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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)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).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.