Introduction

This tutorial introduces users to DataSHIELD commands and syntax. Throughout this document we refer to R, but all commands are run in the same way in Rstudio. This tutorial contains a limited number of examples; further examples are available in each DataSHIELD function manual page that can be accessed via the help function.

Start R/RStudio

Start R, RGui, or RStudio, which you will be using for this analysis training exercise.

Install Packages

The following relevant R packages are required for analysis:

• DSI to login and logout.
• DSOpal used by DSI to access the Opal server.
• dsBaseClient containing all DataSHIELD functions referred to in this tutorial.

install.packages('DSI')
install.packages('DSOpal', dependencies=TRUE)
install.packages('dsBaseClient', repos=c(getOption('repos'), 'http://cran.datashield.org'), dependencies=TRUE)

Load Packages

To load the R packages, type the library function into the command line as given in the example below:

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

Build your login dataframe 

The login dataframe is an R object that is created to store all of the login information necessary to access a DataSHIELD server, and save it (as an R script) for future logins, without having to gather the information each time. It is done by using DataSHIELD functions from the DSI package. It is then assigned to a local object, in the case below called "logindata", to be passed into the function for logging in to servers.

# Build your login dataframe

builder <- DSI::newDSLoginBuilder()
builder$append(server = "server1",  url = "https://opal-demo.obiba.org/",
               user = "dsuser", password = "P@ssw0rd", driver = "OpalDriver", options='list(ssl_verifyhost=0, ssl_verifypeer=0)')
builder$append(server = "server2", url = "https://opal-demo.obiba.org/",
               user = "dsuser", password = "P@ssw0rd", driver = "OpalDriver", options='list(ssl_verifyhost=0, ssl_verifypeer=0)')

logindata <- builder$build()

Login Command

Assign to a local object called "connections" the DSI function to log in to the desired Opal servers. In the DataSHIELD test environment logindata is our login dataframe for the Opal training servers.

connections <- DSI::datashield.login(logins = logindata, assign = TRUE)

The output below indicates that each of the two Opal training servers "server1" and "server2" contain the same 11 variables listed in capital letters under Variables assigned:

Logging into the collaborating servers
  Logged in all servers [================================================================] 100% /24s

Assign tables command

Finally, after successfully making a connection with the server, you must specify which studies, stored in tables, you wish to load into the session. This is done with another of the DSI package functions, "datashield.assign.table". 

DSI::datashield.assign.table(conns = connections, symbol = "DST", table = c("CNSIM.CNSIM1","CNSIM.CNSIM2"))

• The "conns" argument is to create a name for a DSConnection-class object, which will be used by statistical commands to refer to particular studies.
• The "symbol" argument is to create a name by which to refer to the dataframes in each study. Here we have opted for "DST" , an initialism for "DataSHIELD Table" 

• the "table" argument is to specify the names of the tables you wish to connect to as they appear on the servers you are using. The structure, "AAAA.BBBB", "AAAA.CCCC" means that within project AAAA there are tables BBBB and CCCC which we connect to both of, by listing them in an R vector.

An example of the printout after the login process has finished:

Assigned all table (DST <- ...) [======================================================] 100% /25s

Command to logout:

You should get into the habit of putting this command at the end of your scripts, and running it after you are finished. It is particularly important to do so when connecting to shared DataSHIELD servers, to save resources for the analyses of others.

DSI::datashield.logout(connections)

In a later tutorial in this series, you will find the option of saving your workspace before logging out, to be able to log in another day and have all your variables intact and ready to go without having to run everything again!

myvar <- list('LAB_HDL', 'GENDER')
connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "DST", variables=myvar)

Logging into the collaborating servers
  Logged in all servers [================================================================] 100% / 4s

Assigning table data...
  Assigned all tables [==================================================================] 100% / 7s

Variables assigned:
study1 -- LAB_HDL, GENDER
study2 -- LAB_HDL, GENDER

myvar <- list('LAB_HDL', 'GENDER')
connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol='mytable', variables=myvar)

Logging into the collaborating servers
  Logged in all servers [================================================================] 100% / 4s

Assigning table data...
  Assigned all tables [==================================================================] 100% / 6s

Variables assigned:
study1 -- LAB_HDL, GENDER
study2 -- LAB_HDL, GENDER

Conclusion

The other parts in this DataSHIELD tutorial series are:

• 1: Introduction and logging in

• 2: Basic statistics and data manipulations

• 3: Assign functions and tables

• 4: Plotting graphs

• 5: Subsetting

• 6: Modelling