Assign a Opal table to a data.frame identified by a R symbol in the current R session.
Usage
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).
See also
Other assignment functions:
opal.assign(),
opal.assign.data(),
opal.assign.resource(),
opal.assign.script(),
opal.assign.table.tibble()
Examples
if (FALSE) { # \dontrun{
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)
} # }