dsSurvival
is a DataSHIELD package for privacy preserving survival models in DataSHIELD.
There is a well documented tutorial on dsSurvival: Privacy preserving survival models in DataSHIELD, but the servers used in this example (opal-sandbox.mrc-epid.cam.ac.uk) are now access-restricted.
I was wondering if one of the following would be possible:
- To replace the server here with a functional one (probably risky unless there is a dedicated maintainer)
- To release a similarly shaped dataset containing the variables
cens
, age
etc. so that data analysts can try following the tutorial on their own machines.
- A rewrite of the tutorial using dsLite, enabling the use of a custom local dataset.
Thanks in advance
Hi,
The server https://opal-demo.obiba.org is available, using the “survival” profile.
Regards
Yannick
1 Like
Oh, thanks!
Is that “survival” as username?
@yannick
I checked the obiba opal page for demo server info. And there are only two profiles for
Administrator
DataSHIELD user
https://www.obiba.org/pages/products/opal/
I cannot seem to find the “survival” profile.
A profile is not a user profile. Here we are talking about Datashield profiles. See DataSHIELD — Opal documentation
Regards
Yannick
1 Like
Late response, but this reprex should work for accessing the SURVIVAL profile + tables:
library(DSI)
library(DSOpal)
url <- "https://opal-demo.obiba.org"
profile <- "survival"
user <- "dsuser"
password <- "P@ssw0rd"
# Create a login data object
logindata <- data.frame(server = 'DEMO',
url=url,
user = user,
password = password,
profile = profile,
stringsAsFactors = FALSE)
# Log in to the DataSHIELD server
connections <- DSI::datashield.login(logins = logindata, assign = TRUE)
# Assign from a SURVIVAL table
DSI::datashield.assign.table(
conns = connections,
symbol = "DST",
table = c("SURVIVAL.EXPAND_WITH_MISSING1"))
Todo: I would like to expand this with commands to execute after loading in the table.
Not sure I understand your question, but you have dsBase available in this profile:
> datashield.pkg_status(connections)
$package_status
DEMO
dsBase TRUE
dsSurvival TRUE
resourcer TRUE
$version_status
DEMO
dsBase "6.3.0"
dsSurvival "2.1.3"
resourcer "1.4.0"
Regards
Yannick