Assign a Opal table to a data.frame identified by a R symbol in the current R session.

opal.assign.table(
  opal,
  symbol,
  value,
  variables = NULL,
  missings = FALSE,
  identifiers = NULL,
  id.name = NULL,
  updated.name = NULL,
  class = "data.frame",
  async = FALSE
)

Arguments

opal

Opal object or list of opal objects.

symbol

Name of the R symbol.

value

The value to assign evaluated in the following order: a fully qualified name of a variable or a table in Opal.

variables

List of variable names or Javascript expression that selects the variables of a table (ignored if value does not refere to a table). See javascript documentation: http://wiki.obiba.org/display/OPALDOC/Variable+Methods

missings

If TRUE, missing values will be pushed from Opal to R, default is FALSE.

identifiers

Name of the identifiers mapping to use when assigning entities to R (from Opal 2.0).

id.name

Add a vector with the given name representing the entity identifiers (from Opal 2.6). Default is NULL.

updated.name

Deprecated. Add a vector with the given name representing the creation and last update timestamps (from Opal 2.6). Default is NULL.

class

The data frame class into which the table is written: can 'data.frame' (default) or 'tibble' (from Opal 2.6 to 2.13) or 'tibble.with.factors' (from Opal 2.14).

async

R script is executed asynchronously within the session (default is FALSE). If TRUE, the value returned is the ID of the command to look for (from Opal 2.1).

Examples

if (FALSE) {
o <- opal.login('administrator','password', url='https://opal-demo.obiba.org')
# assign a list of variables from table CNSIM1
opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables=list("GENDER","LAB_TSC"))
opal.execute(o, "colnames(D)")
# assign a table CNSIM1 with a identifiers column
opal.assign.table(o, symbol="H", value="datashield.CNSIM1", id.name="id")
opal.execute(o, "colnames(H)")
# assign all the variables matching 'LAB' from table HOP of opal object o
opal.assign.table(o, symbol="D", value="datashield.CNSIM1", variables="name().matches('LAB_')")
opal.execute(o, "colnames(D)")
opal.logout(o)
}