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Opal R

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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

DataSHIELD Client

See the DSOpal documentation.