl options (default is NULL), see httr::httr_options.
• opal.profile, the login profile (R servers cluster name) (default is NULL).
• opal.progress, whether to show progress bar (default is TRUE).
• opal.progress.clear, whether to clear progress bar after it is completed (default is FALSE).
• opal.retry.times, the maximum number of GET requests to attempt (default is 3, no retry when value is 1).
• opal.retry.quiet, whether to print a message displaying how long until the next request (default is FALSE).

Cookbooks

• How to perform DataSHIELD Administration
• How to manage Opal Files
• How to manage Opal Projects
• How to interact with an Opal R Session

DataSHIELD Client

See the DSOpal documentation.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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