Adding Aggregate methods - dsSynthetic

Support Analyst Support
1

Hi all

I was interested in using the package dsSynthetics, with the function ds.syn(). When I try it on the data used in the Vignette it works properly. ( vignette ).

Then, I tried using the same code on the Ninfea italian cohort:

builder <- DSI::newDSLoginBuilder()
builder$append(server = "server1",  url = "https://www.lifecycle.unito.it/",driver = "OpalDriver", 
               user = "----", password = "-----")
logindata <- builder$build()
connections <- DSI::datashield.login(logins = logindata, assign = TRUE, 
                                     symbol = "DST")
synth_data = ds.syn(data = "DST", method = "cart", m = 1, seed = 123)$server1$Data$syn

And I get this error:

"Command 'synDS(\"DST\", \"cart\", 1, NULL, FALSE, 123)' failed on 'server1': No such DataSHIELD 'AGGREGATE' method with name: synDS"

I checked and the synDS function is indeed not in the list of available methods when I run datashield.methods(connections, type = “aggregate”). More generally, it is not the first time I get an error like this for an ASSIGN or AGGREGATE method, that Datashield cannot find.

Does it mean the function is not installed/autorized by the cohort server? Can I install it myself? I looked at the Opal documentation (DataSHIELD — Opal documentation (obiba.org)) but I don’t see any codes to try.

Versions of packages used:

  • dsBase & dsBaseClient: 6.2.0.
  • dsSynthetic: 0.0.2.
  • dsOpal: 1.4.0
  • DSI: 1.5.0

Thanks in advance Inès

2

Inès,

What you are seeing does imply that the dsSynthetic package is not installed on the lifecycle.unito.it server. To install the package will require administrative access to the lifecycle.unito.it server.

I have name of a person at NINFEA who may be of help in this matter, contact me if you think it could help (stuart.wheater@arjuna.com)

Stuart