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', subdir='src')

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)