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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.
Any scripts or data that you put into this service are public.
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