ds.coxph.SLMA: Performs survival analysis using Cox proportional hazards...

In neelsoumya/dsSurvivalClient: dsSurvival: Privacy preserving survival models for federated individual patient meta-analysis in DataSHIELD

Performs survival analysis using Cox proportional hazards model

Description

Passes a formula to a server side environment and returns the summary of Cox proportional hazards model from the server.

Usage

ds.coxph.SLMA(
  formula = NULL,
  dataName = NULL,
  weights = NULL,
  init = NULL,
  ties = "efron",
  singular.ok = TRUE,
  model = FALSE,
  x = FALSE,
  y = TRUE,
  control = NULL,
  combine_with_metafor = FALSE,
  datasources = NULL
)

Arguments

formula	character string (potentially including * symbol without spaces) specifying the formula that you want to pass to the server-side. For more information see Details.
dataName	character string of name of data frame
weights	vector of case weights
init	vector of initial values of the iteration.
ties	character string specifying the method for tie handling. The Efron approximation is used as the default. Other options are 'breslow' and 'exact'.
singular.ok	logical value indicating how to handle collinearity in the model matrix. Default is TRUE. If TRUE, the program will automatically skip over columns of the X matrix that are linear combinations of earlier columns. In this case the coefficients of such columns will be NA and the variance matrix will contain zeros.
model	logical value. If TRUE, the model frame is returned in component model.
x	logical value. If TRUE, the x matrix is returned in component x.
y	logical value. If TRUE, the response vector is returned in component y.
control	object of class survival::coxph.control() specifying iteration limit and other control options. Default is survival::coxph.control()
combine_with_metafor	logical If TRUE the estimates and standard errors for each regression coefficient are pooled across studies using random-effects meta-analysis under maximum likelihood (ML), restricted maximum likelihood (REML) or fixed-effects meta-analysis (FE). Default is FALSE.
datasources	a list of DSConnection-class objects obtained after login. If the datasources argument is not specified the default set of connections will be used: see datashield.connections_default.

Details

This is a function that performs survival analysis using the Cox proportional hazards model.

Server function called: coxphSLMADS.

Value

coxphSLMADS returns to the client-side a summary of the Cox proportional hazards model

Author(s)

Soumya Banerjee and Tom Bishop, 2021

Examples

## Not run: 

  ## Version 1.0.0
  
  # connecting to the Opal servers

  require('DSI')
  require('DSOpal')
  require('dsBaseClient')

  builder <- DSI::newDSLoginBuilder()
  builder$append(server = "study1", 
                 url = "http://192.168.56.100:8080/", 
                 user = "administrator", password = "datashield_test&", 
                 table = "SURVIVAL.EXPAND_NO_MISSING1", driver = "OpalDriver")
  builder$append(server = "study2", 
                 url = "http://192.168.56.100:8080/", 
                 user = "administrator", password = "datashield_test&", 
                 table = "SURVIVAL.EXPAND_NO_MISSING2", driver = "OpalDriver")
  builder$append(server = "study3",
                 url = "http://192.168.56.100:8080/", 
                 user = "administrator", password = "datashield_test&", 
                 table = "SURVIVAL.EXPAND_NO_MISSING3", driver = "OpalDriver")
  logindata <- builder$build()
  
  connections <- DSI::datashield.login(logins = logindata, assign = TRUE, symbol = "D") 
  
  # make sure that the outcome is numeric 
  ds.asNumeric(x.name = "D$cens",
            newobj = "EVENT",
            datasources = connections)

  ds.asNumeric(x.name = "D$survtime",
            newobj = "SURVTIME",
            datasources = connections)

  dsSurvivalClient::ds.Surv(time='SURVTIME', event='EVENT', objectname='surv_object')

  dsSurvivalClient::ds.coxph.SLMA(formula = 'surv_object ~  D$female', 
            dataName = 'D', datasources = connections)
  
  # clear the Datashield R sessions and logout
  datashield.logout(connections)

## End(Not run)

neelsoumya/dsSurvivalClient documentation built on July 1, 2023, 10:32 p.m.