Table assignment — datashield.assign.table • DSI

Assign a table to a R symbol in the Datashield R session.

Usage

datashield.assign.table(
  conns,
  symbol,
  table,
  variables = NULL,
  missings = FALSE,
  identifiers = NULL,
  id.name = NULL,
  async = TRUE,
  success = NULL,
  error = NULL,
  errors.print = getOption("datashield.errors.print", FALSE)
)

Arguments

conns: DSConnection-class object or a list of DSConnection-classs.
symbol: Name of the R symbol.
table: Fully qualified name of a table in the data repository (can be a vector or must be the same in each data repository); or a named list of fully qualified table names (one per server name); or a data frame with 'server' and 'table' columns (such as the one that is used in datashield.login)
variables: List of variable names or Javascript expression that selects the variables of a table. See javascript documentation: http://opaldoc.obiba.org/en/latest/magma-user-guide/variable/
missings: If TRUE, missing values will be pushed from data repository to R, default is FALSE. Ignored if value is an R expression.
identifiers: Name of the identifiers mapping to use when assigning entities to R (if supported by the data repository).
id.name: Name of the column that will contain the entity identifiers. If not specified, the identifiers will be the data frame row names. When specified this column can be used to perform joins between data frames.
async: Whether the result of the call should be retrieved asynchronously. When TRUE (default) the calls are parallelized over the connections, when the connection supports that feature, with an extra overhead of requests.
success: Callback function that will be called each time an assignment is successful. The expected function signature is the connection/study name. Default is NULL (no callback).
error: Callback function that will be called each time the assignment request has failed. The expected function signature is the connection/study name and the error message. Default is NULL (no callback).
errors.print: Boolean, whether to print datashield errors in the console or return a message indicating that they can be retrieved using `datashield.errors`.

Examples

if (FALSE) { # \dontrun{
# assign a list of variables from table CNSIM1
datashield.assign.table(conn, symbol="D", table="CNSIM.CNSIM1",
  variables=list("GENDER","LAB_GLUC"))

# assign all the variables matching 'LAB' from table CNSIM1
datashield.assign.table(conn, symbol="D", table="CNSIM.CNSIM1",
  variables="name().matches('LAB_')")

# assign the tables that are defined in the logindata ('server' and 'table' columns are
# expected) data frame that is used in datashield.login() function. Connections
# are filtered by the list names.
datashield.assign.table(conns, "D", logindata)

# assign the tables that are defined in the provided named list.
# Connections are filtered by the list names.
datashield.assign.table(conns, "D",
  list(server1="CNSIM.CNSIM1", server2="CNSIM.CNSIM2"))

# do assignment with callback functions
datashield.assign.table(conns, "D",
  list(server1="CNSIM.CNSIM1", server2="CNSIM.CNSIM2"),
  success = function(server) {
    # do something with server's success
  },
  error = function(server, error) {
    # do something with server's error message
  })
} # }