1.3. R client#
Warning
We discourage the use of the R client. It is not actively maintained and is not fully implemented. It can not (yet) be used to manage resources, such as creating and deleting users and organizations.
1.3.1. Install#
You can install the R client by running:
devtools::install_github('IKNL/vtg')
1.3.2. Use#
The R client can only create tasks and retrieve their results.
Initialization of the R client can be done by:
setup.client <- function() {
# Username/password should be provided by the administrator of
# the server.
username <- "username@example.com"
password <- "password"
host <- 'https://cotopaxi.vantage6.ai:443'
api_path <- ''
# Create the client & authenticate
client <- vtg::Client$new(host, api_path=api_path)
client$authenticate(username, password)
return(client)
}
# Create a client
client <- setup.client()
Then, this client can be used for the different algorithms. Refer to the README in the repository on how to call the algorithm. Usually this includes installing some additional client-side packages for the specific algorithm you are using.
Example#
This example shows how to run the vantage6 implementation of a federated Cox Proportional Hazard regression model. First you need to install the client side of the algorithm by:
devtools::install_github('iknl/vtg.coxph', subdir="src")
This is the code to run the coxph:
print( client$getCollaborations() )
# Should output something like this:
# id name
# 1 1 ZEPPELIN
# 2 2 PIPELINE
# Select a collaboration
client$setCollaborationId(1)
# Define explanatory variables, time column and censor column
expl_vars <- c("Age","Race2","Race3","Mar2","Mar3","Mar4","Mar5","Mar9",
"Hist8520","hist8522","hist8480","hist8501","hist8201",
"hist8211","grade","ts","nne","npn","er2","er4")
time_col <- "Time"
censor_col <- "Censor"
# vtg.coxph contains the function `dcoxph`.
result <- vtg.coxph::dcoxph(client, expl_vars, time_col, censor_col)