Merge pull request neelsoumya#17 from ESCRI11/v2.3.0task4

ds.finegray correct example

Author: StuartWheater

R/ds.finegray.R

@@ -25,29 +25,52 @@
 #' \dontrun{
 #'   ## Version 1.0.0
 #'
-#'   # connecting to the Opal servers
+#'   # First, set up the connection to the Opal server
 #'   builder <- DSI::newDSLoginBuilder()
 #'   builder$append(server = "study1",
 #'                  url = "http://192.168.56.100:8080/",
-#'                  user = "administrator", password = "datashield_test&",
-#'                  table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver")
+#'                  user = "administrator",
+#'                  password = "datashield_test&",
+#'                  table = "SURVIVAL.EXPAND_WITH_MISSING1",
+#'                  driver = "OpalDriver")
 #'   logindata <- builder$build()
 #'
 #'   connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D")
 #'
+#'   ds.mice(data = 'D', m = 5, method = 'rf', newobj_df = 'D2', seed = 'fixed', newobj_mids = "imputed_mids")
+#'
+#'   ds.asNumeric(x.name = "D2.1$cens",
+#'             newobj = "EVENT",
+#'             datasources = connections)
+#'
+#'   ds.asNumeric(x.name = "D2.1$survtime",
+#'             newobj = "SURVTIME",
+#'             datasources = connections)
+#'
+#'   ds.asNumeric(x.name = "D2.1$starttime",
+#'             newobj = "STARTTIME",
+#'             datasources = connections)
+#'
+#'   ds.asNumeric(x.name = "D2.1$endtime",
+#'             newobj = "ENDTIME",
+#'             datasources = connections)
+#'
+#'   dsSurvivalClient::ds.Surv(time='STARTTIME', time2='ENDTIME',
+#'         event = 'EVENT', objectname='surv_object')
+#'
 #'   # Create a Fine-Gray dataset for competing risks analysis
-#'   ds.finegray(formula = "Surv(time, status) ~ age + sex",
-#'               data = "D",
+#'   ds.finegray(formula = "Surv(endtime, cens) ~ age.60 + female",
+#'               data = "D2.1",
 #'               etype = 1,
 #'               newobj = "fg_data")
 #'
 #'   # Now use the created dataset for a weighted Cox model
-#'   ds.coxph.SLMAassign("Surv(fgstart, fgstop, fgstatus) ~ age + sex",
-#'                       weights = "fgwt",
-#'                       data = "fg_data",
-#'                       newobj = "coxph_model")
+#'   ds.coxphSLMAassign(formula = "survival::Surv(fgstart, fgstop, fgstatus) ~ age.60 + female",
+#'                       dataName = "fg_data",
+#'                       objectname = "coxph_model")
+#'
 #'
-#'   # Clear the Datashield R sessions and logout
+#'   # When finished, clear the session and logout
 #'   datashield.logout(connections)
 #' }
 #'