inst/doc/opal-rsession.R

In opalr: 'Opal' Data Repository Client and 'DataSHIELD' Utils

## ----eval=FALSE---------------------------------------------------------------
#  library(opalr)
#  o <- opal.login("administrator", "password", "https://opal-demo.obiba.org", profile = "default")

## ----eval=FALSE---------------------------------------------------------------
#  opal.assign.table(o, symbol = "df", value = "CNSIM.CNSIM1")

## ----eval=FALSE---------------------------------------------------------------
#  opal.assign.table.tibble(o, symbol = "tbl", value = "CNSIM.CNSIM1")

## ----eval=FALSE---------------------------------------------------------------
#  opal.assign.resource(o, symbol = "rsrc", value = "RSRC.CNSIM3")

## ----eval=FALSE---------------------------------------------------------------
#  opal.assign.script(o, symbol = "hello", value = quote(function(x) { paste0("Hello ", x, "!") }))

## ----eval=FALSE---------------------------------------------------------------
#  opal.symbols(o)

## ----eval=FALSE---------------------------------------------------------------
#  # column names
#  opal.execute(o, script = "names(tbl)")
#  # get variable description from column attributes
#  opal.execute(o, script = "attributes(tbl$GENDER)")
#  # coerce resource to a data.frame and plot histogram of one column
#  plot(opal.execute(o, script = "hist(as.data.frame(rsrc)$LAB_HDL)"))
#  # execute the custom function
#  opal.execute(o, script = "hello('friends')")

## ----eval=FALSE---------------------------------------------------------------
#  GENDER <- opal.execute(o, script = "tbl$GENDER")

## ----eval=FALSE---------------------------------------------------------------
#  opal.execute.source(o, path = "/path/to/some_code.R")

## ----eval=FALSE---------------------------------------------------------------
#  opal.file_write(o, source = "/projects/CNSIM/CNSIM3.zip", "test.zip")

## ----eval=FALSE---------------------------------------------------------------
#  opal.file_read(o, source = "test.zip", destination = "/tmp")

## ----eval=FALSE---------------------------------------------------------------
#  opal.workspace_save(o, save="demo")
#  opal.workspaces(o)

## ----eval=FALSE---------------------------------------------------------------
#  opal.logout(o)