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Follow instructions to Start the Opal VMs.

Recall from the installation instructions, the Opal web interface is a simple check to tell if the VMs have started. Load the following urls, waiting at least 1 minute after starting the training VMs.

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Code Block

xml

Code Block

	xml
	xml

#load libraries
library(DSI)
library(DSOpal)
library(dsBaseClient)

Build your login dataframe

Code Block

language	xml
title	Build your login dataframe

builder <- DSI::newDSLoginBuilder()
builder <- DSI::newDSLoginBuilder()
builder$append(server = "study1server1",  url = "httphttps://192opal-demo.168.56.100:8080/",
               user = "administrator", password = "datashield_test&",
               table = "CNSIM.CNSIM1obiba.org/",
user = "dsuser", password = "P@ssw0rd", driver = "OpalDriver", options='list(ssl_verifyhost=0, ssl_verifypeer=0)')
builder$append(server = "study2server2", url = "httphttps://192.168.56.101:8080/",
              opal-demo.obiba.org/",
user = "administratordsuser", password = "datashield_test&P@ssw0rd", driver = "OpalDriver",             table = "CNSIM.CNSIM2", driver = "OpalDriver"options='list(ssl_verifyhost=0, ssl_verifypeer=0)')

logindata <- builder$build()

logindata <- builder$build()

connections <- DSI::datashield.login(logins = logindata, assign = TRUE)
DSI::datashield.assign.table(conns = connections, symbol = "D""DST", table = c("CNSIM.CNSIM1","CNSIM.CNSIM2"))

Command to logout:

Code Block

language	bash

DSI::datashield.logout(connections)

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Code Block

language	xml

ds.log(x='D$LABDST$LAB_HDL', datasources = connections)

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Code Block

theme	RDark

  Aggregated (exists("DDST")) [=============================================================] 100% / 0s
  Aggregated (classDS("D$LABDST$LAB_HDL")) [====================================================] 100% / 1s
  Assigned expr. (log.newobj <- log(D$LABDST$LAB_HDL,2.71828182845905)) [=======================] 100% / 0s
  Aggregated (exists("log.newobj")) [====================================================] 100% / 0s

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Code Block

language	xml

ds.log(x='D$LABDST$LAB_HDL', newobj='LAB_HDL_log', datasources = connections)

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Code Block

language	xml

ds.assign(toAssign='D$LABDST$LAB_HDL-1.562', newobj='LAB_HDL.c', datasources = connections)

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Code Block

language	xml

ds.table(rvar="D$GENDERDST$GENDER")

Code Block

theme	RDark

  Aggregated (asFactorDS1("D$GENDERDST$GENDER")) [=================================================] 100% / 0s
  Aggregated (tableDS(rvar.transmit = "D$GENDERDST$GENDER", cvar.transmit = NULL, stvar.transmit = NULL, ) ...

 Data in all studies were valid 

Study 1 :  No errors reported from this study
Study 2 :  No errors reported from this study

$output.list
$output.list$TABLE_rvar.by.study_row.props
        study
D$GENDERDST$GENDER         1         2
       0 0.4079193 0.5920807
       1 0.4160839 0.5839161

$output.list$TABLE_rvar.by.study_col.props
        study
D$GENDERDST$GENDER         1         2
       0 0.5048544 0.5132772
       1 0.4951456 0.4867228

$output.list$TABLE_rvar.by.study_counts
        study
D$GENDERDST$GENDER    1    2
       0 1092 1585
       1 1071 1503

$output.list$TABLES.COMBINED_all.sources_proportions
D$GENDERDST$GENDER
   0    1 
0.51 0.49 

$output.list$TABLES.COMBINED_all.sources_counts
D$GENDERDST$GENDER
   0    1 
2677 2574 


$validity.message
[1] "Data in all studies were valid"

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Code Block

language	xml

ds.table(rvar='D$DISDST$DIS_DIAB', cvar='D$GENDERDST$GENDER', datasources = connections)

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Code Block

theme	RDark

  Aggregated (asFactorDS1("D$DISDST$DIS_DIAB")) [===============================================] 100% / 0s
  Aggregated (asFactorDS1("D$GENDERDST$GENDER")) [=================================================] 100% / 0s
  Aggregated (tableDS(rvar.transmit = "D$DISDST$DIS_DIAB", cvar.transmit = "D$GENDERDST$GENDER", ) [======] 100% / 0s

 Data in all studies were valid 

Study 1 :  No errors reported from this study
Study 2 :  No errors reported from this study

$output.list
$output.list$TABLE.STUDY.1_row.props
          D$GENDERDST$GENDER
D$DISDST$DIS_DIAB     0     1
         0 0.502 0.498
         1 0.700 0.300

$output.list$TABLE.STUDY.1_col.props
          D$GENDERDST$GENDER
D$DISDST$DIS_DIAB      0      1
         0 0.9810 0.9920
         1 0.0192 0.0084

$output.list$TABLE.STUDY.2_row.props
          D$GENDERDST$GENDER
D$DISDST$DIS_DIAB     0     1
         0 0.511 0.489
         1 0.660 0.340

$output.list$TABLE.STUDY.2_col.props
          D$GENDERDST$GENDER
D$DISDST$DIS_DIAB      0      1
         0 0.9800 0.9890
         1 0.0196 0.0106

$output.list$TABLES.COMBINED_all.sources_row.props
          D$GENDER
D$DIS_DIAB     0     1
         0 0.507 0.493
         1 0.675 0.325

$output.list$TABLES.COMBINED_all.sources_col.props
          D$GENDERDST$GENDER
D$DISDST$DIS_DIAB      0       1
         0 0.9810 0.99000
         1 0.0194 0.00971

$output.list$TABLE_STUDY.1_counts
          D$GENDERDST$GENDER
D$DISDST$DIS_DIAB    0    1
         0 1071 1062
         1   21    9

$output.list$TABLE_STUDY.2_counts
          D$GENDER
D$DIS_DIAB    0    1
         0 1554 1487
         1   31   16

$output.list$TABLES.COMBINED_all.sources_counts
          D$GENDERDST$GENDER
D$DISDST$DIS_DIAB    0    1
         0 2625 2549
         1   52   25


$validity.message
[1] "Data in all studies were valid"

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Code Block

language	xml

ds.table(rvar='D$DISDST$DIS_DIAB', cvar='D$GENDERDST$GENDER', datasources = connections, report.chisq.tests = TRUE)

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Tip

Also remember you can:

get a function list for any DataSHIELD package and
view the manual help page individual functions
in the DataSHIELD test environment it is possible to print analyses to file (.csv, .txt, .pdf, .png)
take a look at our FAQ page for solutions to common problems such as Changing variable class to use in a specific DataSHIELD function.
Get support from our DataSHIELD forum.

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Old Version 6

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Build your login dataframe